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All Classes All Packages

$

$3D_atom_query - Static variable in class com.actelion.research.util.Sketch
 
$3D_basis_objs - Static variable in class com.actelion.research.util.Sketch
 
$3D_dihed_chiral - Static variable in class com.actelion.research.util.Sketch
 
$3D_exclus_dradius - Static variable in class com.actelion.research.util.Sketch
 
$3D_exclus_ignore - Static variable in class com.actelion.research.util.Sketch
 
$3D_exclus_radius - Static variable in class com.actelion.research.util.Sketch
 
$3D_marker_rf - Static variable in class com.actelion.research.util.Sketch
 
$3D_maxval - Static variable in class com.actelion.research.util.Sketch
 
$3D_minval - Static variable in class com.actelion.research.util.Sketch
 
$3D_name - Static variable in class com.actelion.research.util.Sketch
 
$3D_num_basis_objs - Static variable in class com.actelion.research.util.Sketch
 
$3D_point_ddist - Static variable in class com.actelion.research.util.Sketch
 
$3D_point_dir - Static variable in class com.actelion.research.util.Sketch
 
$3D_point_dist - Static variable in class com.actelion.research.util.Sketch
 
$3D_tolerance - Static variable in class com.actelion.research.util.Sketch
 
$Abbrev_atch - Static variable in class com.actelion.research.util.Sketch
 
$Arc_endpts - Static variable in class com.actelion.research.util.Sketch
 
$ArrowDir - Static variable in class com.actelion.research.util.Sketch
 
$ArrowShaftSp - Static variable in class com.actelion.research.util.Sketch
 
$ArrowSize - Static variable in class com.actelion.research.util.Sketch
 
$ArrowStyle - Static variable in class com.actelion.research.util.Sketch
 
$ArrowType - Static variable in class com.actelion.research.util.Sketch
 
$Atom_aamap_num - Static variable in class com.actelion.research.util.Sketch
 
$Atom_aamapped - Static variable in class com.actelion.research.util.Sketch
 
$Atom_alias - Static variable in class com.actelion.research.util.Sketch
 
$Atom_AttachLen - Static variable in class com.actelion.research.util.Sketch
 
$Atom_can_reverse - Static variable in class com.actelion.research.util.Sketch
 
$Atom_chg - Static variable in class com.actelion.research.util.Sketch
 
$Atom_coords - Static variable in class com.actelion.research.util.Sketch
 
$Atom_dispflags - Static variable in class com.actelion.research.util.Sketch
 
$Atom_DotWidth - Static variable in class com.actelion.research.util.Sketch
 
$Atom_exact_change - Static variable in class com.actelion.research.util.Sketch
 
$Atom_fixed - Static variable in class com.actelion.research.util.Sketch
 
$Atom_h0bit - Static variable in class com.actelion.research.util.Sketch
 
$Atom_hpos - Static variable in class com.actelion.research.util.Sketch
 
$Atom_hshow - Static variable in class com.actelion.research.util.Sketch
 
$Atom_list - Static variable in class com.actelion.research.util.Sketch
 
$Atom_margin_width - Static variable in class com.actelion.research.util.Sketch
 
$Atom_msdif - Static variable in class com.actelion.research.util.Sketch
 
$Atom_npos - Static variable in class com.actelion.research.util.Sketch
 
$Atom_number - Static variable in class com.actelion.research.util.Sketch
 
$Atom_NumSize - Static variable in class com.actelion.research.util.Sketch
 
$Atom_Orig_coords - Static variable in class com.actelion.research.util.Sketch
 
$Atom_rad - Static variable in class com.actelion.research.util.Sketch
 
$Atom_rbcount - Static variable in class com.actelion.research.util.Sketch
 
$Atom_rgroupAtch - Static variable in class com.actelion.research.util.Sketch
 
$Atom_rxn_stereo - Static variable in class com.actelion.research.util.Sketch
 
$Atom_stereo_care - Static variable in class com.actelion.research.util.Sketch
 
$Atom_substcount - Static variable in class com.actelion.research.util.Sketch
 
$Atom_symbol - Static variable in class com.actelion.research.util.Sketch
 
$Atom_tplatchpt - Static variable in class com.actelion.research.util.Sketch
 
$Atom_type - Static variable in class com.actelion.research.util.Sketch
 
$Atom_unsat - Static variable in class com.actelion.research.util.Sketch
 
$Atom_valence - Static variable in class com.actelion.research.util.Sketch
 
$Atom_value - Static variable in class com.actelion.research.util.Sketch
 
$Atom_zcoord - Static variable in class com.actelion.research.util.Sketch
 
$Begsketch - Static variable in class com.actelion.research.util.Sketch
 
$BigMetaData - Static variable in class com.actelion.research.util.Sketch
 
$Bond_alt_stereo - Static variable in class com.actelion.research.util.Sketch
 
$Bond_atoms - Static variable in class com.actelion.research.util.Sketch
 
$Bond_bond_spacing - Static variable in class com.actelion.research.util.Sketch
 
$Bond_crossed - Static variable in class com.actelion.research.util.Sketch
 
$Bond_dbl_side - Static variable in class com.actelion.research.util.Sketch
 
$Bond_dbl_width - Static variable in class com.actelion.research.util.Sketch
 
$Bond_hash_spacing - Static variable in class com.actelion.research.util.Sketch
 
$Bond_qtopo - Static variable in class com.actelion.research.util.Sketch
 
$Bond_rxn_center - Static variable in class com.actelion.research.util.Sketch
 
$Bond_stereo_care - Static variable in class com.actelion.research.util.Sketch
 
$Bond_stereo_type - Static variable in class com.actelion.research.util.Sketch
 
$Bond_topo - Static variable in class com.actelion.research.util.Sketch
 
$Bond_type - Static variable in class com.actelion.research.util.Sketch
 
$Circ_Arc_Points - Static variable in class com.actelion.research.util.Sketch
 
$Comment - Static variable in class com.actelion.research.util.Sketch
 
$Crop_coords - Static variable in class com.actelion.research.util.Sketch
 
$Endsketch - Static variable in class com.actelion.research.util.Sketch
 
$Fill_color - Static variable in class com.actelion.research.util.Sketch
 
$Fill_RGB2Color - Static variable in class com.actelion.research.util.Sketch
 
$Fill_style - Static variable in class com.actelion.research.util.Sketch
 
$Font - Static variable in class com.actelion.research.util.Sketch
 
$Is_A_Model - Static variable in class com.actelion.research.util.Sketch
 
$Locked - Static variable in class com.actelion.research.util.Sketch
 
$MDLEditText - Static variable in class com.actelion.research.util.Sketch
 
$MetaData - Static variable in class com.actelion.research.util.Sketch
 
$Model_Rotated - Static variable in class com.actelion.research.util.Sketch
 
$Mol_type - Static variable in class com.actelion.research.util.Sketch
 
$Name - Static variable in class com.actelion.research.util.Sketch
 
$Nostruct_label - Static variable in class com.actelion.research.util.Sketch
 
$Nostruct_regno - Static variable in class com.actelion.research.util.Sketch
 
$Obj - Static variable in class com.actelion.research.util.Sketch
 
$Obj_Atom - Static variable in class com.actelion.research.util.Sketch
 
$Obj_Bond - Static variable in class com.actelion.research.util.Sketch
 
$Obj_Chiral - Static variable in class com.actelion.research.util.Sketch
 
$Obj_coords - Static variable in class com.actelion.research.util.Sketch
 
$Obj_Mol - Static variable in class com.actelion.research.util.Sketch
 
$Parent - Static variable in class com.actelion.research.util.Sketch
 
$Pen_color - Static variable in class com.actelion.research.util.Sketch
 
$Pen_RGB2Color - Static variable in class com.actelion.research.util.Sketch
 
$Pen_style - Static variable in class com.actelion.research.util.Sketch
 
$Pen_style_token - Static variable in class com.actelion.research.util.Sketch
 
$Pen_width - Static variable in class com.actelion.research.util.Sketch
 
$Pen_widthUnit - Static variable in class com.actelion.research.util.Sketch
 
$Poly_points - Static variable in class com.actelion.research.util.Sketch
 
$Poly_smoothed - Static variable in class com.actelion.research.util.Sketch
 
$RGroupNo - Static variable in class com.actelion.research.util.Sketch
 
$RLogic - Static variable in class com.actelion.research.util.Sketch
 
$Roundrect_curve - Static variable in class com.actelion.research.util.Sketch
 
$RxnAtch - Static variable in class com.actelion.research.util.Sketch
 
$SGroupAtch - Static variable in class com.actelion.research.util.Sketch
 
$SGroupAtchPt - Static variable in class com.actelion.research.util.Sketch
 
$SGroupBracketLen - Static variable in class com.actelion.research.util.Sketch
 
$SGroupContext - Static variable in class com.actelion.research.util.Sketch
 
$SGroupLinkVal - Static variable in class com.actelion.research.util.Sketch
 
$SGroupName - Static variable in class com.actelion.research.util.Sketch
 
$SGroupNewAtch - Static variable in class com.actelion.research.util.Sketch
 
$SGroupType - Static variable in class com.actelion.research.util.Sketch
 
$Totobjs - Static variable in class com.actelion.research.util.Sketch
 
$Transparent - Static variable in class com.actelion.research.util.Sketch
 
$Version - Static variable in class com.actelion.research.util.Sketch
 

A

a - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
 
a - Variable in class com.actelion.research.util.BurtleHasherABC
 
A - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
a_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'A-i' from the table.
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
 
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
a1t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a1t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
a2t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a2t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
a3 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
a3 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
a3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a3t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a4 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
a4t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
AbstractDepictor - Class in com.actelion.research.chem
 
AbstractDepictor(StereoMolecule) - Constructor for class com.actelion.research.chem.AbstractDepictor
 
AbstractDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.AbstractDepictor
 
AbstractDepictor.DepictorDot - Class in com.actelion.research.chem
 
AbstractDepictor.DepictorLine - Class in com.actelion.research.chem
 
AbstractDescriptorHandlerFP<U> - Class in com.actelion.research.chem.descriptor
 
AbstractDescriptorHandlerFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
AbstractDescriptorHandlerLongFP<U> - Class in com.actelion.research.chem.descriptor
 
AbstractDescriptorHandlerLongFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
AbstractDrawingObject - Class in com.actelion.research.chem
 
AbstractDrawingObject() - Constructor for class com.actelion.research.chem.AbstractDrawingObject
 
AbstractExtendedDepictor<T,​C> - Class in com.actelion.research.share.gui.editor.chem
 
AbstractExtendedDepictor(Reaction, List<IDrawingObject>, boolean, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
AbstractExtendedDepictor(StereoMolecule[], int, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
Use this constructor for markush structures.
AbstractExtendedDepictor(StereoMolecule[], List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
AbstractExtendedDepictor(StereoMolecule, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
AbstractForceField - Class in com.actelion.research.chem.forcefield
 
AbstractForceField(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.AbstractForceField
 
AbstractParser - Class in com.actelion.research.chem.io
A parser is used to load and save molecules from the filesystem.
AbstractParser() - Constructor for class com.actelion.research.chem.io.AbstractParser
 
AbstractScoringEngine - Class in com.actelion.research.chem.docking.scoring
 
AbstractScoringEngine(StereoMolecule, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
accept(double, double) - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
 
accept(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
Return true if this file should be shown in the directory pane, false if it shouldn't.
ACCEPTOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
ACCEPTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
AcceptorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
 
AcceptorPoint(AcceptorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
AcceptorPoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
AcceptorPoint(StereoMolecule, int, List<Integer>, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
Action - Interface in com.actelion.research.share.gui.editor.actions
Basic Interface for all editor actions
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomLabelDialog
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JBondQueryFeatureDialog
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JChemistryView
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawArea
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawDialog
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JStructureView
 
actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JTextDrawingObjectDialog
 
add(byte[]) - Method in class com.actelion.research.util.datamodel.IntArray
 
add(byte, byte) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
Adds a pair of nodes to this solution.
add(double) - Method in class com.actelion.research.calc.Matrix
 
add(double) - Method in class com.actelion.research.util.Angle
 
add(double) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
add(double[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
add(double, double, double) - Method in class com.actelion.research.chem.Coordinates
 
add(float[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
Caution! After finishing all adding's realize() has to be called!
add(int) - Method in class com.actelion.research.util.datamodel.IntArray
 
add(int) - Method in class com.actelion.research.util.hash.HashSetInt
If the key is already present nothing will happen.
add(int[]) - Method in class com.actelion.research.util.datamodel.IntArray
 
add(int[]) - Method in class com.actelion.research.util.hash.HashSetInt
 
add(int, int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
 
add(int, long) - Method in class com.actelion.research.chem.CanonizerBaseValue
 
add(int, T) - Method in class com.actelion.research.util.UniqueList
 
add(long) - Method in class com.actelion.research.chem.CanonizerBaseValue
 
add(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
add(SubFlexophoreGenerator.ViolatedConditionsCount) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
 
add(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Adds two vectors together by component.
add(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
add(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
add(ListWithIntVecIdCode) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
add(Angle) - Method in class com.actelion.research.util.Angle
 
add(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
 
add(DoubleArray) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
add(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
 
add(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
 
add(ErrorHashMap) - Method in class com.actelion.research.util.ErrorHashMap
 
add(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
 
add(Point2D) - Method in class com.actelion.research.share.gui.Polygon
 
add(Exception) - Method in class com.actelion.research.util.ErrorHashMap
 
add(String, int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
 
add(String, String) - Method in class com.actelion.research.util.CommandLineParser
 
add(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntArray
 
add(List<Integer>) - Method in class com.actelion.research.util.hash.HashSetInt
 
add(T) - Method in class com.actelion.research.util.SortedList
Adds object to the list provided that it doesn't contain an object being considered equal by compareTo().
add(T) - Method in class com.actelion.research.util.UniqueList
 
add2CompleteCol(Matrix) - Method in class com.actelion.research.calc.Matrix
The value in the col from the input matrix is added to all values in the corresponding col in the matrix.
add2DCoordinatesColumn(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Creates a new column to hold encoded 2-dimensional atom coordinates for the structures stored in the associated structure column.
add2Row(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
 
add3DCoordinatesColumn(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Creates a new column to hold encoded 3-dimensional atom coordinates for the structures stored in the associated structure column.
addAll(List<Exception>) - Method in class com.actelion.research.util.ErrorHashMap
 
addAllBits(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
addAlphanumericalColumn(String) - Method in class com.actelion.research.chem.io.DWARFileCreator
Creates a new standard column to hold any alphanumerical content.
addArrOriginalAtomIndexRGroups(AtomIndexLinkerId) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
addAtom(double, double) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addAtom(double, double, double) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addAtom(int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addAtom(int) - Method in class com.actelion.research.chem.Molecule3D
Add an atom with the given atomicNo
addAtom(Molecule3D, int) - Method in class com.actelion.research.chem.Molecule3D
Add an atom by copying its properties from the given Molecule3D This has to be overriden by subclasses
addAtom(String) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addAtomIndices(HashSetInt, List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
Adds the atom indices to the hash set.
addAtomList(StringBuilder) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
addAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
addAtoms(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
addBit(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
Dont't forget to calculate the hash!
addBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
addBond(int, int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
addCatalyst(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
 
addCatalyst(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
 
addChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
 
addColumnProperty(int, String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
This method may be used to define column properties, e.g.
addCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addCompound(T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addCompound(T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
 
addCore(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
 
addData(List<T>) - Method in class com.actelion.research.util.Pipeline
 
addData(T) - Method in class com.actelion.research.util.Pipeline
 
addDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
 
addDescriptorColumn(String, String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Creates a new column to hold a chemical descriptor for the structures stored in the associated structure column.
addDrawAreaListener(DrawAreaListener) - Method in class com.actelion.research.gui.JDrawArea
 
addDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
 
addElement(String, double) - Method in class com.actelion.research.chem.prediction.IncrementTable
 
addEnergyTerm(EnergyTerm) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
addExtension(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
Adds a filetype "dot" extension to filter against.
addFacultative(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
The fragment is added if it is not already in the hash map.
addFeatureMatch(TreeMatcher.FeatureMatch) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
addFragment(ExtendedMolecule, int, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
This adds a fragment from sourceMol to this molecule by first copying rootAtom and then all connected atoms and bonds by traversing the graph breadth first.
addGradient(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
addHandle() - Method in class com.actelion.research.gui.wmf.WMF
 
addHydrogenAtoms(StereoMolecule) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Adds explicit hydrogen atoms where they are implicit by filling valences and adapting for atom charges.
addHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Add the missing hydrogens for the ligand
addHydrogens(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Adds the missing hydrogens (no optimization)
addHydrogensAroundLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
addImplicitHydrogens() - Method in class com.actelion.research.chem.conf.AtomAssembler
 
addImplicitHydrogens(int) - Method in class com.actelion.research.chem.conf.AtomAssembler
 
addImplicitHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
 
addImplicitHydrogens(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
 
addIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
addIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
addIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
addInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
addInteraction(int, int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
addLayoutComponent(String, Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
Adds a feature to the LayoutComponent attribute of the VerticalFlowLayout object
addListener(ForceFieldChangeListener) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
Return the variance across all atoms in a molecule for the specified coordinate.
addListener(ForceFieldChangeListener) - Method in interface com.actelion.research.chem.forcefield.ForceField
 
addMatching(TreeMatcher.TreeMatching) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
addMissingChirality(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
 
addMissingChirality(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
The problem is that sometimes we need to add chiral bond that was not planned because it is the same group This is the case for example for the valine where the 2 C of the methyl groups are diastereotopic
addMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
 
addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
 
addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
 
addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
 
addMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
Copies all atoms and bonds of mol to the end of this Molecule's atom and bond tables.
addMolecule(StereoMolecule, double, double) - Method in class com.actelion.research.share.gui.editor.Model
 
addMoleculeList(Collection<StereoMolecule>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
addMoleculeList(Collection<StereoMolecule>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
addNode(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
addNode(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
addNoise(double, double, double) - Method in class com.actelion.research.util.DoubleVec
 
addOrChangeAtom(double, double, int, int, int, int, String) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addOrChangeBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
addOriginalAtomIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
addPoint(double, double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
addPoint(PointDouble) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
addPoint(Point) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
add a point to the vector of points
addProduct(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
 
addProduct(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
 
addProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
 
addReactant(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
 
addReactant(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
 
addRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
addResidue(Molecule3D) - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
an amino acid is added to the protein structure and a peptide coupling is performed, if coupling cannot be performed, the function results false and the residue is not added
addRGroup(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule.
addRing(double, double, int, boolean) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
AddRingAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 2/1/13 Time: 4:03 PM
AddRingAction(Model, int, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.AddRingAction
 
addRingToAtom(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addRingToBond(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
addRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
Adds aor subtracts a random value to the original value.
addRow(double[]) - Method in class com.actelion.research.calc.Matrix
 
addRow(int[]) - Method in class com.actelion.research.calc.Matrix
 
addShift(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.DistanceRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.PlaneRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TorsionRule
 
addString(String) - Method in class com.actelion.research.chem.SortedStringList
 
addString(String) - Method in class com.actelion.research.chem.UniqueStringList
 
addStructureColumn(String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
This adds a column to host canonical structure representations (idcodes).
addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
 
addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JDrawDialog
 
addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
 
addSubstituent(Molecule, int) - Method in class com.actelion.research.chem.Molecule
Adds and connects the substituent molecule to the connectionAtom of this molecule.
addSubstituent(Molecule, int, boolean) - Method in class com.actelion.research.chem.Molecule
Adds and connects the substituent molecule to the connectionAtom of this molecule.
addToElement(int, int, double) - Method in class com.actelion.research.calc.Matrix
 
addToExistingSet(long[]) - Method in class com.actelion.research.chem.DiversitySelector
 
addToIntArray(int[], int) - Static method in class com.actelion.research.chem.CanonizerMesoHelper
 
addValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
 
advanceToNext() - Method in class com.actelion.research.chem.io.CompoundFileParser
Dont't call this method directly.
advanceToNext() - Method in class com.actelion.research.chem.io.DWARFileParser
 
advanceToNext() - Method in class com.actelion.research.chem.io.ODEFileParser
 
advanceToNext() - Method in class com.actelion.research.chem.io.SDFileParser
 
align() - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
 
align() - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
align(Coordinates, Matrix, Coordinates) - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
 
align(PheSAMolecule, MolecularVolume, MolecularVolume, StereoMolecule, double) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
 
align(PheSAMolecule, PheSAMolecule, StereoMolecule[], double, boolean) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
 
AlignmentResult(double, double[][], int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
 
alignTwoMolsInPlace(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
 
alignTwoMolsInPlace(StereoMolecule, StereoMolecule, double) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
 
allFieldsEquals(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
ALMOST_ZERO - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
alpha - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
ALPHA - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
alpha_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'alpha-i' from the table.
alpha_pref - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
 
ALTERNATE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
AMemorizedObject - Class in com.actelion.research.util.graph.complete
AMemorizedObject
AMemorizedObject() - Constructor for class com.actelion.research.util.graph.complete.AMemorizedObject
 
AMERICAN - com.actelion.research.util.Formatter.LocaleFormat
 
AMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
AMIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
AMINO_ACIDS - Static variable in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
 
AminoAcidLabeled - Class in com.actelion.research.chem.io.pdb.converter
AminoAcidLabeled
AminoAcidLabeled(StereoMolecule, String, String) - Constructor for class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
 
AminoAcidsLabeledContainer - Enum in com.actelion.research.chem.io.pdb.converter
AminoAcidsLabeledContainer The txt file was generated with com.actelion.research.chem.parsers.pdb.ProcessLabeledAminoAcids
analyse(String) - Method in class com.actelion.research.util.DateAnalysis
Checks, whether entry consists of three elements separated by one or more non-word characters (neither digit nor letter) that might be day, month and year.
analyzeFragmentMembership() - Method in class com.actelion.research.share.gui.editor.Model
 
analyzeMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
analyzeReaction() - Method in class com.actelion.research.share.gui.editor.Model
 
AND(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Makes an logical AND and calculates the hash code.
angle - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
angle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns the angle between this vector and that vector.
Angle - Class in com.actelion.research.chem.forcefield.mmff.table
Angle table, corresponds to the MMFFANG.PAR parameters table provided in the MMFF literature.
Angle - Class in com.actelion.research.chem.forcefield.mmff.type
The angle type class provides static functions for getting angle and stretch bend MMFF type.
Angle - Class in com.actelion.research.util
This class provides various operations on angles, while making sure that the values is always in the rangle from -pi >= v > pi.
Angle() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Angle
 
Angle() - Constructor for class com.actelion.research.util.Angle
 
Angle(double) - Constructor for class com.actelion.research.util.Angle
 
Angle(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Angle
 
Angle(Angle) - Constructor for class com.actelion.research.util.Angle
 
AngleBend - Class in com.actelion.research.chem.forcefield.mmff
Angle bending energy term class.
AngleBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.AngleBend
Construct a new angle bend energy term.
AngleConstraint - Class in com.actelion.research.chem.potentialenergy
 
AngleConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.AngleConstraint
 
ANSI_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
append(String) - Method in class com.actelion.research.util.datamodel.ByteVec
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.DistanceRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.PlaneRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TorsionRule
 
apply(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
 
applyTo(AbstractDrawingObject) - Method in class com.actelion.research.chem.DepictorTransformation
 
applyTo(DepictorTransformation) - Method in class com.actelion.research.chem.DepictorTransformation
 
applyTo(Molecule) - Method in class com.actelion.research.chem.DepictorTransformation
 
applyTo(Point2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
 
applyTo(Rectangle2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
 
applyTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
 
approveSelection() - Method in class com.actelion.research.gui.JFileChooserOverwrite
 
arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
arccos(double) - Static method in class com.actelion.research.util.Angle
 
arcsin(double) - Static method in class com.actelion.research.util.Angle
 
arctan(double, double) - Static method in class com.actelion.research.util.Angle
 
areAtomsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
 
areBonded(Residue) - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
areBondsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
 
areNodesMapping(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
Dynamic calculation of similarity threshold.
areNodesMapping(int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
areRowsEqual(int, int) - Method in class com.actelion.research.calc.Matrix
 
arom(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the Arom bool of an atom given its MMFF type.
AROM - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
AROM_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
AROM_RING - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
AROM_RING_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
AromaticityResolver - Class in com.actelion.research.chem
 
AromaticityResolver(ExtendedMolecule) - Constructor for class com.actelion.research.chem.AromaticityResolver
Creates a new AromaticityResolver for molecule mol.
aromatize(Molecule3D, ArrayList<Integer>[], RingCollection, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
 
aromatize(Molecule3D, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
 
AromRingPoint - Class in com.actelion.research.chem.phesa.pharmacophore
 
AromRingPoint(AromRingPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
AromRingPoint(StereoMolecule, int, List<Integer>) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
ARR_TAGS - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
arrange(double, boolean) - Method in class com.actelion.research.chem.coords.FragmentAssociation
 
arrangeReaction(Reaction, Dimension) - Static method in class com.actelion.research.chem.ChemistryHelper
 
arrangeWith(InventorFragment) - Method in class com.actelion.research.chem.coords.InventorFragment
 
arrAtomLabelRGroups - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ArrayUtils - Class in com.actelion.research.util
 
ArrayUtils() - Constructor for class com.actelion.research.util.ArrayUtils
 
ArrayUtilsCalc - Class in com.actelion.research.calc
 
ArrayUtilsCalc() - Constructor for class com.actelion.research.calc.ArrayUtilsCalc
 
arrDistHists - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
Arrow - Class in com.actelion.research.share.gui
 
Arrow(DrawConfig, double, double, double, double) - Constructor for class com.actelion.research.share.gui.Arrow
 
ArrowAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 5/16/13 Time: 3:46 PM
ArrowAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ArrowAction
 
arrRGroupsAtomicNo - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
arrRGroupsSymbol - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
aspec(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the ASPEC type of an atom given its MMFF type.
assemble() - Method in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
 
assessCLogP(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
Ambiguous bonds are normalized.
assessDruglikeness(StereoMolecule, ThreadMaster) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
 
assessPSA(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
assessRisk(StereoMolecule, int, ThreadMaster) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
 
assessSolubility(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
 
ASSIGN_PARITIES_TO_TETRAHEDRAL_N - Static variable in class com.actelion.research.chem.Canonizer
 
assignCol(int, Matrix) - Method in class com.actelion.research.calc.Matrix
 
assignCol(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
 
assignRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
 
assignRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
 
assignRow(int, DoubleVec) - Method in class com.actelion.research.calc.Matrix
 
assignRow(int, Vector<Double>) - Method in class com.actelion.research.calc.Matrix
 
atom - Variable in class com.actelion.research.chem.coords.InventorCharge
 
atom - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Atom - Class in com.actelion.research.chem.forcefield.mmff.table
Atom table, corresponds to the MMFFPROP.PAR parameters table provided in the MMFF literature.
Atom - Class in com.actelion.research.chem.forcefield.mmff.type
The Atom type class provides static functions to perform atom typing on atoms in a Molecule.
Atom() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Atom
 
Atom(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Atom
 
ATOM_BITS - Static variable in class com.actelion.research.chem.Canonizer
 
ATOM_LABEL_R1 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R10 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R11 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R12 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R13 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R14 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R15 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R16 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R2 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R3 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R4 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R5 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R6 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R7 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R8 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_LABEL_R9 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATOM_TYPE - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
 
AtomAssembler - Class in com.actelion.research.chem.conf
 
AtomAssembler(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.AtomAssembler
 
atomAtomSubStrucMatch(StereoMolecule, int, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
AtomComparator - Class in com.actelion.research.chem
 
AtomComparator() - Constructor for class com.actelion.research.chem.AtomComparator
 
AtomFunctionAnalyzer - Class in com.actelion.research.chem
 
AtomFunctionAnalyzer() - Constructor for class com.actelion.research.chem.AtomFunctionAnalyzer
 
AtomHighlightAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
ATOMIC_NO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
AtomicFloat - Class in com.actelion.research.util.concurrent
 
AtomicFloat() - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
 
AtomicFloat(float) - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
 
AtomicGaussian - Class in com.actelion.research.chem.phesa
 
AtomicGaussian(int, int, Coordinates) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
 
AtomicGaussian(AtomicGaussian) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
 
atomicNo - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
atomId - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
AtomIndexLinkerId - Class in com.actelion.research.chem.descriptor.flexophore.entity
AtomIndexLinkerId
AtomIndexLinkerId() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
AtomIndexLinkerId(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
AtomMapAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 5/22/13 Time: 4:00 PM
AtomMapAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
AtomRecord - Class in com.actelion.research.chem.io.pdb.parser
ModelAtom
AtomRecord(int, String, String, String, String, int, String, double, double, double, double, double, String) - Constructor for class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
AtomTypeCalculator - Class in com.actelion.research.chem
 
AtomTypeCalculator() - Constructor for class com.actelion.research.chem.AtomTypeCalculator
 
AtomTypeList - Class in com.actelion.research.chem
 
AtomTypeList(int) - Constructor for class com.actelion.research.chem.AtomTypeList
Creates an empty AtomTypeList, which must be populated by multiply calling processMolecule() and finally calling finalizeProcessMolecules() once.
AtomTypeList(String, int) - Constructor for class com.actelion.research.chem.AtomTypeList
Creates a new AtomTypeList from a given file using the given mode.
AtomTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
 
ATTACHED_HYDROGEN_COUNT - Static variable in class com.actelion.research.chem.Molecule3D
 
ATTACHED_HYDROGEN_COUNT_SHIFT - Static variable in class com.actelion.research.chem.Molecule3D
 
ATTR_ACCEPTOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_ALIPHATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_AROMATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_DONOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_NEGATIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ATTR_POSITIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ATTR_YES - Static variable in class com.actelion.research.util.ConstantsDWAR
 
autoMap() - Method in interface com.actelion.research.chem.reaction.AutoMapper
 
autoMap() - Method in class com.actelion.research.chem.reaction.MoleculeAutoMapper
 
AutoMapper - Interface in com.actelion.research.chem.reaction
Project: User: rufenec Date: 6/17/2014 Time: 10:04 AM
autoScroll() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
 
avr() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
AxialStereoRule - Class in org.openmolecules.chem.conf.so
Handles attropisomery as well as chiral allenes
AxialStereoRule(StereoMolecule, int[], int[], boolean, boolean) - Constructor for class org.openmolecules.chem.conf.so.AxialStereoRule
 

B

b - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
 
b - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
b - Variable in class com.actelion.research.util.BurtleHasherABC
 
B - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
B_sq - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
back(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
 
back(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
 
BACKBONE - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
 
BACKBONE - Static variable in class com.actelion.research.chem.Molecule3D
 
BadAtomTypeException - Exception in com.actelion.research.chem.forcefield.mmff
The BadAtomTypeException is thrown when there is a bad atom type in a molecule.
BadAtomTypeException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
 
BadAtomTypeException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
 
BadRingAromException - Exception in com.actelion.research.chem.forcefield.mmff
The BadRingAromException is thrown when there is a problem with the MMFF ring aromaticity assignment.
BadRingAromException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
 
BadRingAromException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
 
BASE_LOG - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
BASIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
BASIC_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
 
bcc() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
 
bccutil(int, int[], int[], LinkedList<Graph.Edge>, int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
 
bci_binary_search(int, int, int, int, boolean) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
Binary search in the bci table.
beta - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
between(Coordinates, Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
Updates this to contain a point on the straight line through c1 and c2.
BiGramInt(int[]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
 
BiGramInt(int, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
 
BIN_SIZE - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
BIN_SIZE - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
binary(int[], int[], Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
Binary search on a collection of values in columns in a table.
binary(int, int, int, int, boolean, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
Binary searches for a value and returns the index to it.
binary(int, int, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
Helper function that acts like Search.binary(int[], int[], Searchable) but takes a single int for cols and vals to search just one column.
BinaryDecoder - Class in com.actelion.research.util
 
BinaryDecoder(BufferedReader) - Constructor for class com.actelion.research.util.BinaryDecoder
 
BinaryDecoder(BufferedReader, int, int) - Constructor for class com.actelion.research.util.BinaryDecoder
 
bindingSiteAtoms - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
BINS_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
Defines the resolution for the range.
BitArray128 - Class in com.actelion.research.chem.properties.complexity
 
BitArray128() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
 
BitArray128(int) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
 
BitArray128(BitArray128) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
Deep copy
BitArray128Factory - Class in com.actelion.research.chem.properties.complexity
 
BitArray128Factory() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128Factory
 
bitCount(int) - Static method in class com.actelion.research.util.BitUtils
Deprecated.
use Integer.bitCount() instead.
bitCount(long) - Static method in class com.actelion.research.util.BitUtils
 
BitUtils - Class in com.actelion.research.util
 
BitUtils() - Constructor for class com.actelion.research.util.BitUtils
 
BLACK - Static variable in class com.actelion.research.gui.hidpi.ColorUtils
 
BLACK - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
BLACKNESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BLUE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
blurrSingleBinHistograms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
bndk - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Bndk - Class in com.actelion.research.chem.forcefield.mmff.table
Bndk table, corresponds to the MMFFBNDK.PAR parameters table provided in the MMFF literature.
Bndk(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bndk
 
BOMSkipper - Class in com.actelion.research.io
 
BOMSkipper() - Constructor for class com.actelion.research.io.BOMSkipper
 
bond - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Bond - Class in com.actelion.research.chem.forcefield.mmff.table
Bond table, corresponds to the MMFFBOND.PAR parameters table provided in the MMFF literature.
Bond - Class in com.actelion.research.chem.forcefield.mmff.type
The bond type class provides static functions for getting the MMFF bond type (either by bond or by the atoms of a bond).
Bond() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Bond
 
Bond(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bond
 
BOND_CUTOFF_SQ - Static variable in class com.actelion.research.chem.io.pdb.parser.Residue
 
BondAngleSet - Class in com.actelion.research.chem.conf
 
BondAngleSet(StereoMolecule, BondLengthSet) - Constructor for class com.actelion.research.chem.conf.BondAngleSet
Calculates and caches a list of bond angle estimates for any two neighbours of any atom of the molecule.
BondBaseAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
BondBaseAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
BondConstraint - Class in com.actelion.research.chem.potentialenergy
 
BondConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.BondConstraint
 
BondHighlightAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
BondHighlightAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
BondLengthSet - Class in com.actelion.research.chem.conf
 
BondLengthSet(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondLengthSet
Calculates and caches a list of bond length estimates from molecule.
BondRotationHelper - Class in com.actelion.research.chem.conf
 
BondRotationHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondRotationHelper
 
bondsAreParallel(double, double) - Method in class com.actelion.research.chem.ExtendedMolecule
 
BondsCalculator - Class in com.actelion.research.chem.io.pdb.converter
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders based on the 3D coordinates of the atoms
BondsCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.BondsCalculator
 
BondStretch - Class in com.actelion.research.chem.forcefield.mmff
Bond stretching energy term class.
BondStretch(Tables, MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
Creates a new bond stretch given a force field and a bond.
BondStretch(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
Creates a new bond stretch given a force field and two bonded atoms.
BondVector2IdCode - Class in com.actelion.research.chem.mcs
 
BondVector2IdCode(StereoMolecule) - Constructor for class com.actelion.research.chem.mcs.BondVector2IdCode
 
BOTTOM - Static variable in class com.actelion.research.gui.VerticalFlowLayout
Description of the Field
brighter(Color, float) - Static method in class com.actelion.research.util.ColorHelper
Creates a new Color that is a brighter version of this Color.
Bromine - Static variable in class com.actelion.research.chem.PeriodicTable
 
BS_DIBPATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BS_HATCHED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BS_HOLLOW - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BS_PATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
BS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
build() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
BURIED_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
BurtleHasher - Class in com.actelion.research.util
http://burtleburtle.net/bob/c/lookup3.c ------------------------------------------------------------------------------- lookup3.c, by Bob Jenkins, May 2006, Public Domain.
BurtleHasher() - Constructor for class com.actelion.research.util.BurtleHasher
 
BurtleHasherABC - Class in com.actelion.research.util
 
BurtleHasherABC(long, long, long) - Constructor for class com.actelion.research.util.BurtleHasherABC
 
buttonPressed(int) - Method in class com.actelion.research.gui.JDrawArea
 
ByteArray - Class in com.actelion.research.util
 
ByteArrayComparator - Class in com.actelion.research.util
 
ByteArrayComparator() - Constructor for class com.actelion.research.util.ByteArrayComparator
 
byteArrayToDouble(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
byteArrayToDoubleArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
byteArrayToInt(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
byteArrayToIntArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
ByteVec - Class in com.actelion.research.util.datamodel
ByteVec:
ByteVec(byte[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
 
ByteVec(int) - Constructor for class com.actelion.research.util.datamodel.ByteVec
 
ByteVec(int[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
 
ByteVec(ByteVec) - Constructor for class com.actelion.research.util.datamodel.ByteVec
Deep copy
ByteVec(String) - Constructor for class com.actelion.research.util.datamodel.ByteVec
Hash code is calculated.

C

c - Variable in class com.actelion.research.util.BurtleHasherABC
 
C - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
CacheEntry(Coordinates[][], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
 
calcFeatureSim(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
calcMin(StereoMolecule) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
calculate() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
calculate() - Method in class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
 
calculate() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
 
calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
calculates the total volume and size of the node from its elements
calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
calculate(double, double, double, double, int[]) - Static method in class com.actelion.research.chem.prediction.DrugScoreCalculator
 
calculate(StereoMolecule) - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
 
calculate(List<PharmacophoreNode>, List<PharmacophoreNode>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
calculateAverageBondLength() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
calculateBondOrders(Molecule3D) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
Calculate the bond orders of the molecule (without knowing the hydrogens).
calculateCollisionTolerance() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
calculateCorrelation(INumericalDataColumn, INumericalDataColumn, int) - Method in class com.actelion.research.calc.CorrelationCalculator
Calculates the correlation coefficient between two columns of data.
calculateDescriptor(int[]) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
Calculates the torsion descriptor for the current coordinates.
calculateHash() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
 
calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
 
calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
calculateHash(T) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
Stores the hash in f.
calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntArray
 
calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntVec
 
calculateHashCode(IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
calculateHeight() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
 
calculateHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
calculateHeight() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
calculateHeight() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
calculateHeight() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
calculateMassCovarianceMatrix(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
calculateMatrix(INumericalDataColumn[], int) - Method in class com.actelion.research.calc.CorrelationCalculator
Calculates a half correlation matrix of all passed numerical columns
calculatePreferredAttachmentAngle(double, double, int, double) - Method in class com.actelion.research.chem.coords.InventorFragment
 
calculateProbabilities() - Method in class com.actelion.research.chem.AtomTypeList
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.AxialStereoRule
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.DistanceRule
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.PlaneRule
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TorsionRule
 
calculateScore(ResultFragmentsStatistic) - Method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
28.08.2013
calculateSimilarity() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
calculateStrain(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
calculateTorsion(int[]) - Method in class com.actelion.research.chem.conf.Conformer
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
calculateTorsion(int[]) - Method in class com.actelion.research.chem.Molecule
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
calculateTorsionExtended(Conformer, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
Calculates a signed torsion like calculateTorsion().
calculateTorsionExtended(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
Calculates a signed torsion like calculateTorsion().
calculateVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
calculateWidth() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
 
calculateWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
calculateWidth() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
calculateWidth() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
calculateWidth() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
calculationFailed(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
calculationFailed(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
calculationFailed(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
calculationFailed(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
calculationFailed(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
calculationFailed(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
calculationFailed(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
calculationFailed(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
cAllowedAtomicNo - Static variable in class com.actelion.research.chem.Mutation
 
cAllowLogModeForNegativeOrZeroValues - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
candidatePose - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
canDrop() - Method in class com.actelion.research.gui.JChemistryView
 
canDrop() - Method in class com.actelion.research.gui.JStructureView
 
canonize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
canonizeCharge(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Normalizes charge distribution in single- and multifragment molecules.
canonizeCharge(boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Normalizes charge distribution in single- and multifragment molecules.
Canonizer - Class in com.actelion.research.chem
 
Canonizer(StereoMolecule) - Constructor for class com.actelion.research.chem.Canonizer
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
Canonizer(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Canonizer
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
CanonizerBaseValue - Class in com.actelion.research.chem
 
CanonizerBaseValue(int) - Constructor for class com.actelion.research.chem.CanonizerBaseValue
 
CanonizerMesoHelper - Class in com.actelion.research.chem
 
CanonizerMesoHelper(ExtendedMolecule, int[], boolean[], byte[], byte[], byte[], byte[], byte[], byte[], boolean[], boolean[], boolean[]) - Constructor for class com.actelion.research.chem.CanonizerMesoHelper
 
CanonizerUtil - Class in com.actelion.research.chem
 
CanonizerUtil() - Constructor for class com.actelion.research.chem.CanonizerUtil
 
CanonizerUtil.IDCODE_TYPE - Enum in com.actelion.research.chem
 
CanonizerUtil.StrongHasher - Class in com.actelion.research.chem
64 bit hash, derived from numerical recipes Will move this class later to dd_core.
canWriteAndDeleteInPath(File) - Static method in class com.actelion.research.util.IO
 
CAPACITY_INEVITABLE_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
Carbon - Static variable in class com.actelion.research.chem.PeriodicTable
 
CARBOXYL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
cat(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
CATALYST_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
cAtomCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
 
cAtomCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
 
cAtomCIPParityRorM - Static variable in class com.actelion.research.chem.Molecule
 
cAtomCIPParitySorP - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorBlue - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorDarkGreen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorDarkRed - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorGreen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorMagenta - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorNone - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorOrange - Static variable in class com.actelion.research.chem.Molecule
 
cAtomColorRed - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagAllylic - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagConfigurationUnknown - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagMarked - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlags2RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlags3RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlags4RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsESR - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsHelper - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsParity - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsRingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagStabilized - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagStereoProblem - Static variable in class com.actelion.research.chem.Molecule
 
cAtomFlagsValence - Static variable in class com.actelion.research.chem.Molecule
 
cAtomLabel - Static variable in class com.actelion.research.chem.Molecule
 
cAtomParity1 - Static variable in class com.actelion.research.chem.Molecule
 
cAtomParity2 - Static variable in class com.actelion.research.chem.Molecule
 
cAtomParityIsPseudo - Static variable in class com.actelion.research.chem.Molecule
 
cAtomParityNone - Static variable in class com.actelion.research.chem.Molecule
 
cAtomParityUnknown - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFAny - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFAromState - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFCharge - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFChargeBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFChargeShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFExcludeGroup - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFFlatNitrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFHydrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFHydrogenBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFHydrogenShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNeighbourBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNeighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNeighbourShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNoMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot0Hydrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot0Neighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot0PiElectrons - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot1Hydrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot1Neighbour - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot1PiElectron - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot2Hydrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot2Neighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot2PiElectrons - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot2RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot3Hydrogen - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot3Neighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot3RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot4Neighbours - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNot4RingBonds - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNotChain - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNotCharge0 - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNotChargeNeg - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFNotChargePos - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFPiElectronBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFPiElectrons - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFPiElectronShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingSize - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingState - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityBits - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityHint - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityInvert - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityRacemize - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityRetain - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFRxnParityShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalState - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalStateD - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalStateNone - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalStateS - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalStateShift - Static variable in class com.actelion.research.chem.Molecule
 
cAtomRadicalStateT - Static variable in class com.actelion.research.chem.Molecule
 
cAtomValence - Static variable in class com.actelion.research.chem.Molecule
 
cAutoStartMacro - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cBondCIPParityEorP - Static variable in class com.actelion.research.chem.Molecule
 
cBondCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
 
cBondCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
 
cBondCIPParityZorM - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagDelocalized - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagRing - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagsCIPParityShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagsESR - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
 
cBondFlagsParity - Static variable in class com.actelion.research.chem.Molecule
 
cBondParityEor1 - Static variable in class com.actelion.research.chem.Molecule
 
cBondParityNone - Static variable in class com.actelion.research.chem.Molecule
 
cBondParityUnknown - Static variable in class com.actelion.research.chem.Molecule
 
cBondParityZor2 - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFAllFeatures - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFAromState - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBondTypes - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBondTypesBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBondTypesShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridge - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeMin - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeMinBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeMinShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeSpan - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeSpanBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFBridgeSpanShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFDelocalized - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFDouble - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFMetalLigand - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFNotRing - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRing - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingSize - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingState - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFSingle - Static variable in class com.actelion.research.chem.Molecule
 
cBondQFTriple - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeCross - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeDeleted - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeDelocalized - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeDouble - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeDown - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeIncreaseOrder - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeMaskSimple - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeMaskStereo - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeMetalLigand - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeSingle - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeTriple - Static variable in class com.actelion.research.chem.Molecule
 
cBondTypeUp - Static variable in class com.actelion.research.chem.Molecule
 
cButtonCleanStructure - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cButtonClear - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cButtonsPerColumn - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cButtonUndo - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cChainCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cChiralityDiastereomers - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityEpimers - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityIsomerCountMask - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityKnownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityMeso - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityNotChiral - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityRacemic - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityUnknown - Static variable in class com.actelion.research.chem.Molecule
 
cChiralityUnknownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
 
cCLogPUnknown - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
 
cColorGray - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cColumnName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnNameRowList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnProperty - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyBinBase - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyBinIsDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyBinIsLog - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyBinSize - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyCommentDepartment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyCommentUploadStatus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyCyclicDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDataMin - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDescriptorVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDetailCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDetailName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDetailSource - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDetailType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyDisplayGroup - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyFormula - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyGroupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyImagePath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyIsClusterNo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyIsDisplayable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyIsFragment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchAllowMultiple - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchCommand - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchDecoration - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLaunchOption - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupDetailURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupEncode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupFilterRemoveMinus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyLookupURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyOpenExternalName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyOpenExternalPath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyOrbitType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyParentColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReactionPart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReferencedColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReferenceStrengthColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReferenceType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReferenceTypeRedundant - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyReferenceTypeTopDown - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyRelatedCatalystColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyRelatedIdentifierColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertySpecialType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertySuperpose - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertySuperposeAlign - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertySuperposeMolecule - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnPropertyUseThumbNail - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnRelationTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnType2DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnType3DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnTypeAtomColorInfo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnTypeIDCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnTypeReactionMapping - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnTypeReactionObjects - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnTypeRXNCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnUnassignedCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cColumnUnassignedItemText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cCommonOxidationState - Static variable in class com.actelion.research.chem.Molecule
 
cCountModeExistance - Static variable in class com.actelion.research.chem.SSSearcher
 
cCountModeFirstMatch - Static variable in class com.actelion.research.chem.SSSearcher
 
cCountModeOverlapping - Static variable in class com.actelion.research.chem.SSSearcher
 
cCountModeRigorous - Static variable in class com.actelion.research.chem.SSSearcher
 
cCountModeSeparated - Static variable in class com.actelion.research.chem.SSSearcher
 
cDataDependentPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataDependentPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeAutomatic - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeNumerical - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeString - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDataTypeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDefaultAtomValence - Static variable in class com.actelion.research.chem.Molecule
 
cDefaultDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDefaultMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
 
cDeleteCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cDetailDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDetailDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDetailID - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDetailIndexSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cDModeAtomNo - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeBondNo - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeHiliteAllQueryFeatures - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeNoColorOnESRAndCIP - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeNoImplicitAtomLabelColors - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeNoStereoProblem - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeNoTabus - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeShowMapping - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeShowSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeShowSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeShowSymmetrySimple - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeSuppressChiralText - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeSuppressCIPParity - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cDModeSuppressESR - Static variable in class com.actelion.research.chem.AbstractDepictor
 
CDPBondAttach(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
 
CDPBondBegin(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondBegin
 
CDPBondEnd(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondEnd
 
CDPElement(short) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
 
CDPPoint2D(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
 
cDruglikenessUnknown - Static variable in class com.actelion.research.chem.prediction.DruglikenessPredictor
 
CDXConstants - Class in com.actelion.research.gui.clipboard.external
 
CDXConstants() - Constructor for class com.actelion.research.gui.clipboard.external.CDXConstants
 
CDXDocument() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
 
CDXPage() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
 
CDXReactionStep(int[], int[]) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
 
center - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
center() - Method in class com.actelion.research.chem.conf.Conformer
Translate this conformer's coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
center() - Method in class com.actelion.research.chem.Molecule
Translate this molecule's 3D-coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
center(Coordinates) - Method in class com.actelion.research.chem.Coordinates
Calculates the center point between this and c and sets this to the center point.
center(Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
Updates this to contains the center between c1 and c2.
CENTER - Static variable in class com.actelion.research.gui.VerticalFlowLayout
Description of the Field
cEntrySeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cEntrySeparatorBytes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cESRGroupBits - Static variable in class com.actelion.research.chem.Molecule
 
cESRMaxGroups - Static variable in class com.actelion.research.chem.Molecule
 
cESRTypeAbs - Static variable in class com.actelion.research.chem.Molecule
 
cESRTypeAnd - Static variable in class com.actelion.research.chem.Molecule
 
cESRTypeOr - Static variable in class com.actelion.research.chem.Molecule
 
cExtensionNameFileExplanation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cExtensionNameMacroList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cFileExplanationEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cFileExplanationStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cFileTypeDataWarrior - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDataWarriorCompatibleData - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDataWarriorMacro - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDataWarriorQuery - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDataWarriorTemplate - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDataWarriorTemplateContaining - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeDirectory - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeGIF - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeJPG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeMask - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeMOL - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeMOL2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypePDB - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypePictureFile - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypePNG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeRD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeRDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeRDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeRXN - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeSD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeSDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeSDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeSOM - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeSVG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeText - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeTextCommaSeparated - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeTextTabDelimited - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFileTypeUnknown - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
 
cFistCursor - Static variable in class com.actelion.research.util.CursorHelper
 
chainHiliteColor() - Static method in class com.actelion.research.gui.JDrawArea
 
cHandCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cHandPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
 
changeAtom(int, int, int, int, int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
ChangeAtomAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
ChangeAtomAction(Model, int) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
 
changeAtomCharge(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
changeAtomCharge(int, boolean) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
ChangeAtomPropertiesAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
ChangeAtomPropertiesAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
 
changeBond(int, int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
ChangeChargeAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
ChangeChargeAction(Model, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
 
changed() - Method in class com.actelion.research.share.gui.editor.Model
 
changed(Action) - Method in interface com.actelion.research.share.gui.editor.actions.ToolbarSelectionChange
 
charge - Variable in class com.actelion.research.chem.coords.InventorCharge
 
Charge - Class in com.actelion.research.chem.forcefield.mmff.table
 
Charge - Class in com.actelion.research.chem.forcefield.mmff.type
The charge class provides static functions for calculating formal and partial charges on a molecule.
Charge() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Charge
 
Charge(Tables, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Charge
 
CHARGE_NEG_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
CHARGE_POS_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
charge_term - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
ChargePoint - Class in com.actelion.research.chem.phesa.pharmacophore
 
ChargePoint(ChargePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
ChargePoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
CHARSET_ENCODING - Static variable in class com.actelion.research.util.ConstantsDWAR
 
check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
check(String, String) - Method in interface com.actelion.research.chem.forcefield.mmff.Sdf.OnMolecule
 
checkBiggestFragmentForUnwanted(StereoMolecule, List<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
checkCommandWithValue(String) - Method in class com.actelion.research.util.CommandLineParser
 
checkHiliting(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
checkHiliting(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
checkHiliting(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
 
cHelperBitCIP - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitIncludeNitrogenParities - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitNeighbours - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitParities - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitRings - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitRingsSimple - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitsStereo - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
 
cHelperBitSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
 
cHelperCIP - Static variable in class com.actelion.research.chem.Molecule
 
cHelperNeighbours - Static variable in class com.actelion.research.chem.Molecule
 
cHelperNone - Static variable in class com.actelion.research.chem.Molecule
 
cHelperParities - Static variable in class com.actelion.research.chem.Molecule
 
cHelperRings - Static variable in class com.actelion.research.chem.Molecule
 
cHelperRingsSimple - Static variable in class com.actelion.research.chem.Molecule
 
cHelperSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
 
cHelperSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
 
cHelperSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
 
CHEM_SIM_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
ChemDrawCDX - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
ChemDrawCDX.CDPAtomCharge - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPAtomCIP - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPAtomEnhGroup - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPAtomEnhStereoType - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPAtomIsotope - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPAtomRadical - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPBondAttach - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPBondBegin - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPBondDisplay - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPBondEnd - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPBondType - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPElement - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPPoint2D - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPProducts - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPReactants - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPShowAtomStereo - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPShowBondStereo - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPShowEnhAtomStereo - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDPText - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDXDocument - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDXPage - Class in com.actelion.research.gui.clipboard.external
 
ChemDrawCDX.CDXReactionStep - Class in com.actelion.research.gui.clipboard.external
 
ChemistryDataFormats - Class in com.actelion.research.chem.dnd
 
ChemistryDataFormats() - Constructor for class com.actelion.research.chem.dnd.ChemistryDataFormats
 
ChemistryFlavors - Class in com.actelion.research.chem.dnd
 
ChemistryFlavors() - Constructor for class com.actelion.research.chem.dnd.ChemistryFlavors
 
ChemistryHelper - Class in com.actelion.research.chem
 
ChemPLP - Class in com.actelion.research.chem.docking.scoring
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!
ChemPLP(Molecule3D, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.ChemPLP
 
CHEMPLP - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
 
chge - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
chi(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
Returns the 'chi' (or pauEle) parameter from the table at the given index.
CHI - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
CHI - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
cHighRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cHitlistData - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cHitlistDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cHitlistDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cHitlistName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
Chlorine - Static variable in class com.actelion.research.chem.PeriodicTable
 
chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
 
cIDCodeCurrentVersion - Static variable in class com.actelion.research.chem.Canonizer
 
cIDCodeVersion2 - Static variable in class com.actelion.research.chem.Canonizer
 
cIDCodeVersion3 - Static variable in class com.actelion.research.chem.Canonizer
 
cIndexMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
 
cIndexVersion - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
 
cInvisibleCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cKeyIDCode - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
 
ClassificationData - Class in com.actelion.research.chem.reaction
 
classify(StereoMolecule, int) - Method in class com.actelion.research.chem.conf.TorsionDetail
Determines uniquely an identifying name for the rotatable bond and its vicinity.
cLassoCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cLassoPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
 
CleanAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 10:09 AM
CleanAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CleanAction
 
cleanDate(String) - Static method in class com.actelion.research.util.Formatter
 
cleanDateTime(String) - Static method in class com.actelion.research.util.Formatter
 
cleanMolecule(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
cleanReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
cleanStructure() - Method in class com.actelion.research.gui.JDrawPanel
 
cleanupCoordinates(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
clear() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
clear() - Method in class com.actelion.research.chem.DepictorTransformation
 
clear() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
clear() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
clear() - Method in class com.actelion.research.chem.Molecule
Empties the molecule to serve as container for constructing a new molecule, e.g.
clear() - Method in class com.actelion.research.chem.Molecule3D
 
clear() - Method in class com.actelion.research.chem.reaction.Reaction
 
clear() - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
clear() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
clear() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
clear() - Method in class com.actelion.research.util.datamodel.IntArray
 
clear() - Method in class com.actelion.research.util.datamodel.IntVec
 
clear() - Method in class com.actelion.research.util.ErrorHashMap
 
clear() - Method in class com.actelion.research.util.hash.HashSetInt
 
clear() - Method in class com.actelion.research.util.IntQueue
 
clear() - Method in class com.actelion.research.util.Pipeline
 
clear() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
ClearAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/24/13 Time: 5:09 PM
ClearAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ClearAction
 
clearAll() - Method in class com.actelion.research.gui.JDrawArea
 
clearCovers(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
clearHiliting() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
clearHiliting() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
clearHiliting() - Method in class com.actelion.research.chem.TextDrawingObject
 
clearInfo() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
clearOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
clearRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
clearRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
cLineSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cLineSeparatorByte - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
clip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
CLIP_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
CLIP_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
CLIP_LH_ANGLES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
CLIP_MASK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
CLIP_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
CLIP_TT_ALWAYS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
ClipboardHandler - Class in com.actelion.research.gui.clipboard
Title: Actelion Library
ClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ClipboardHandler
 
ClipboardHelper - Class in com.actelion.research.jfx.gui.misc
Created by baerr on 7/28/14.
clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
CLogPPredictor - Class in com.actelion.research.chem.prediction
 
CLogPPredictor() - Constructor for class com.actelion.research.chem.prediction.CLogPPredictor
 
clone() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
clone() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
clone() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
clone() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
clone() - Method in class com.actelion.research.chem.TextDrawingObject
 
clone() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
clone() - Method in class com.actelion.research.util.DoubleVec
 
close() - Method in class com.actelion.research.chem.io.CompoundFileParser
Closes the underlying reader.
close() - Method in class com.actelion.research.io.StringReadChannel
 
close() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
close() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
cLowRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
ClusterNode - Class in com.actelion.research.chem.descriptor.flexophore
 
ClusterNode(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
cMacroListEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cMacroListStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cMatchAromDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
 
cMatchAtomCharge - Static variable in class com.actelion.research.chem.SSSearcher
 
cMatchAtomMass - Static variable in class com.actelion.research.chem.SSSearcher
 
cMatchDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
 
cMaxAtomicNo - Static variable in class com.actelion.research.chem.Molecule
 
cMaxConnAtoms - Static variable in class com.actelion.research.chem.ExtendedMolecule
 
cMaxDateOrDoubleCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cMaxTextCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
CMNT_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
 
cModeChiralTextAboveMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeChiralTextBelowMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeChiralTextOnFrameBottom - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeChiralTextOnFrameTop - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeInflateToAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeInflateToHighResAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeInflateToMaxAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cModeMaxBondLength - Static variable in class com.actelion.research.chem.AbstractDepictor
 
cMoleculeColorDefault - Static variable in class com.actelion.research.chem.Molecule
 
cMoleculeColorNeutral - Static variable in class com.actelion.research.chem.Molecule
 
cNativeFileCreated - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cNativeFileHeaderEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cNativeFileHeaderStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cNativeFileRowCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cNativeFileVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cNewLineString - Static variable in class com.actelion.research.chem.io.RDFileParser
 
cNewLineString - Static variable in class com.actelion.research.chem.io.SDFileParser
 
cNoRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
coeff - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
collectionUpdated(int, int) - Method in interface com.actelion.research.gui.CompoundCollectionListener
 
collectionUpdated(int, int) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
color - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
 
COLOR_BLUE - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_DARK_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_DARK_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_FOR_CENTER_SELECTION - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
COLOR_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_MAGENTA - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_ORANGE - Static variable in class com.actelion.research.chem.AbstractDepictor
 
COLOR_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
 
ColorHelper - Class in com.actelion.research.util
 
ColorHelper() - Constructor for class com.actelion.research.util.ColorHelper
 
COLORS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Colors for visualization of the Flexophore mapping.
colorToString(Color) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
 
ColorUtils - Class in com.actelion.research.gui.hidpi
Defines a color with some utility methods.
ColorUtils() - Constructor for class com.actelion.research.gui.hidpi.ColorUtils
 
cols() - Method in class com.actelion.research.calc.Matrix
 
com.actelion.research.calc - package com.actelion.research.calc
 
com.actelion.research.calc.combinatorics - package com.actelion.research.calc.combinatorics
 
com.actelion.research.calc.filter - package com.actelion.research.calc.filter
 
com.actelion.research.calc.geometry - package com.actelion.research.calc.geometry
 
com.actelion.research.calc.graph - package com.actelion.research.calc.graph
 
com.actelion.research.calc.histogram - package com.actelion.research.calc.histogram
 
com.actelion.research.calc.regression.linear.simple - package com.actelion.research.calc.regression.linear.simple
 
com.actelion.research.calc.statistics.median - package com.actelion.research.calc.statistics.median
 
com.actelion.research.chem - package com.actelion.research.chem
 
com.actelion.research.chem.alignment3d - package com.actelion.research.chem.alignment3d
 
com.actelion.research.chem.conf - package com.actelion.research.chem.conf
 
com.actelion.research.chem.conf.torsionstrain - package com.actelion.research.chem.conf.torsionstrain
 
com.actelion.research.chem.contrib - package com.actelion.research.chem.contrib
 
com.actelion.research.chem.coords - package com.actelion.research.chem.coords
 
com.actelion.research.chem.descriptor - package com.actelion.research.chem.descriptor
 
com.actelion.research.chem.descriptor.flexophore - package com.actelion.research.chem.descriptor.flexophore
 
com.actelion.research.chem.descriptor.flexophore.calculator - package com.actelion.research.chem.descriptor.flexophore.calculator
 
com.actelion.research.chem.descriptor.flexophore.completegraphmatcher - package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
 
com.actelion.research.chem.descriptor.flexophore.entity - package com.actelion.research.chem.descriptor.flexophore.entity
 
com.actelion.research.chem.descriptor.flexophore.generator - package com.actelion.research.chem.descriptor.flexophore.generator
 
com.actelion.research.chem.descriptor.flexophore.redgraph - package com.actelion.research.chem.descriptor.flexophore.redgraph
 
com.actelion.research.chem.descriptor.pharmacophoretree - package com.actelion.research.chem.descriptor.pharmacophoretree
 
com.actelion.research.chem.dnd - package com.actelion.research.chem.dnd
 
com.actelion.research.chem.docking - package com.actelion.research.chem.docking
 
com.actelion.research.chem.docking.scoring - package com.actelion.research.chem.docking.scoring
 
com.actelion.research.chem.docking.scoring.chemscore - package com.actelion.research.chem.docking.scoring.chemscore
 
com.actelion.research.chem.docking.scoring.idoscore - package com.actelion.research.chem.docking.scoring.idoscore
 
com.actelion.research.chem.docking.scoring.plp - package com.actelion.research.chem.docking.scoring.plp
 
com.actelion.research.chem.forcefield - package com.actelion.research.chem.forcefield
 
com.actelion.research.chem.forcefield.mmff - package com.actelion.research.chem.forcefield.mmff
 
com.actelion.research.chem.forcefield.mmff.table - package com.actelion.research.chem.forcefield.mmff.table
 
com.actelion.research.chem.forcefield.mmff.type - package com.actelion.research.chem.forcefield.mmff.type
 
com.actelion.research.chem.interactionstatistics - package com.actelion.research.chem.interactionstatistics
 
com.actelion.research.chem.io - package com.actelion.research.chem.io
 
com.actelion.research.chem.io.pdb.converter - package com.actelion.research.chem.io.pdb.converter
 
com.actelion.research.chem.io.pdb.parser - package com.actelion.research.chem.io.pdb.parser
 
com.actelion.research.chem.mcs - package com.actelion.research.chem.mcs
 
com.actelion.research.chem.name - package com.actelion.research.chem.name
 
com.actelion.research.chem.optimization - package com.actelion.research.chem.optimization
 
com.actelion.research.chem.phesa - package com.actelion.research.chem.phesa
 
com.actelion.research.chem.phesa.pharmacophore - package com.actelion.research.chem.phesa.pharmacophore
 
com.actelion.research.chem.phesaflex - package com.actelion.research.chem.phesaflex
 
com.actelion.research.chem.potentialenergy - package com.actelion.research.chem.potentialenergy
 
com.actelion.research.chem.prediction - package com.actelion.research.chem.prediction
 
com.actelion.research.chem.properties.complexity - package com.actelion.research.chem.properties.complexity
 
com.actelion.research.chem.properties.fractaldimension - package com.actelion.research.chem.properties.fractaldimension
 
com.actelion.research.chem.reaction - package com.actelion.research.chem.reaction
 
com.actelion.research.chem.shredder - package com.actelion.research.chem.shredder
 
com.actelion.research.gui - package com.actelion.research.gui
 
com.actelion.research.gui.clipboard - package com.actelion.research.gui.clipboard
 
com.actelion.research.gui.clipboard.external - package com.actelion.research.gui.clipboard.external
 
com.actelion.research.gui.dnd - package com.actelion.research.gui.dnd
 
com.actelion.research.gui.hidpi - package com.actelion.research.gui.hidpi
 
com.actelion.research.gui.wmf - package com.actelion.research.gui.wmf
 
com.actelion.research.io - package com.actelion.research.io
 
com.actelion.research.jfx.dataformat - package com.actelion.research.jfx.dataformat
 
com.actelion.research.jfx.gui - package com.actelion.research.jfx.gui
 
com.actelion.research.jfx.gui.chem - package com.actelion.research.jfx.gui.chem
 
com.actelion.research.jfx.gui.misc - package com.actelion.research.jfx.gui.misc
 
com.actelion.research.share.gui - package com.actelion.research.share.gui
 
com.actelion.research.share.gui.editor - package com.actelion.research.share.gui.editor
 
com.actelion.research.share.gui.editor.actions - package com.actelion.research.share.gui.editor.actions
 
com.actelion.research.share.gui.editor.chem - package com.actelion.research.share.gui.editor.chem
 
com.actelion.research.share.gui.editor.dialogs - package com.actelion.research.share.gui.editor.dialogs
 
com.actelion.research.share.gui.editor.geom - package com.actelion.research.share.gui.editor.geom
 
com.actelion.research.share.gui.editor.io - package com.actelion.research.share.gui.editor.io
 
com.actelion.research.share.gui.editor.listeners - package com.actelion.research.share.gui.editor.listeners
 
com.actelion.research.util - package com.actelion.research.util
 
com.actelion.research.util.concurrent - package com.actelion.research.util.concurrent
 
com.actelion.research.util.convert - package com.actelion.research.util.convert
 
com.actelion.research.util.datamodel - package com.actelion.research.util.datamodel
 
com.actelion.research.util.datamodel.table - package com.actelion.research.util.datamodel.table
 
com.actelion.research.util.graph.complete - package com.actelion.research.util.graph.complete
 
com.actelion.research.util.hash - package com.actelion.research.util.hash
 
CombinationGenerator - Class in com.actelion.research.calc.combinatorics
CombinationGenerator
CombinationGenerator() - Constructor for class com.actelion.research.calc.combinatorics.CombinationGenerator
 
combineIntsToLong(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
CommandAction - Class in com.actelion.research.share.gui.editor.actions
Abstract class for handling of all the actions which handle single type of actions: the action is executed when pressing the button and the current drawing action will remain unchanged
CommandAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CommandAction
 
CommandLineParser - Class in com.actelion.research.util
CommandLineParser Simple command line parser.
CommandLineParser() - Constructor for class com.actelion.research.util.CommandLineParser
 
CommandLineParser(String[]) - Constructor for class com.actelion.research.util.CommandLineParser
 
CommandLineParser(String, String) - Constructor for class com.actelion.research.util.CommandLineParser
 
CommonSubGraphHelper - Class in com.actelion.research.chem.reaction
 
CommonSubGraphHelper() - Constructor for class com.actelion.research.chem.reaction.CommonSubGraphHelper
 
compact() - Method in class com.actelion.research.chem.Molecule3D
 
compare(byte[], byte[]) - Method in class com.actelion.research.util.ByteArrayComparator
 
compare(int[], int[]) - Method in class com.actelion.research.util.IntArrayComparator
 
compareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
compareArrays(byte[], byte[]) - Static method in class com.actelion.research.util.ByteArray
 
compareArrays(byte[], byte[], int) - Static method in class com.actelion.research.util.ByteArray
 
compareTo(CanonizerBaseValue) - Method in class com.actelion.research.chem.CanonizerBaseValue
 
compareTo(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
 
compareTo(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE; Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
compareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
compareTo(ClusterNode) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
compareTo(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
compareTo(PPNodeVizTriangle) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
compareTo(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
Compares this object with another.
compareTo(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
 
compareTo(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
 
compareTo(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
 
compareTo(IdentifiedObject<T>) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
compareTo(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
 
compareTo(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
 
compareTo(SolutionCompleteGraph) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
compareTo(RigidFragmentCache.CacheEntry) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
 
compareTo(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.
CompleteGraphMatcher<T extends ICompleteGraph> - Class in com.actelion.research.util.graph.complete
CompleteGraphMatcher
CompleteGraphMatcher(IObjectiveCompleteGraph<T>) - Constructor for class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
CompoundCollectionListener - Interface in com.actelion.research.gui
 
CompoundCollectionModel<T> - Interface in com.actelion.research.gui
 
CompoundCollectionPane<T> - Class in com.actelion.research.gui
 
CompoundCollectionPane(CompoundCollectionModel<T>, boolean) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
This is a visual component to display and edit a compound collection maintained by a CompoundCollectionModel.
CompoundCollectionPane(CompoundCollectionModel<T>, boolean, int, int, int) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
 
CompoundFileFilter - Class in com.actelion.research.chem.io
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
CompoundFileFilter() - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
Creates a file filter.
CompoundFileFilter(String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
Creates a file filter that accepts files with the given extension.
CompoundFileFilter(String[]) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
Creates a file filter from the given string array.
CompoundFileFilter(String[], String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
Creates a file filter from the given string array and description.
CompoundFileFilter(String, String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
Creates a file filter that accepts the given file type.
CompoundFileHelper - Class in com.actelion.research.chem.io
 
CompoundFileHelper() - Constructor for class com.actelion.research.chem.io.CompoundFileHelper
 
CompoundFileParser - Class in com.actelion.research.chem.io
 
CompoundFileParser() - Constructor for class com.actelion.research.chem.io.CompoundFileParser
 
CompoundTableConstants - Interface in com.actelion.research.chem.io
 
compressMolTable() - Method in class com.actelion.research.chem.Molecule
 
compressMolTable() - Method in class com.actelion.research.chem.Molecule3D
 
cond() - Method in class com.actelion.research.calc.SingularValueDecomposition
Two norm condition number
CONF_GIVEN_SINGLE_CONFORMATION - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
ConformationRule - Class in org.openmolecules.chem.conf.so
 
ConformationRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.ConformationRule
 
ConformationSelfOrganizer - Class in org.openmolecules.chem.conf.so
 
ConformationSelfOrganizer(StereoMolecule, boolean) - Constructor for class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
Generates a new ConformationSelfOrganizer from the given molecule.
Conformer - Class in com.actelion.research.chem.conf
 
Conformer(Conformer) - Constructor for class com.actelion.research.chem.conf.Conformer
Creates a new conformer as an exact copy of the given one.
Conformer(Conformer, StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
Use at own risk!! Initializes the conformer as a copy of c but replaces the StereoMolecule by the supplied molecule.
Conformer(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
Creates a Conformer, i.e.
ConformerGenerator - Class in org.openmolecules.chem.conf.gen
This class generates 3D-conformers of a given molecule using the following strategy: All rotatable, non-ring bonds are determined.
ConformerGenerator() - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
Instantiates a ConformerGenerator for creating non-reproducible conformers.
ConformerGenerator(boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
Instantiates a ConformerGenerator for creating non-reproducible conformers.
ConformerGenerator(long, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
ConformerGenerator(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
ConformerGenerator(long, RigidFragmentProvider) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
ConformerSet - Class in com.actelion.research.chem.conf
 
ConformerSet() - Constructor for class com.actelion.research.chem.conf.ConformerSet
 
ConformerSet(String) - Constructor for class com.actelion.research.chem.conf.ConformerSet
 
ConformerSetGenerator - Class in com.actelion.research.chem.conf
 
ConformerSetGenerator() - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
STRATEGY_LIKELY_RANDOM was evaluated to be the best strategy for reproducing bioactive conformers (J.W.
ConformerSetGenerator(boolean) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
 
ConformerSetGenerator(boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
 
ConformerSetGenerator(int, int, boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
 
connected(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Returns the rotatable bonds (sorted).
connected(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
 
connectFragments(Conformer, boolean[], int[]) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
Checks both rigid fragments that are connected by this bond, whether they have been attached to the conformer yet, i.e.
ConnectionPoint - Static variable in class com.actelion.research.chem.PeriodicTable
 
CONSIDER_DIASTEREOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
 
CONSIDER_ENANTIOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
 
CONSIDER_STEREOHETEROTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
 
Constants - Class in com.actelion.research.chem.forcefield.mmff
The Constants class holds numerical constants that are reused in multiple classes.
ConstantsAminoAcidsLabeled - Class in com.actelion.research.chem.io.pdb.converter
ConstantsAminoAcidsLabeled
ConstantsAminoAcidsLabeled() - Constructor for class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
 
ConstantsDWAR - Class in com.actelion.research.util
ConstantsDWAR
ConstantsDWAR() - Constructor for class com.actelion.research.util.ConstantsDWAR
 
ConstantsFlexophore - Class in com.actelion.research.chem.descriptor.flexophore
 
ConstantsFlexophore() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
 
ConstantsFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
 
ConstantsFlexophoreGenerator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
ConstantsFlexophoreHardPPPoints - Class in com.actelion.research.chem.descriptor.flexophore
 
ConstantsFlexophoreHardPPPoints() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
ConstantsHistogram - Class in com.actelion.research.calc.histogram
ConstantsHistogram
ConstantsHistogram() - Constructor for class com.actelion.research.calc.histogram.ConstantsHistogram
 
ContainerBitArray - Class in com.actelion.research.chem.properties.complexity
 
ContainerBitArray(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
ContainerFragBondsSolutions - Class in com.actelion.research.chem.properties.complexity
 
ContainerFragBondsSolutions(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
Fragments are represented as bit arrays.
ContainerListWithIntVec - Class in com.actelion.research.chem.mcs
 
ContainerListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ContainerListWithIntVec
 
ContainerMemory<S extends AMemorizedObject> - Class in com.actelion.research.util.graph.complete
ContainerMemory
ContainerMemory(int, IFactory<S>) - Constructor for class com.actelion.research.util.graph.complete.ContainerMemory
 
contains(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
Checks, whether this drawing object contains the point at x,y
contains(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
contains(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
 
contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
 
contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
contains(double, double) - Method in class com.actelion.research.share.gui.Polygon
 
contains(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
contains(int) - Method in class com.actelion.research.util.hash.HashSetInt
 
contains(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
contains(Point2D) - Method in class com.actelion.research.share.gui.Polygon
 
contains(String) - Method in class com.actelion.research.chem.SortedStringList
 
contains(String) - Method in class com.actelion.research.util.CommandLineParser
 
contains(List<int[]>, int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
contains(T) - Method in class com.actelion.research.util.SortedList
 
contains(T) - Method in class com.actelion.research.util.UniqueList
 
containsAtLeastOneAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
containsColumn(String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
containsFragmentOpenRing(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
 
containsHeteroAtom(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
containsInteractionID(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
containsLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
containsRow(DoubleVec) - Method in class com.actelion.research.calc.Matrix
 
containsSolelyAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
containsUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
contentChanged(DrawAreaEvent) - Method in interface com.actelion.research.gui.DrawAreaListener
 
convert(String) - Static method in class com.actelion.research.util.convert.String2DoubleArray
 
convert(ArrayList) - Static method in class com.actelion.research.util.convert.String2DoubleArray
 
convertDataToPrimitiveTypes(List<Molecule3D>) - Static method in class com.actelion.research.chem.io.AbstractParser
 
convertPath(int[][], int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
convertStereoBondsToSingleBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Converts any stereo bond attached with its pointed tip to this atom into a single bond.
convertToValidFileNameCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
Not allowed are: \ / : * ? < > |
CoordinateInventor - Class in com.actelion.research.chem.coords
 
CoordinateInventor() - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
Creates an CoordinateInventor, which removes unneeded hydrogen atoms and creates new atom coordinates for all(!) atoms.
CoordinateInventor(int) - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
Creates an CoordinateInventor, which removes unneeded hydrogens, if mode flags include MODE_REMOVE_HYDROGEN.
coordinates - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
 
Coordinates - Class in com.actelion.research.chem
Class to encapsulate 3D coordinates
Coordinates() - Constructor for class com.actelion.research.chem.Coordinates
 
Coordinates(double, double, double) - Constructor for class com.actelion.research.chem.Coordinates
 
Coordinates(Coordinates) - Constructor for class com.actelion.research.chem.Coordinates
 
coordinatesAre3D(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
coordinatesAre3D(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
coordinatesAre3D(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
coordinatesAreAbsolute(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
coordinatesAreAbsolute(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
coordinatesAreAbsolute(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
COORDS_ARE_3D - Static variable in class com.actelion.research.chem.Canonizer
 
coordVariance(int) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
cOptAvBondLen - Static variable in class com.actelion.research.chem.AbstractDepictor
 
copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
copy(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
copy(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
copy(Matrix) - Method in class com.actelion.research.calc.Matrix
Copies a matrix ma into this, the pointer to ma1 is not changed.
copy(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
copy(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
copy(MolDistHistViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
copy(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
Copy of node into this.
copy(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
Copy of node into this
copy(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
copy(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
 
copy(Object) - Static method in class com.actelion.research.util.ArrayUtils
Copy an array
copy(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
CopyAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 5/16/13 Time: 3:31 PM
CopyAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CopyAction
 
copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule
Creates a new atom in destMol and copies all source atom properties including atom list, custom label, flags, and mapNo to it.
copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule3D
 
copyAtoms(Molecule3D, Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
copyBond(Molecule, int, int, int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
 
copyBond(Molecule, int, int, int, int, int, boolean) - Method in class com.actelion.research.chem.Molecule
 
copyColumn(Matrix, int, int) - Method in class com.actelion.research.calc.Matrix
 
copyFrom(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
Copies the conformer's atom coordinates to this Conformer.
copyFrom(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
Copies the molecule's atom coordinates to this Conformer.
copyImage(Image) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Copies an Image to the clipboard
copyImage(Image) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
copyImage(Image) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
 
copyIntArray(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
copyIntoThis(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
copyIntoThis(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
Deep copy The index is not copied
copyIntoThis(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
Has to be a deep copy
copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
copyMetaFile(byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
Copy a windows enhance metafile to the Windows clipboard
copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
 
copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
copyMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
Copies this molecule including parity settings, if valid.
copyMolecule(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Copies a molecule to the clipboard in various formats: ENHMETAFILE with an embedded sketch MDLSK Sketch MDLCT MDL molfile
copyMolecule(StereoMolecule) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
copyMolecule(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
 
copyMolecule(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
copyMoleculeByAtoms(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of atoms to be included.
copyMoleculeByBonds(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of bonds to be included.
copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.Molecule
Copies name,isFragment,chirality and validity of parity & CIP flags.
copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.StereoMolecule
Copies name, isFragment, chirality.
copyMoleculeToClipboard(String, byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
copyOf(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
copyPharmacophorePoint() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
 
copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
copyReaction(Reaction) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Copies a reaction to the clipboard in various formats: MDLSK Sketch MDLCT MDL molfile
copyReaction(Reaction) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
copyReaction(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Copies a reaction to the clipboard in various formats: CTAB with an embedded sketch MDLSK Sketch serialized
copyReaction(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
copyReactionToClipboard(byte[], byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
copySizedMoleculeToClipboard(String, byte[], byte[], int, int) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
copyText(String) - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
 
copyTo(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
Copies this conformer's atom coordinates to mol.
coreToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
correlation() - Method in class com.actelion.research.calc.Matrix
Generate a correlation matrix, each column contains values of a pulling.
CorrelationCalculator - Class in com.actelion.research.calc
 
CorrelationCalculator() - Constructor for class com.actelion.research.calc.CorrelationCalculator
 
cos() - Method in class com.actelion.research.util.Angle
 
cosAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
cosAngle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns the cosine of the angle between this vector and that vector.
Cosine(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Vectors have to be normed!
COSINE - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
COSINE - Static variable in class com.actelion.research.util.DoubleVec
 
countIntegerInText(String) - Static method in class com.actelion.research.util.StringFunctions
 
countOccurence(String, char) - Static method in class com.actelion.research.util.StringFunctions
 
countWordInText(String) - Static method in class com.actelion.research.util.StringFunctions
 
COVALENT_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
These covalent single bond radii values were taken from the following source: 'Molecular Double-Bond Covalent Radii for Elements Li–E112', 2009, Pyykkö and Atsumi, doi: 10.1002/chem.200901472
covariance() - Method in class com.actelion.research.calc.Matrix
Generate a covariance matrix, each column contains values of a pulling.
covrad - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
CovRad - Class in com.actelion.research.chem.forcefield.mmff.table
CovRad table, used in the bond stretch empirical calculations of 'kb' and 'r0'.
CovRad(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.CovRad
 
cParentSpecialColumnTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cParity1And - Static variable in class com.actelion.research.chem.Canonizer
 
cParity1Or - Static variable in class com.actelion.research.chem.Canonizer
 
cParity2And - Static variable in class com.actelion.research.chem.Canonizer
 
cParity2Or - Static variable in class com.actelion.research.chem.Canonizer
 
cPointedHandCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cPointerCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cPolarAtomTypeName - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
cPropertiesAll - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomAllylic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomCharged - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomRingCount - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomRingSize - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesBasicType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomNeighbours - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomNeighboursExact - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnAtomTypeSimple - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesConnBondOrder - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cPropertiesForCLogP - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesForCLogPCharges - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesForMutator - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesForSolubility - Static variable in class com.actelion.research.chem.AtomTypeCalculator
 
cPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cPSAUnknown - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
cRangeNotAvailable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cRangeSeparation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
crd(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the CRD type of an atom given its MMFF type.
cReactionHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionHiliteModeReactionCenter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionPartDelimiter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionPartProducts - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionPartReactants - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cReactionPartReaction - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
create() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
 
create() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
create() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
create(Conformer, int[], String) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
 
create(Conformer, int, int[], Coordinates, double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
 
create(Conformer, Conformer, int, int) - Static method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
create(Conformer, Conformer, int, int, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
 
create(Conformer, Conformer, int, int, int[], int[]) - Static method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
 
create(Conformer, Conformer, int, int, int, boolean, boolean, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
 
create(Conformer, Conformer, int, int, Map<String, Double>) - Static method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
create(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
create(StereoMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
Creates a list with ModelExhaustiveStatistics.
create(IDCodeCoord) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
 
create(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
 
create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
 
create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
 
create(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
 
create(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
 
create(String, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
 
create(List<PPGaussian>, Coordinates) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleCreator
 
CREATE_PSEUDO_STEREO_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
 
CREATE_SYMMETRY_RANK - Static variable in class com.actelion.research.chem.Canonizer
 
createArrow(Rectangle2D) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
createAtomPropertiesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
createAtomQueryFeatureDialog(StereoMolecule, int, boolean) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
createBarycenter(Coordinates...) - Static method in class com.actelion.research.chem.Coordinates
 
createBondFeaturesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
createBonds(Molecule3D, boolean) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
Calculates the bonds of a molecule by checking the distance between all atoms.
createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.WMF
 
createCache(String[], String, int, boolean, int, RigidFragmentProvider) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
This is a helper method to generate a custom cache and optionally a set of cache files from one or more compound files.
createCanonicalOrientation(Conformer, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
createColor(double, double, double, double) - Method in class com.actelion.research.share.gui.DrawConfig
 
createColor(long) - Static method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
createColor(Color, float) - Static method in class com.actelion.research.util.ColorHelper
Creates a new color with the hue taken from color c, but adjusted in brightness to match the desired perceived brightness.
createColor(Color, int) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
 
createCursor(int) - Static method in class com.actelion.research.util.CursorHelper
 
createDefaultDocument() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
 
createDepictor(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
createDepictor(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
 
createDepictor(StereoMolecule, boolean, DrawConfig) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
createDescriptor(ConformerSet) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
createDescriptor(Reaction) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
This descriptor contains non-hashed counts of predefined overlapping small fragments of organic functional groups.
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
This descriptor requires proper up/down bonds, because it encodes stereo parities.
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
This descriptor requires proper up/down bonds, because it encodes stereo parities.
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
This descriptor requires proper up/down bonds, because it encodes stereo parities.
createDescriptor(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm
createDescriptor(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
createDescriptor(U) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
createDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
createDescriptorSingleConf(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
createDisabledIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
 
createExtendedDepictor() - Method in class com.actelion.research.share.gui.editor.Model
 
createFileFilter(int, boolean) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
 
createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.MetaFile
 
createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.WMF
 
createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.MetaFile
 
createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.WMF
 
createFragment(StereoMolecule, int[], int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
 
createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
 
createFromGivenConformation(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
createGenericTautomer() - Method in class com.actelion.research.chem.TautomerHelper
If no tautomers can be formed then a copy of the original molecule is returned.
createHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
createHTMLView(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
Create an html renderer for the given component and string of html.
createIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
 
createImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
Creates an image from the fileName.
createImage(String) - Static method in class com.actelion.research.gui.JDrawToolbar
 
createIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
createIndexTables() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
createInitialOrientation(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
createInstance(String) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
createLaFCompatibleImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
Creates an image from the fileName.
createLongIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
createMolecule(int, int) - Method in class com.actelion.research.chem.StereoMolecule
 
createMolFromSketchBuffer(StereoMolecule, byte[]) - Static method in class com.actelion.research.util.Sketch
 
createMolFromSketchFile(StereoMolecule, String) - Static method in class com.actelion.research.util.Sketch
 
createMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
Modifies mol in-place to represent the most central ring system of the original mol.
createMultipleConformations(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
Conformation generator of Thomas Sander
createMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
Modifies mol in-place to represent the Murcko scaffold from the original mol.
createNodeIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
This index is used to track the fate of the nodes MvK 17.07.2007
createObject() - Method in class com.actelion.research.util.graph.complete.FactorySolution
 
createObject() - Method in interface com.actelion.research.util.graph.complete.IFactory
 
createObject(String) - Static method in class com.actelion.research.chem.DrawingObjectFactory
 
createParser(String) - Static method in class com.actelion.research.chem.io.CompoundFileParser
Creates the proper parser for the given type of compound file (currently SD or DWAR).
createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
 
createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
 
createPolygon() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
createReactionFromSketchBuffer(Reaction, byte[]) - Static method in class com.actelion.research.util.Sketch
 
createReactionFromSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
 
createReactionSmiles(Reaction) - Static method in class com.actelion.research.chem.IsomericSmilesCreator
 
createResidue(Map<String, AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
 
createSketchFromMol(Molecule) - Static method in class com.actelion.research.util.Sketch
 
createSketchFromReaction(Reaction) - Static method in class com.actelion.research.util.Sketch
 
createSketchFromReactionOLd(Reaction) - Static method in class com.actelion.research.util.Sketch
 
createTorsionSet(int[], int[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
Creates a new TorsionSet object from a torsion index array.
createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
Provide the next set of torsion angles using a specific strategy and considering, which angle combinations were already tried, which had failed, and (depending on the strategy) considering the likelyhoods of particular torsions.
createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
 
createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
Determine the next likely set of torsion angles and return the TorsionSet containing an array of indexes referring to the torsion value in the RotatableBond and containing the contribution of this conformer to all non colliding ones.
createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
Build a new set of torsion angles by pure or biased random picking.
createVisualDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
createVisualDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
creatorMolDistHistViz - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
CreatorMolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore.generator
CreatorMolDistHistViz
CreatorMolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
cRiskNameA - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskNameN - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskTypeIrritant - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskTypeMutagenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskTypeReproductiveEffective - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskTypes - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
cRiskTypeTumorigenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
crop(Molecule3D, Coordinates, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
cropLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
cross(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
cross(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Computes the vector cross product between this vector and that vector.
CROSSHAIR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
cRoundedMass - Static variable in class com.actelion.research.chem.Molecule
 
cSelectRectCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cSelectRectPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cSolubilityUnknown - Static variable in class com.actelion.research.chem.prediction.SolubilityPredictor
 
cStringTypeDouble - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
 
cStringTypeIDCode - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
 
cStringTypeText - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
 
cStructureHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cStructureHiliteModeCurrentRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cStructureHiliteModeFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cStructureHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cStructureHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeMaximum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeMean - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeMedian - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeMinimum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeNormal - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeSum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSummaryModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSuperposeAlignValueShape - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cSuperposeValueReferenceRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
Csv - Class in com.actelion.research.chem.forcefield.mmff
Basic CSV parser.
Csv() - Constructor for class com.actelion.research.chem.forcefield.mmff.Csv
 
cTemplateTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextCursor - Static variable in class com.actelion.research.util.CursorHelper
 
cTextExclusionTypeContains - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextExclusionTypeEndsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextExclusionTypeEquals - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextExclusionTypeRegEx - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextExclusionTypeStartsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTextMultipleCategories - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cTool3Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cTool4Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cTool5Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cTool6Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cTool7Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAromRing - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomBr - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomC - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomCl - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomF - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomH - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomI - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomN - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomO - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomOther - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomP - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomS - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolAtomSi - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolChain - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolDelete - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolDownBond - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolESR - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolESRAbs - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolESRAnd - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolESROr - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolLassoPointer - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolMapper - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolNegCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolPosCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolStdBond - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolText - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolUnknownParity - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolUpBond - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cToolZoom - Static variable in class com.actelion.research.gui.JDrawToolbar
 
cubicDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
cubicDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
cubicDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
cUnknownRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
CursorHelper - Class in com.actelion.research.util
 
CursorHelper() - Constructor for class com.actelion.research.util.CursorHelper
 
cut(double[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
Resize an array of Object
CUT_LEFT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
CUT_NONE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
CUT_RIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
CutAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 5/16/13 Time: 3:43 PM
CutAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CutAction
 
CUTOFF_RADIUS - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
cVersion - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
cViewConfigTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cViewNameEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cViewNameStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
cZoomCursor - Static variable in class com.actelion.research.util.CursorHelper
 

D

d - Variable in class com.actelion.research.util.LittleEndianDataInputStream
 
D - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
da(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'DA' from the table.
da1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
da2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
daeps - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
darad - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
darker(Color, float) - Static method in class com.actelion.research.util.ColorHelper
Creates a new Color that is a darker version of this Color.
DATA_FORMATS - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
DataProcessor - Class in com.actelion.research.calc
 
DataProcessor() - Constructor for class com.actelion.research.calc.DataProcessor
 
DATE_FORMAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
DateAnalysis - Class in com.actelion.research.util
 
DateAnalysis() - Constructor for class com.actelion.research.util.DateAnalysis
 
debug - Static variable in class com.actelion.research.chem.MolfileParser
 
debug - Static variable in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
debug - Static variable in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
DEBUG - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
DEBUG - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a binary fingerprint from a String into an int[].
decode(byte[]) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
decode(byte[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
decode(byte[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
decode(byte[], byte[], byte[], String, byte[], boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a binary fingerprint from a String into an int[].
decode(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
decode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
decode(String) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
decode(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
decode(String) - Method in class com.actelion.research.chem.phesa.AtomicGaussian
 
decode(String) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
decode(String) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
decode(String) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
 
decode(String) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
 
decode(String, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
 
decode(String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
decode(String, int, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a Reaction object by interpreting a reaction string encoded by this class.
decode(String, StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
decode(String, String, String, String, String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
decodeCatalysts(byte[]) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Generates an array of all catalysts of the encoded reaction string as bytes.
decodeCoordsOnly(String, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
 
decodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a list of fragment/has-value counts from an encoded byte sequence into a byte[].
decodeCounts(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a list of fragment/has-value counts from an encoded String.
decodeFull(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
 
decodeHistograms(String, MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
 
decodeIntArray(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes an int[] without upper limit.
decodeIntArray(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes an int[] without upper limit.
decodeLong(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a binary fingerprint from a String into a long[].
decodeLong(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes a binary fingerprint from a String into a long[].
decodeMolecules(byte[], byte[], byte[], boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
decodeMolecules(String, boolean, boolean, boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
decodeNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
decodePairs(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
decodePairs(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
def - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Def - Class in com.actelion.research.chem.forcefield.mmff.table
Equivalence table, corresponds to MMFFDEF.PAR parameters table provided in the MMFF literature.
Def(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Def
 
DEFAULT - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
DEFAULT_BG - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
DEFAULT_BOND_LENGTH - Static variable in class com.actelion.research.chem.conf.BondLengthSet
 
DEFAULT_BOND_STDDEV - Static variable in class com.actelion.research.chem.conf.BondLengthSet
 
DEFAULT_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
DEFAULT_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
DEFAULT_ELEM_WIDTH - Static variable in class com.actelion.research.chem.SVGDepictor
 
DEFAULT_IMAGE_HEIGHT - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
DEFAULT_IMAGE_WIDTH - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
DEFAULT_MERGE_SPAN - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
DEFAULT_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
DEFAULT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
DEFAULT_SIZE - Static variable in class com.actelion.research.chem.TextDrawingObject
 
DEFAULT_STYLE - Static variable in class com.actelion.research.chem.TextDrawingObject
 
DEFAULT_VAL - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
DefaultCompoundCollectionModel<T> - Class in com.actelion.research.gui
 
DefaultCompoundCollectionModel() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel
 
DefaultCompoundCollectionModel.IDCode - Class in com.actelion.research.gui
This version of the DefaultCompoundCollectionModel collects molecules as IDCodes.
DefaultCompoundCollectionModel.IDCodeWithName - Class in com.actelion.research.gui
This version of the DefaultCompoundCollectionModel collects molecules as String[2] with idcodes & idcoords (index 0) and molecule name (index 1).
DefaultCompoundCollectionModel.Molecule - Class in com.actelion.research.gui
This version of the DefaultCompoundCollectionModel collects molecules as StereoMolecules.
DefaultCompoundCollectionModel.Native - Class in com.actelion.research.gui
This version of the DefaultCompoundCollectionModel collects IDCodes and StereoMolecules without conversion into their native type.
DEG2RAD - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
 
degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.
degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
 
Delegator<T> - Class in com.actelion.research.share.gui
 
Delegator(T) - Constructor for class com.actelion.research.share.gui.Delegator
 
DeleteAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 3/26/13 Time: 4:15 PM
DeleteAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DeleteAction
 
deleteAtom(int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteAtom(int) - Method in class com.actelion.research.chem.Molecule3D
High level function for constructing a molecule.
deleteAtomOrBond(double, double) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.conf.Conformer
Removes atoms Coordinates objects from those atoms that are marked in the given array.
deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteAtoms(int[]) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteAtoms(List<Integer>) - Method in class com.actelion.research.chem.Molecule3D
 
deleteBond(int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteBond(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
deleteBondAndSurrounding(int) - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
deleteHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
deleteMarkedAtomsAndBonds() - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
deleteMolecule() - Method in class com.actelion.research.chem.Molecule
Deprecated.
deleteMolecule(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
 
deleteObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
deleteObject(int) - Method in class com.actelion.research.gui.wmf.WMF
 
deleteSelectedAtoms() - Method in class com.actelion.research.chem.Molecule
High level function for constructing a molecule.
DELTA_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
DENSITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
 
Depictor - Class in com.actelion.research.chem
 
Depictor(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor
 
Depictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor
 
Depictor2D - Class in com.actelion.research.chem
 
Depictor2D(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor2D
 
Depictor2D(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor2D
 
DepictorLine() - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
 
DepictorLine(double, double, double, double) - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
 
DepictorTransformation - Class in com.actelion.research.chem
 
DepictorTransformation() - Constructor for class com.actelion.research.chem.DepictorTransformation
 
DepictorTransformation(double, double, double) - Constructor for class com.actelion.research.chem.DepictorTransformation
 
DepictorTransformation(DepictorTransformation) - Constructor for class com.actelion.research.chem.DepictorTransformation
 
DepictorTransformation(Rectangle2D.Double, Rectangle2D.Double, double, int) - Constructor for class com.actelion.research.chem.DepictorTransformation
 
derivative() - Method in class com.actelion.research.util.FastSpline
Returns the derivative of the polynomial spline function as a PolynomialSplineFunction
derivative() - Method in class com.actelion.research.util.FastSpline.Polynome
 
DESCRIBE_ALL - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
DESCRIBE_MAPPED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Only mapped atoms are described.
DESCRIPTOR_BINARY_SKELETONSPHERES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_CenteredSkeletonFragments - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_END - Static variable in class com.actelion.research.chem.AbstractDrawingObject
 
DESCRIPTOR_EXTENDED_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_FFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_Flexophore - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_FULL_FRAGMENT_SET - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_HashedCFp - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_IntegerVector - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_MAX_COMMON_SUBSTRUCT - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_OrganicFunctionalGroups - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_PFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_PhysicoChemicalProperties - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_PTREE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_ReactionFP - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_ShapeAlign - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_ShapeAlignSingleConf - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_SkeletonSpheres - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_START - Static variable in class com.actelion.research.chem.AbstractDrawingObject
 
DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_TopoPPHistDist - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_TYPE - Static variable in class com.actelion.research.chem.AbstractDrawingObject
 
DESCRIPTOR_TYPE_MOLECULE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_TYPE_REACTION - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DESCRIPTOR_TYPE_UNKNOWN - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
 
DescriptorConstants - Interface in com.actelion.research.chem.descriptor
 
DescriptorEncoder - Class in com.actelion.research.chem.descriptor
DescriptorEncoder encodes int[] based descriptors into byte arrays that may be used to instantiate Strings
DescriptorEncoder() - Constructor for class com.actelion.research.chem.descriptor.DescriptorEncoder
 
DescriptorHandler<T,​U> - Interface in com.actelion.research.chem.descriptor
DescriptorHandler is the base Interface for any molecular descriptor handling StereoMolecules or Reactions
DescriptorHandlerFactory - Interface in com.actelion.research.chem.descriptor
 
DescriptorHandlerFFP512 - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
DescriptorHandlerFlexophore - Class in com.actelion.research.chem.descriptor
DescriptorHandlerFlexophore
DescriptorHandlerFlexophore() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
DescriptorHandlerFlexophore(int, int, double, double, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
DescriptorHandlerFlexophore(String) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
DescriptorHandlerFunctionalGroups - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerFunctionalGroups() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
DescriptorHandlerHashedCFp - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerHashedCFp() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
DescriptorHandlerLongCFP - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerLongCFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
DescriptorHandlerLongFFP512 - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerLongFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
DescriptorHandlerLongPFP512 - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerLongPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
DescriptorHandlerPFP512 - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
DescriptorHandlerPTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
DescriptorHandlerPTree() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
DescriptorHandlerReactionFP - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerReactionFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
DescriptorHandlerShape - Class in com.actelion.research.chem.phesa
 
DescriptorHandlerShape() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShape(boolean) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShape(boolean, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShape(boolean, int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShape(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShape(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
DescriptorHandlerShapeOneConf - Class in com.actelion.research.chem.phesa
 
DescriptorHandlerShapeOneConf() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
 
DescriptorHandlerShapeOneConf(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
 
DescriptorHandlerShapeOneConf(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
 
DescriptorHandlerSkeletonSpheres - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerSkeletonSpheres() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
DescriptorHandlerStandard2DFactory - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerStandard2DFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
 
DescriptorHandlerStandardFactory - Class in com.actelion.research.chem.descriptor
 
DescriptorHandlerStandardFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
 
DescriptorHelper - Class in com.actelion.research.chem.descriptor
 
DescriptorHelper() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHelper
 
DescriptorInfo - Class in com.actelion.research.chem.descriptor
 
DescriptorInfo(String, String, String, int, boolean, boolean, boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorInfo
 
det() - Method in class com.actelion.research.calc.LUDecomposition
Determinant
det() - Method in class com.actelion.research.calc.Matrix
Matrix determinant
detect() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
 
detect() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
 
determineAromaticity(boolean[], boolean[], int[], boolean) - Method in class com.actelion.research.chem.RingCollection
 
devide(double) - Method in class com.actelion.research.calc.Matrix
 
devide(Matrix) - Method in class com.actelion.research.calc.Matrix
 
devide(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
devide(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
devide(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
devideCols(Matrix) - Method in class com.actelion.research.calc.Matrix
 
devideDivisorBigger(Matrix) - Method in class com.actelion.research.calc.Matrix
 
devideRow(int, double) - Method in class com.actelion.research.calc.Matrix
 
DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
 
DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
 
DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_MDLMOLFILE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
 
DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
DF_REACTION_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_SERIALIZED_MOLECULE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_SERIALIZED_OBJECT - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
 
DF_SERIALIZED_REACTION - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_SERIALIZEDMOLECULE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
DF_SERIALIZEDREACTANT - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
DF_SERIALIZEDSTRUCTURETRANSFERDATA - Static variable in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
 
DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
DF_SMILES - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
dfI2 - Static variable in class com.actelion.research.util.Formatter
 
dfI3 - Static variable in class com.actelion.research.util.Formatter
 
dfs(Molecule3D, int, Set<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
dfs(Molecule3D, int, Set<Integer>, int, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
dfsb - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Dfsb - Class in com.actelion.research.chem.forcefield.mmff.table
 
Dfsb(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Dfsb
 
diagonalize() - Method in class com.actelion.research.calc.Matrix
 
DialogResult - Enum in com.actelion.research.share.gui
Return values from Dialog calls
DiastereoIDTest - Class in com.actelion.research.chem.contrib
 
DiastereoIDTest() - Constructor for class com.actelion.research.chem.contrib.DiastereoIDTest
 
DiastereotopicAtomID - Class in com.actelion.research.chem.contrib
 
DiastereotopicAtomID() - Constructor for class com.actelion.research.chem.contrib.DiastereotopicAtomID
 
DIB_PAL_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
DIB_RGB_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
difference(double, double) - Static method in class com.actelion.research.util.Angle
Determines the normalized difference between a2 and a1, i.e.
difference(Angle, Angle) - Static method in class com.actelion.research.util.Angle
Determines the normalized difference between a2 and a1, i.e.
disableCollidingTorsionRules(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
disableIfColliding(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.TorsionRule
 
disablePlaneRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
disableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
dispose() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
dist() - Method in class com.actelion.research.chem.Coordinates
 
dist(InteractionSimilarityTable.InteractionDescriptor) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
DIST_CUTOFF - Static variable in class com.actelion.research.chem.phesa.Gaussian3D
 
distance(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
distance(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Computes the euclidean distance between two Vector3s.
distance(ByteVec, ByteVec, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
distance(DoubleVec, DoubleVec, int) - Static method in class com.actelion.research.util.DoubleVec
 
DistanceRule - Class in org.openmolecules.chem.conf.so
 
DistanceRule() - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
Creates a dummy rule to be neglected
DistanceRule(int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
 
DistanceRule(int[], int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
 
DistanceRule(int[], int[], double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
Constructor for 2 bonds in between.
distanceSquared(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
DistHist - Class in com.actelion.research.chem.descriptor.flexophore
 
DistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
 
DistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
 
DistHist(DistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
 
DistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
 
DistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
 
DistHistHelper - Class in com.actelion.research.chem.descriptor.flexophore
DistHistHelper
DistHistHelper() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
 
DistHistHelper.RangeStatistics - Class in com.actelion.research.chem.descriptor.flexophore
 
DISTINGUISH_RACEMIC_OR_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
 
distModel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
distSq() - Method in class com.actelion.research.chem.Coordinates
 
distSquareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
DiversitySelector - Class in com.actelion.research.chem
 
DiversitySelector() - Constructor for class com.actelion.research.chem.DiversitySelector
 
DiversitySelector.DiversitySelectorRecord - Class in com.actelion.research.chem
 
DockingEngine - Class in com.actelion.research.chem.docking
 
DockingEngine(Molecule3D, Molecule3D) - Constructor for class com.actelion.research.chem.docking.DockingEngine
 
DockingEngine(Molecule3D, Molecule3D, int, int, DockingEngine.ScoringFunction, DockingEngine.StartPosition) - Constructor for class com.actelion.research.chem.docking.DockingEngine
 
DockingEngine.DockingResult - Class in com.actelion.research.chem.docking
 
DockingEngine.ScoringFunction - Enum in com.actelion.research.chem.docking
 
DockingEngine.StartPosition - Enum in com.actelion.research.chem.docking
 
DockingFailedException - Exception in com.actelion.research.chem.docking
 
DockingFailedException(String) - Constructor for exception com.actelion.research.chem.docking.DockingFailedException
 
DockingResult(StereoMolecule, double) - Constructor for class com.actelion.research.chem.docking.DockingEngine.DockingResult
 
DockingUtils - Class in com.actelion.research.chem.docking
 
dockMolecule(StereoMolecule) - Method in class com.actelion.research.chem.docking.DockingEngine
 
doModal() - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
 
doModalAt(double, double) - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
 
DONOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
DONOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
DonorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
 
DonorPoint(DonorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
DonorPoint(StereoMolecule, int, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
dot(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
dot(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Computes the vector dot product between this vector and that vector.
DoubleArray - Class in com.actelion.research.util.datamodel
DoubleArray 26 Jun 2010 MvK: Start implementation
DoubleArray() - Constructor for class com.actelion.research.util.datamodel.DoubleArray
 
DoubleArray(double[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
Deep constructor
DoubleArray(int) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
 
DoubleArray(int[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
 
DoubleArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
 
doubleArrayToByteArray(double[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
DoubleFormat - Class in com.actelion.research.util
 
DoubleFormat() - Constructor for class com.actelion.research.util.DoubleFormat
 
doubleToByteArray(double) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
doubleValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
DoubleVec - Class in com.actelion.research.util
 
DoubleVec(double[]) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(double[], boolean) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(int) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(int[]) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(DoubleVec) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(DoubleVec, boolean) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(Vector<Double>) - Constructor for class com.actelion.research.util.DoubleVec
 
DoubleVec(Vector<Double>, boolean) - Constructor for class com.actelion.research.util.DoubleVec
 
DownBondAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 1:51 PM
DownBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DownBondAction
 
DRAFT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.JChemistryView
 
dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
 
dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.JChemistryView
 
dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
dragGestureRecognized(DragGestureEvent) - Method in class com.actelion.research.gui.JChemistryView
 
DragGlassPane - Class in com.actelion.research.jfx.gui.chem
Project: User: rufenec Date: 2/21/14 Time: 6:14 PM
DragGlassPane() - Constructor for class com.actelion.research.jfx.gui.chem.DragGlassPane
 
dragIsValidAndStarts() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
 
dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
draw() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
draw(IDrawContext) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
draw(IDrawContext, DepictorTransformation) - Method in class com.actelion.research.share.gui.Arrow
 
draw(IDrawContext, DepictorTransformation) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.TextDrawingObject
 
draw(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.TextDrawingObject
 
DrawAction - Class in com.actelion.research.share.gui.editor.actions
Basic class which handles all actions which interact with the drawing surface
DrawAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DrawAction
 
drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
DrawAreaEvent - Class in com.actelion.research.gui
 
DrawAreaEvent(Object, int, boolean) - Constructor for class com.actelion.research.gui.DrawAreaEvent
 
DrawAreaListener - Interface in com.actelion.research.gui
 
drawAtomHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
drawAtomKeyStrokes(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
 
drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
 
drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
 
drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
 
drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
drawBondHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
DrawConfig - Class in com.actelion.research.share.gui
User: rufenec Creation Date: 8/24/2016
DrawConfig() - Constructor for class com.actelion.research.share.gui.DrawConfig
 
drawDashedLine(double, double, double, double, int[]) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
drawDashedLine(double, double, double, double, int[]) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
drawDot(double, double) - Method in class com.actelion.research.chem.AbstractDepictor
 
drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
 
drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
 
drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
 
drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
 
drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
drawGlyphVector(GlyphVector, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(BufferedImage, BufferedImageOp, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawImage(Image, AffineTransform, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
DrawingObject - Class in com.actelion.research.share.gui.editor.chem
Project: User: rufenec Date: 5/16/13 Time: 12:31 PM
DrawingObject() - Constructor for class com.actelion.research.share.gui.editor.chem.DrawingObject
 
DrawingObjectFactory - Class in com.actelion.research.chem
 
DrawingObjectList - Class in com.actelion.research.chem
 
DrawingObjectList() - Constructor for class com.actelion.research.chem.DrawingObjectList
 
DrawingObjectList(DrawingObjectList) - Constructor for class com.actelion.research.chem.DrawingObjectList
 
DrawingObjectList(String) - Constructor for class com.actelion.research.chem.DrawingObjectList
 
drawLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
drawLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.AbstractDepictor
 
drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.Depictor
 
drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.Depictor2D
 
drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.SVGDepictor
 
drawPolygon(double[], double[], int) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawPolygon(IPolygon) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
drawPolygon(IPolygon) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
drawRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawRenderableImage(RenderableImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawRenderedImage(RenderedImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawString(String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
 
drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor
 
drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor2D
 
drawString(String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
 
drawString(String, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
drawString(String, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawString(AttributedCharacterIterator, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
drawText(String, double, double, boolean, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
drawText(String, double, double, boolean, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
driver1() - Static method in class com.actelion.research.util.BurtleHasher
 
driver3() - Static method in class com.actelion.research.util.BurtleHasher
 
drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
 
dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
DruglikenessPredictor - Class in com.actelion.research.chem.prediction
 
DruglikenessPredictor() - Constructor for class com.actelion.research.chem.prediction.DruglikenessPredictor
 
DrugScoreCalculator - Class in com.actelion.research.chem.prediction
Created by rufenec on 26/10/15.
DrugScoreCalculator() - Constructor for class com.actelion.research.chem.prediction.DrugScoreCalculator
 
DSTINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
DUMMY_INTERACT_ID - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
dump(ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
DW_FRAGMENTS_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
DWAQ_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
 
DWAR_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
 
DWARFileCreator - Class in com.actelion.research.chem.io
 
DWARFileCreator(BufferedWriter) - Constructor for class com.actelion.research.chem.io.DWARFileCreator
Use a DWARFileCreator for writing native DataWarrior files without a CompoundTableModel.
DWARFileParser - Class in com.actelion.research.chem.io
 
DWARFileParser(File) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a File with coordinate mode MODE_COORDINATES_PREFER_2D.
DWARFileParser(File, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a File with the specified coordinate mode.
DWARFileParser(Reader) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a Reader with coordinate mode MODE_COORDINATES_PREFER_2D.
DWARFileParser(Reader, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a Reader with the specified coordinate mode.
DWARFileParser(String) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a file name with coordinate mode MODE_COORDINATES_PREFER_2D.
DWARFileParser(String, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
Constructs a DWARFileParser from a file name with the specified coordinate mode.
DWARFileParser.SpecialField - Class in com.actelion.research.chem.io
 

E

edge - Variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
 
editableProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
Electrostatic - Class in com.actelion.research.chem.forcefield.mmff
Nonbonded electrostatic energy term class.
Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
Constructor with default values for distModel and dielConst.
Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double, boolean, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
Construct a new electrostatic energy term.
Element - Class in com.actelion.research.chem
 
Element() - Constructor for class com.actelion.research.chem.Element
 
Element(int, String, String, double, double, double, double) - Constructor for class com.actelion.research.chem.Element
 
eliminationRuleString(TorsionSetEliminationRule) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
ELUSIVE - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
EmpiricalLigandStrain - Class in com.actelion.research.chem.potentialenergy
 
EmpiricalLigandStrain(Conformer, int[], BondRotationHelper) - Constructor for class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
 
enableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
encode() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
 
encode() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
encode() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
encode() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
encode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
encode(double[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
Convenience method to encode a array with a given precision.
encode(float[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
 
encode(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
encode(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Encodes a binary fingerprint stored as int[].
encode(int[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
Convenience method to encode a array with a given precision.
encode(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
encode(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
encode(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
encode(PharmacophoreNode) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
encode(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
encode(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
encode(Reaction, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order.
encode(Reaction, boolean, int) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order.
encode(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
encode(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
ENCODE_ATOM_CUSTOM_LABELS - Static variable in class com.actelion.research.chem.Canonizer
 
ENCODE_ATOM_SELECTION - Static variable in class com.actelion.research.chem.Canonizer
 
encodeCoordsOnly() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
encodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Encodes a fragment/hash-value count list.
encodeFull() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
EncodeFunctions - Class in com.actelion.research.chem.phesa
February 2018 Author: J.
EncodeFunctions() - Constructor for class com.actelion.research.chem.phesa.EncodeFunctions
 
encodeHistograms(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
 
encodeHTML(String) - Static method in class com.actelion.research.util.StringFunctions
 
encodeIntArray(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Encodes an int[] containing positive values without upper limit.
encodeLong(long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Encodes a binary fingerprint stored as long[].
encodePairs(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
Encodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
EncoderFloatingPointNumbers - Class in com.actelion.research.util
 
EncoderFloatingPointNumbers(double[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
More values can be added after the constructor was called.
EncoderFloatingPointNumbers(float[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
 
EncoderIntegerNumbers - Class in com.actelion.research.util
Encodes integer numbers into a string.
EncoderIntegerNumbers(int[]) - Constructor for class com.actelion.research.util.EncoderIntegerNumbers
More values can be added after the constructor was called.
end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
 
end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
 
end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
 
ENERGY_CUTOFF - Static variable in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
EnergyTerm - Interface in com.actelion.research.chem.forcefield.mmff
Interface class for energy terms.
ENOL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParser
 
ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
ensureHelperArrays(int) - Method in class com.actelion.research.chem.ExtendedMolecule
While the Molecule class covers all primary molecule information, its derived class ExtendedMolecule handles secondary, i.e.
ensureHelperArrays(int) - Method in class com.actelion.research.chem.StereoMolecule
ensureHelperArrays() is the essential method when working with molecules.
enumerateExtensionCutFast(int, int[], List<Integer>, Set<Integer>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
retrieve nodes that are part of extension match ("extension nodes") as well as the nodes that are part of a cut subtree (source nodes) from a cut-string
enumerateExtensionCutFull(int, int[], List<Integer>, List<Integer>, List<List<Integer>>, List<List<Integer>>, List<Integer>, Set<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
retrieves nodes that are part of extension match ("extension nodes") as well as the different subtrees resulting from the cuts with a list of their edges (in bfs order) as well as the parents of the edges
EPS - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
equal(byte[], byte[]) - Static method in class com.actelion.research.util.StringFunctions
 
equal(Matrix) - Method in class com.actelion.research.calc.Matrix
 
equal(Matrix, double) - Method in class com.actelion.research.calc.Matrix
 
equal(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
 
equal(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
 
equal(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
 
equalAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
realize() may be called first.
equalDimension(Matrix) - Method in class com.actelion.research.calc.Matrix
Checks two matrices for equal dimensions.
equals(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
equals(int[], int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
equals(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
 
equals(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.
equals(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
 
equals(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
Returns true, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
equals(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
 
equals(SortedStringList) - Method in class com.actelion.research.chem.SortedStringList
 
equals(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
 
equals(SortedList<T>) - Method in class com.actelion.research.util.SortedList
 
equals(Object) - Method in class com.actelion.research.chem.Coordinates
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
equals(Object) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
 
equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
Returns true if this SortedPair is equal with another object.
equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Checks for equality between two vectors.
equals(Object) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
equals(Object) - Method in class com.actelion.research.chem.MolecularFormula
 
equals(Object) - Method in class com.actelion.research.chem.Molecule3D
 
equals(Object) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
equals(Object) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
equals(Object) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
equals(Object) - Method in class com.actelion.research.chem.shredder.Fragment
 
equals(Object) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
 
equals(Object) - Method in class com.actelion.research.util.datamodel.ByteVec
 
equals(Object) - Method in class com.actelion.research.util.datamodel.IntArray
 
equals(Object) - Method in class com.actelion.research.util.datamodel.IntVec
 
equals(Object) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
equals(Object) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
equals(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.
erasePrimes(int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
ErrorHashMap - Class in com.actelion.research.util
ErrorHashMap 2005 MvK: Start implementation
ErrorHashMap() - Constructor for class com.actelion.research.util.ErrorHashMap
 
errors - Variable in class com.actelion.research.chem.io.AbstractParser
 
escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.MetaFile
 
escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.WMF
 
escapeDanglingMetaCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
Escapes the meta characters in a regular expression pattern with \\.
esrTypeFromRow(int) - Static method in class com.actelion.research.share.gui.editor.Model
 
ESTER - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
ETO_CLIPPED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
ETO_GRAYED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
ETO_OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
EUCLIDEAN - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
EUCLIDEAN - Static variable in class com.actelion.research.util.DoubleVec
 
EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.DoubleVec
 
euclideanDist(PointDouble, PointDouble) - Static method in class com.actelion.research.util.datamodel.PointDouble
 
euclideanDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
 
euclideanDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Euclidean distance
euclideanDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Euclidean distance
EuclideanDistanceFast(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Euclidean distance without sqrt
EUROPEAN - com.actelion.research.util.Formatter.LocaleFormat
 
Evaluable - Interface in com.actelion.research.chem.optimization
 
EvaluableFlexibleOverlap - Class in com.actelion.research.chem.phesaflex
 
EvaluableFlexibleOverlap(PheSAAlignment, StereoMolecule, StereoMolecule, double, boolean[], double[], Map<String, Object>) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
EvaluableFlexibleOverlap(EvaluableFlexibleOverlap) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
EvaluableOverlap - Class in com.actelion.research.chem.phesa
 
EvaluableOverlap(EvaluableOverlap) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
 
EvaluableOverlap(PheSAAlignment, double[]) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
 
EvaluableOverlap(PheSAAlignment, double[], double) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
 
evaluateNativePose() - Method in class com.actelion.research.chem.docking.DockingEngine
 
exactly(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Checks if this OutOfPlane term is exactly equal to a given set of four atoms.
ExceptionConformationGenerationFailed - Exception in com.actelion.research.chem.descriptor.flexophore
 
ExceptionConformationGenerationFailed(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.ExceptionConformationGenerationFailed
 
EXCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
 
execute(String[]) - Static method in class com.actelion.research.util.Platform
Start an executable with parameters.
execute(String, String...) - Static method in class com.actelion.research.util.Platform
Start an executable with parameters.
ExhaustiveFragmentGeneratorAtoms - Class in com.actelion.research.chem.mcs
 
ExhaustiveFragmentGeneratorAtoms() - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
 
ExhaustiveFragmentGeneratorBonds - Class in com.actelion.research.chem.mcs
 
ExhaustiveFragmentGeneratorBonds(int, int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
ExhaustiveFragmentGeneratorParallizer - Class in com.actelion.research.chem.mcs
 
ExhaustiveFragmentGeneratorParallizer(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
 
ExhaustiveFragmentsStatistics - Class in com.actelion.research.chem.properties.complexity
 
ExhaustiveFragmentsStatistics(int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
ExhaustiveFragmentsStatistics(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
ExhaustiveFragmentsStatistics(int, int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
ExhaustiveMCSGeneratorParallel - Class in com.actelion.research.chem.mcs
 
ExhaustiveMCSGeneratorParallel(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
 
EXIT_VECTOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
EXIT_VECTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
ExitVectorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
 
ExitVectorPoint(ExitVectorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
ExitVectorPoint(StereoMolecule, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
EXTENDED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
EXTENDED_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
 
ExtendedDepictor - Class in com.actelion.research.chem
 
ExtendedDepictor(Reaction, DrawingObjectList, boolean, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
 
ExtendedDepictor(StereoMolecule[], int, DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
Use this constructor for markush structures.
ExtendedDepictor(StereoMolecule[], DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
 
ExtendedDepictor(StereoMolecule, DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
 
ExtendedMolecule - Class in com.actelion.research.chem
While the Molecule class covers all primary molecule information as atom and bond properties, the atom connectivity and coordinates, its derived class ExtendedMolecule handles secondary, i.e.
ExtendedMolecule() - Constructor for class com.actelion.research.chem.ExtendedMolecule
 
ExtendedMolecule(int, int) - Constructor for class com.actelion.research.chem.ExtendedMolecule
 
ExtendedMolecule(Molecule) - Constructor for class com.actelion.research.chem.ExtendedMolecule
 
ExtendedMoleculeFunctions - Class in com.actelion.research.chem
ExtendedMoleculeFunctions
ExtendedMoleculeFunctions() - Constructor for class com.actelion.research.chem.ExtendedMoleculeFunctions
 
extendedToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
EXTENSION_MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
EXTENSION_MATCHES - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
extract(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
Delivers a list of indices that describes sub structures of the given molecule.
extract(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
extractAliphaticRingsAndEndStandingAliphaticGroups(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
 
extractAromaticRing(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
extractCol(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
extractFieldName(String) - Method in class com.actelion.research.chem.io.SDFileParser
 
extractForGivenResolution(IntVec, int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
Converts the IntVec into an array.
extractFragment(Molecule3D, T, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Extract the Ligand from mol and copy it into res
extractFragment(Molecule3D, T, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
extractFragments(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return all connex components with more than 5 atoms
extractInverse(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
extractLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Extract the Ligand from mol and copy it into res
extractLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return all ligands with more than 5 atoms
extractMols() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
extractValue(String) - Static method in class com.actelion.research.chem.io.ODEFileParser
 
extractX(List<ScorePoint>) - Static method in class com.actelion.research.util.datamodel.ScorePoint
 

F

FACTOR_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
FactorySolution - Class in com.actelion.research.util.graph.complete
FactorySolution
FactorySolution() - Constructor for class com.actelion.research.util.graph.complete.FactorySolution
 
FAILED_BYTES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
FAILED_OBJECT - Static variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
FAILED_STRING - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
FAKE_ATOM_NO - Static variable in class com.actelion.research.gui.JDrawArea
 
FAKE_ATOM_NO - Static variable in class com.actelion.research.share.gui.editor.Model
 
FALSE - com.actelion.research.chem.forcefield.mmff.RingBoolean
 
FastSpline - Class in com.actelion.research.util
Represents a polynomial spline function.
FastSpline(double[], FastSpline.Polynome[]) - Constructor for class com.actelion.research.util.FastSpline
Construct a polynomial spline function with the given segment delimiters and interpolating polynomials.
FastSpline.Polynome - Class in com.actelion.research.util
 
FeatureCalculator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
calculates features for all atoms in a molecule: H-bond acceptors/donors, negatively/positively ionizable, aromatic, lipophilic
FeatureCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
 
FeatureMatch(int[][]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
FF_DECORATIVE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FF_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FF_MODERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FF_ROMAN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FF_SCRIPT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FF_SWISS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
fget(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
Gets a floating point value from a given row and column.
fieldIndex - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
FILE_SUPPORT_NONE - Static variable in class com.actelion.research.gui.CompoundCollectionPane
 
FILE_SUPPORT_OPEN_AND_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
 
FILE_SUPPORT_OPEN_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
 
FILE_SUPPORT_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
 
fileExists(File) - Static method in class com.actelion.research.gui.FileHelper
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
fileExists(File, long) - Static method in class com.actelion.research.gui.FileHelper
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
FileHelper - Class in com.actelion.research.gui
 
FileHelper(Component) - Constructor for class com.actelion.research.gui.FileHelper
 
fill(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillCircle(double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
 
fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor
 
fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor2D
 
fillCircle(double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
 
fillCircle(double, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
fillElipse(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
fillElipse(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillPolygon(double[], double[], int) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
fillPolygon(double[], double[], int) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
fillRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
fillText(String, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
fillText(String, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
filter(byte[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
 
filter(byte[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
filter(double[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
 
filter(int[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
 
filter(int[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
FILTER - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
FILTER_SUB - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
Filter for sliding window to blurr distance histograms 07.04.2020
finalize() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
finalize() - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
 
finalize() - Method in class com.actelion.research.io.StringReadChannel
 
finalizeMolecule(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Remove all atoms without connections.
finalizeProcessMolecules() - Method in class com.actelion.research.chem.AtomTypeList
 
finalizeThreads() - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
findAlignment(double[][]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
findAlignment(double[][], boolean) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
findAlleneCenterAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
If atom is one of the two ends of an allene then returns allene center atom.
findAlleneEndAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
Crawls along a chain of sp-hybridized atoms starting from atom2 (which may not be sp-hybridized) away from its sp-hybridized neighbour atom1.
findAtom(double, double) - Method in class com.actelion.research.chem.Molecule
 
findAtom(StereoMolecule, Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
findBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Checks whether atom is one of the two atoms of an axial chirality bond of BINAP type.
findBond(double, double) - Method in class com.actelion.research.chem.Molecule
 
findFragmentInMolecule() - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
 
findFragmentInMolecule() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
 
findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcher
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcher
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms that are not flagged to be excluded from matching.
findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
findFragmentInMoleculeWithoutIndex(int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
findIdentical(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
findIn(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
 
findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.AngleBend
Helper function that builds a list of AngleBends for a molecule.
findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.BondStretch
Finds all bond stretch energy terms in the current molecule.
findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Finds all out of plane angles in the current molecule.
findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
Helper function that builds a list of StretchBends for a molecule.
findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
Helper function that builds a list of TorsionAngles for a molecule.
findIn(Tables, MMFFMolecule, Separation) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
Overloaded wrapper function for 'findIn' which sets default values for the nonbonded cutoff, dielectric model and dielectric constant.
findIn(Tables, MMFFMolecule, Separation, double) - Static method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
Finds all van der Waals energy terms in the current molecule.
findIn(Tables, MMFFMolecule, Separation, double, boolean, double) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
Finds all Electrostatic energy terms in the current molecule.
findInitialSplits() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
findLargest(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
findMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.
findMurckoScaffold(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
This method flags all atoms that are a member of the Murcko fragment of mol.
findPrimeInRow(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
findRearAtoms(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
findRingSystem(int, boolean, boolean[], boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Starting from startAtom this method locates a system of annelated or bridged ring systems with all members bonds being a ring bond.
findRotatableBonds(StereoMolecule) - Static method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor().
findRotatableBonds(StereoMolecule, boolean, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
Locates all relevant rotatable bonds, i.e.
findSmallest(double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
findStarInCol(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
findUncoveredZero(int[], double[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
FingerPrintGenerator - Class in com.actelion.research.chem.descriptor
Generator of a path-based Fingerprint Not thread safe!
FingerPrintGenerator() - Constructor for class com.actelion.research.chem.descriptor.FingerPrintGenerator
 
FISCHER_PROJECTION_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
To interpret a stereo center as fisher projection, all non stereo bonds must be vertical and all stereo bonds must be horizontal.
FIXED_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FLAG_CENTER_ATOM - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
 
FLAG1 - Static variable in class com.actelion.research.chem.Molecule3D
 
flagBackbone(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
FLD_CMNT - Static variable in class com.actelion.research.chem.StructureInfo
 
FLD_DENSITY - Static variable in class com.actelion.research.chem.StructureInfo
 
FLD_ID - Static variable in class com.actelion.research.chem.StructureInfo
 
FLD_NAME - Static variable in class com.actelion.research.chem.StructureInfo
 
FLD_PURITY - Static variable in class com.actelion.research.chem.StructureInfo
 
flexible - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
FlexibleShapeAlignment - Class in com.actelion.research.chem.phesaflex
Performs flexible Alignment of two Molecules that are prealigned.
FlexibleShapeAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
FlexibleShapeAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
FlexibleShapeAlignment(StereoMolecule, StereoMolecule, MolecularVolume, MolecularVolume, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
FlexophoreCreateFunctions - Class in com.actelion.research.chem.descriptor.flexophore.generator
FlexophoreCreateFunctions
FlexophoreCreateFunctions() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
 
FlexophorePoint - Class in com.actelion.research.chem.descriptor.flexophore.entity
FlexophorePoint
FlexophorePoint(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
flip(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
flip(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
 
flipOneSide(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
floatValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
Fluorine - Static variable in class com.actelion.research.chem.PeriodicTable
 
flush() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
ForceField - Interface in com.actelion.research.chem.forcefield
 
forceFieldAllowsOpenValences() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
For using a different forcefield you may override all three forceField...
ForceFieldChangeListener - Interface in com.actelion.research.chem.forcefield
 
forceFieldInitialize() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
For using a different forcefield you may override all three forceField...
forceFieldMinimize(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
For using a different forcefield you may override all three forceField...
ForceFieldMMFF94 - Class in com.actelion.research.chem.forcefield.mmff
 
ForceFieldMMFF94(StereoMolecule, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Forcefield constructor.
ForceFieldMMFF94(StereoMolecule, String, Map<String, Object>) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Forcefield constructor.
format(double, DecimalFormat, int) - Static method in class com.actelion.research.calc.Matrix
 
format(int) - Static method in class com.actelion.research.calc.Matrix
 
format(Object) - Static method in class com.actelion.research.util.Formatter
 
format(String) - Static method in class com.actelion.research.util.StringFunctions
Keeps the minus.
format(String, char) - Static method in class com.actelion.research.util.StringFunctions
Keeps the minus.
format0(Double) - Static method in class com.actelion.research.util.Formatter
 
format1(Double) - Static method in class com.actelion.research.util.Formatter
 
format2(Double) - Static method in class com.actelion.research.util.Formatter
 
format2DefinedLengthLeading(String, int) - Static method in class com.actelion.research.util.StringFunctions
 
format2DefinedLengthTrailing(String, int) - Static method in class com.actelion.research.util.StringFunctions
 
format3(Double) - Static method in class com.actelion.research.util.Formatter
 
format4(Double) - Static method in class com.actelion.research.util.Formatter
 
format8(Double) - Static method in class com.actelion.research.util.Formatter
 
formatDate(Date) - Static method in class com.actelion.research.util.Formatter
 
formatDateTime(Date) - Static method in class com.actelion.research.util.Formatter
 
formatDateTimeShort(Date) - Static method in class com.actelion.research.util.Formatter
 
formatDescription(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
formatE(Double) - Static method in class com.actelion.research.util.Formatter
 
formatMax2(Double) - Static method in class com.actelion.research.util.Formatter
 
formatMax3(Double) - Static method in class com.actelion.research.util.Formatter
 
Formatter - Class in com.actelion.research.util
 
Formatter() - Constructor for class com.actelion.research.util.Formatter
 
Formatter.LocaleFormat - Enum in com.actelion.research.util
 
formatTime(Date) - Static method in class com.actelion.research.util.Formatter
 
formatToCharactersAndDigits(String) - Static method in class com.actelion.research.util.StringFunctions
 
formatToPrintableCharactersOnly(String) - Static method in class com.actelion.research.util.StringFunctions
This function was implemented because in AxoSOMSampleView was a new line in SMILES molConvert from ChemAxon that is not detected by replaceAll("\n", "");
formatYYYYMMDD() - Static method in class com.actelion.research.util.Formatter
 
FormulaParser - Class in com.actelion.research.chem.io.pdb.parser
FormulaParser
FormulaParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.FormulaParser
 
FractalDimensionMolecule - Class in com.actelion.research.chem.properties.fractaldimension
FractalDimensionMolecule
FractalDimensionMolecule(int, boolean) - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
FractalDimensionMoleculeMain - Class in com.actelion.research.chem.properties.fractaldimension
FractalDimensionMoleculeMain
FractalDimensionMoleculeMain() - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
 
Fragment - Class in com.actelion.research.chem.shredder
Fragment Jan 18, 2013 MvK Start implementation
Fragment(String) - Constructor for class com.actelion.research.chem.shredder.Fragment
 
Fragment(String, String) - Constructor for class com.actelion.research.chem.shredder.Fragment
 
Fragment3D - Class in com.actelion.research.chem.shredder
 
Fragment3D(String, String, TorsionDescriptor, int[]) - Constructor for class com.actelion.research.chem.shredder.Fragment3D
 
FragmentAssociation - Class in com.actelion.research.chem.coords
Created by thomas on 9/23/16.
FragmentAssociation(InventorFragment, InventorFragment) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
Uses center of gravity of the fragments as anchor points
FragmentAssociation(InventorFragment, InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
 
FragmentDefinedByBondsHasher - Class in com.actelion.research.chem.properties.complexity
 
FragmentDefinedByBondsHasher() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
 
FragmentDefinedByBondsIdCode - Class in com.actelion.research.chem.properties.complexity
 
FragmentDefinedByBondsIdCode() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
FragmentDefinedByBondsIdCode(FragmentDefinedByBondsIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
FragmentDefinedByBondsIdCode(IBitArray) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
Fragmenter3D - Class in com.actelion.research.chem.shredder
 
Fragmenter3D(int, int, int, int, int) - Constructor for class com.actelion.research.chem.shredder.Fragmenter3D
 
fromString(String) - Static method in class com.actelion.research.chem.phesa.AtomicGaussian
 
fromString(String) - Static method in class com.actelion.research.chem.phesa.VolumeGaussian
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophorePointFactory
 
fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
FULL_HOSE_CODE - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
 
FUNC_GROUP_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
 
FUNCTIONAL_GROUP - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
FUNCTIONAL_GROUP_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
 
FunctionalGroupClassifier - Class in com.actelion.research.chem.reaction
 
FunctionalGroupClassifier(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.FunctionalGroupClassifier
 
FUNCTIONALITY_WEIGHTS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
FUNCTOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
fusion(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
This method will append a Molecule3D to the end.
FW_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FW_BOLD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FW_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FW_NORMAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
FW_THIN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 

G

g_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'G-i' from the table.
Gaussian3D - Class in com.actelion.research.chem.phesa
 
Gaussian3D() - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
 
Gaussian3D(int, int, Coordinates, double) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
 
Gaussian3D(Gaussian3D) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
 
GDIPolyPolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
generate() - Method in class com.actelion.research.chem.phesa.PheSABindingHypothesis
 
generate(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
 
generate(StereoMolecule, Map<Integer, List<Integer>>, List<Set<Integer>>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react
generateConformerAndSetCoordinates(ConformerGenerator, int, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
08.03.2017 Method set to public for debugging purposes.
generateConformerFromTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Computes a conformer from a TorsionSet object.
generateConformerSet(StereoMolecule) - Method in class com.actelion.research.chem.conf.ConformerSetGenerator
 
generateFragments() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
 
generateFragments() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
 
generateFragmentsAllBonds() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
generateFragmentsForSingleBond(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
generateMutationList(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
Creates a list of possible mutations and their probabilities
generateOneConformer(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
Generates the coordinates for one conformer in the calling thread.
generateOneConformerInPlace(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
This convenience method returns the StereoMolecule that has been passed to the constructor after modifying its atom coordinates to reflect the conformer internally created by generateOneConformer().
generateRandomArray(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
generateSmiles(ExtendedMolecule) - Method in class com.actelion.research.chem.SmilesCreator
public String generateSmiles (Molecule inMol) Effect on instance variable: -> increment this.mVisitedMolAtoms -> increment this.mDisconnections, if inMol consists of several isolated molecules (or atoms).
generateSubPharmacophores(MolDistHist, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
generateSubPharmacophores(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
Generates a list of sub-fragments.
generateSubPharmacophores(MolDistHistViz, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
generateSubPharmacophores(List<MolDistHistViz>, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
generateSubPharmacophoresCheckedRange(MolDistHist, int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
GeometryCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
Utility class to perform 3D geometry calculations on molecules
GeometryCalculator - Class in com.actelion.research.chem.io.pdb.converter
Utility class to perform 3D geometry calculations on molecules
GeometryCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
 
GeometryCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
 
geomFactory - Variable in class com.actelion.research.share.gui.editor.Model
 
GeomFactory - Class in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 3:15 PM
GeomFactory(DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.geom.GeomFactory
 
get() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
get() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
 
get() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
get() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
get() - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
get() - Method in class com.actelion.research.util.datamodel.ByteVec
 
get() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
get() - Method in class com.actelion.research.util.datamodel.IntArray
 
get() - Method in class com.actelion.research.util.datamodel.IntVec
 
get() - Method in class com.actelion.research.util.DoubleVec
 
get() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
 
get(double, double) - Static method in class com.actelion.research.calc.Logarithm
 
get(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
get(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
 
get(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
Returns a bit list.
get(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
get(int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
Returns list with indices for fragments with size atoms.
get(int) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
 
get(int) - Method in class com.actelion.research.share.gui.Polygon
 
get(int) - Method in class com.actelion.research.util.datamodel.ByteVec
 
get(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
get(int) - Method in class com.actelion.research.util.datamodel.IntArray
 
get(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
get(int) - Method in class com.actelion.research.util.DoubleVec
 
get(int) - Method in class com.actelion.research.util.IntQueue
 
get(int) - Method in class com.actelion.research.util.SortedList
Returns object at given index, or null if index==-1
get(int) - Method in class com.actelion.research.util.UniqueList
 
get(int, int) - Method in class com.actelion.research.calc.Matrix
 
get(int, int) - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
This should get an integer value given a column and row.
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
 
get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
get(int, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
get(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
Returns the relation of a given pair of atoms.
get(Object) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
get(String) - Method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
 
get(String) - Method in class com.actelion.research.util.CommandLineParser
 
get_bci_f(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
 
get_bci_len() - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
 
get_bci_n(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
 
getAbs() - Method in class com.actelion.research.calc.Matrix
 
getAbsoluteAtomParity(int) - Method in class com.actelion.research.chem.StereoMolecule
This returns the absolute(!) atom parity from the canonization procedure.
getAbsoluteBondParity(int) - Method in class com.actelion.research.chem.StereoMolecule
This returns the absolute(!) bond parity from the canonization procedure.
getAbsoluteMass(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
 
getAbsoluteWeight() - Method in class com.actelion.research.chem.MolecularFormula
 
getAcceptedFormats(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
getAcceptorCount() - Method in class com.actelion.research.chem.PropertyCalculator
 
getAcceptorID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getAdded() - Method in class com.actelion.research.util.Pipeline
 
getAdjacencyList(int, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
 
getAlignment() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
getAlignment() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getAlkyneAtomCount() - Method in class com.actelion.research.chem.conf.TorsionDetail
 
getAllAtoms() - Method in class com.actelion.research.chem.Molecule
 
getAllBonds() - Method in class com.actelion.research.chem.Molecule
 
getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCS
All molecules which are sub structures of an other molecule in the list are removed.
getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCSFast
All molecules which are sub structures of an other molecule in the list are removed.
getAllConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getAllConnAtomsPlusMetalBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getAllHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getAllOutOf(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
Get all possible index combinations, order independent.
getAllSubStrings(String, int) - Static method in class com.actelion.research.util.StringFunctions
 
getAllSubtrees() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getAndSet(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.coords.InventorAngle
 
getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.Molecule
 
getAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
Returns the preferred angle between to three atoms in a row as positive value <= pi.
getAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
Gets the angle formed between the 2 vectors ([0,PI])
getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
 
getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
 
getAngle(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
Gets the Angle between 3 atoms
getAngle(Molecule, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
 
getAngle(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
Gets the Angle between 3 atoms
getAngleDif(double, double) - Static method in class com.actelion.research.chem.Molecule
 
getAngleXY(Coordinates) - Method in class com.actelion.research.chem.Coordinates
Calculates the angle of the line from this location to c projected into the x/y plane.
getAnisou() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getAppendedSorted(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
getArea() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getArea(double, double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
 
getAreaRightTriangle(double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
 
getAromaticRingCount() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getArray() - Method in class com.actelion.research.calc.Matrix
 
getArrayAsInt() - Method in class com.actelion.research.calc.Matrix
 
getArrayCopy() - Method in class com.actelion.research.calc.Matrix
 
getArrIndexFrag() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
 
getArrIndexParentNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
getArrNode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getArrowBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getAsBoolean(String) - Method in class com.actelion.research.util.CommandLineParser
Use contains(...) if only the flag is used.
getAsDir(String) - Method in class com.actelion.research.util.CommandLineParser
 
getAsDouble(String) - Method in class com.actelion.research.util.CommandLineParser
 
getAsFile(String) - Method in class com.actelion.research.util.CommandLineParser
 
getAsInt(String) - Method in class com.actelion.research.util.CommandLineParser
 
getAtom() - Method in class com.actelion.research.chem.CanonizerBaseValue
 
getAtomAbnormalValence(int) - Method in class com.actelion.research.chem.Molecule
Get an atom's defined maximum valance if different from the default one.
getAtomAmino(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomAndBondCounts(byte[], int, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Determines atom and bond counts of the given idcode
getAtomAndBondCounts(String, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Determines atom and bond counts of the given idcode
getAtomBfactor(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomChainId(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomCharge(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomCIPParity(int) - Method in class com.actelion.research.chem.Molecule
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
getAtomColor(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomCoordinates() - Method in class com.actelion.research.chem.Molecule
 
getAtomCount(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getAtomCount(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getAtomCustomLabel(int) - Method in class com.actelion.research.chem.Molecule
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
getAtomCustomLabelBytes(int) - Method in class com.actelion.research.chem.Molecule
This method is more efficient than getAtomCustomLabel(), because internally atom custom labels are stored as a byte[].
getAtomDescription(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomESRGroup(int) - Method in class com.actelion.research.chem.Molecule
This is MDL's enhanced stereo representation (ESR).
getAtomESRType(int) - Method in class com.actelion.research.chem.Molecule
This is MDL's enhanced stereo representation (ESR).
getAtomFlags(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
 
getAtomHashkey(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return a long representing the atom and its neighbours
getAtomicGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getAtomicNo() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getAtomicNo() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getAtomicNo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getAtomicNo(int) - Method in class com.actelion.research.chem.Molecule
In addition to the natural atomic numbers, we support additional pseudo atomic numbers.
getAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getAtomicNoFromInteractionType(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getAtomicNoFromLabel(String) - Static method in class com.actelion.research.chem.Molecule
 
getAtomicNoRGroup(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Starts with 1 and goes until 16
getAtomicNumber(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getAtomId() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getAtomIds(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
 
getAtomIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
 
getAtomIndexConnectionFlexophorePoint() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
getAtomIndexFirstLinkerAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
getAtomIndexLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
getAtomIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
getAtomKeySet() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getAtomKeyStrokeValidity(String) - Method in class com.actelion.research.share.gui.editor.Model
 
getAtomLabel(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomList() - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
getAtomList(int) - Method in class com.actelion.research.chem.Molecule
The list of atoms that are allowed at this position during sub-structure search.
getAtomListString(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomMapNo(int) - Method in class com.actelion.research.chem.Molecule
Returns an atom mapping number within the context of a reaction.
getAtomMass(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getAtomName(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomPairsBondsTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
 
getAtomParity(int) - Method in class com.actelion.research.chem.Molecule
The atom parity is a calculated property available above/equal helper level cHelperParities.
getAtomPi(int) - Method in class com.actelion.research.chem.ExtendedMolecule
This is different from the Hendrickson pi-value, which considers pi-bonds to carbons only.
getAtomPi(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.
getAtomPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the atom chirality.
getAtomQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
Returns all set query features for this atom.
getAtomRadical(int) - Method in class com.actelion.research.chem.Molecule
Gets an atom's radical state as singulet,dublet,triplet or none
getAtomRegionNumbers(int[]) - Method in class com.actelion.research.chem.TautomerHelper
Identifies connected tautomeric regions and assign region numbers to all atoms.
getAtomRingBondCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getAtomRingCount(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates the number of independent rings of which 'atom' is a member.
getAtomRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getAtomRingSize(int) - Method in class com.actelion.research.chem.RingCollection
An atom's ring size is the size of the smallest ring the atom is a member of.
getAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getAtoms() - Method in class com.actelion.research.chem.ExtendedMolecule
A validated molecule (after helper array creation) contains a sorted list of all atoms with the plain (neglegible) hydrogen atoms at the end of the list.
getAtoms() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getAtomSequence(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAtomsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getAtomsOnPath(Molecule3D, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Finds on all atoms going on a path from a1 to a2.
getAtomStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
getAtomToGroups(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getAtomToGroups(Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
For each molecule in mol one group is created.
getAtomType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
 
getAtomType(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
Get the MMFF atom type of an atom.
getAtomType(InteractionAtomTypeCalculator.FunctionalGroup, int, boolean, int, boolean) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getAtomType(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getAtomTypeList() - Method in class com.actelion.research.chem.AtomTypeList
 
getAtomTypes() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getAtomVolumes(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
 
getAtomX(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
getAtomX(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomY(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
getAtomY(int) - Method in class com.actelion.research.chem.Molecule
 
getAtomZ(int) - Method in class com.actelion.research.chem.Molecule
 
getAttachedHydrogenCount(int) - Method in class com.actelion.research.chem.Molecule3D
 
getAuthor() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getAuxiliaryInfo(String) - Method in class com.actelion.research.chem.Molecule3D
 
getAuxiliaryInfos() - Method in class com.actelion.research.chem.Molecule3D
 
getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getAverageBondLength() - Method in class com.actelion.research.chem.Molecule
Calculates and returns the mean bond length.
getAverageBondLength() - Method in class com.actelion.research.chem.reaction.Reaction
 
getAverageBondLength(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates and returns the mean bond length of all bonds including or not including hydrogen bonds.
getAverageBondLength(int, int) - Method in class com.actelion.research.chem.Molecule
Calculates and returns the mean bond length of all bonds 0...bonds.
getAverageBondLength(int, int, double) - Method in class com.actelion.research.chem.Molecule
Calculates and returns the mean bond length of all bonds 0...bonds.
getAverageBondLength(int, int, double, Coordinates[]) - Method in class com.actelion.research.chem.Molecule
Calculates and returns the mean bond length of all bonds 0...bonds.
getAverageBondLength(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getAverageTopologicalAtomDistance() - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates for every non-H atom the mean value of all shortest routes (bonds in between) to any other atom of the same fragment.
getBackbone(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getBackboneCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns a hash code representing the structure or its largest fragment without stereo information and with all unsaturated bonds converted to single bonds.
getBackboneHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
 
getBackbones(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getBackbones(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Gets the backbone
getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
getBackgroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
 
getBackgroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getBackSpaceKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getBar() - Static method in class com.actelion.research.gui.JMessageBar
 
getBase() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
getBase() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
getBaseName(File) - Static method in class com.actelion.research.util.IO
 
getBaseName(String) - Static method in class com.actelion.research.util.IO
 
getBegin() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
getBegin() - Method in class com.actelion.research.util.IntQueue
 
getBestCollidingTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
If no collision free torsion set can be constructed, this method is called to get the torsion set with the least atom collision strain.
getBestMatchingSolution() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
getBiasFactor(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
 
getBiggestFragment(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBiggestFragmentIDCode(String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBin(int) - Method in class com.actelion.research.calc.histogram.Histogram
 
getBindingSiteAtoms(StereoMolecule, Set<Integer>, MoleculeGrid, boolean) - Static method in class com.actelion.research.chem.docking.DockingEngine
 
getBinIndex(double) - Method in class com.actelion.research.calc.histogram.Histogram
 
getBinomialCoefficient(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
Calculate binomial coefficient or n choose k
getBins() - Method in class com.actelion.research.calc.histogram.Histogram
 
getBinWidth() - Method in class com.actelion.research.calc.histogram.Histogram
 
getBitArray() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
getBitSetBits(BitSet) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
 
getBitsSet() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
getBitsSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
getBitsSet() - Method in class com.actelion.research.util.datamodel.ByteVec
 
getBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
 
getBitsSet(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
 
getBond() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getBond(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
getBondAndFragmentCollisionIntensities(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
Calculates for every rotatable bond and for every rigid fragment a collision intensity sum for the given torsion/conformer state from the collision rules already known.
getBondAngle(int, int) - Method in class com.actelion.research.chem.Molecule
 
getBondAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getBondAtom(int, int) - Method in class com.actelion.research.chem.Molecule
 
getBondBridgeMaxSize(int) - Method in class com.actelion.research.chem.Molecule
 
getBondBridgeMinSize(int) - Method in class com.actelion.research.chem.Molecule
 
getBondCIPParity(int) - Method in class com.actelion.research.chem.Molecule
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
getBondCount(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
 
getBondESRGroup(int) - Method in class com.actelion.research.chem.Molecule
This is MDL's enhanced stereo representation (ESR).
getBondESRType(int) - Method in class com.actelion.research.chem.Molecule
This is MDL's enhanced stereo representation (ESR).
getBondID(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Constructs a bond classification index from a specific bond in a molecule.
getBondIDString(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
 
getBondIndex(int, boolean, boolean, int, int, int, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information.
getBondIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
 
getBondIndex(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.
getBondLength(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an estimate of the bond length based on atom and bond characteristics.
getBondLength(int) - Method in class com.actelion.research.chem.Molecule
 
getBondLengthFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an estimate of the bond length based on atom and bond characteristics.
getBondNo(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBondOrder(int) - Method in class com.actelion.research.chem.Molecule
Returns the formal bond order.
getBondOrder(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBondParity(int) - Method in class com.actelion.research.chem.Molecule
Returns the pre-calculated bond parity, e.g.
getBondParity(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBondPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the bond chirality.
getBondQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
 
getBondRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getBondRingSize(int) - Method in class com.actelion.research.chem.RingCollection
A bond's ring size is the size of the smallest ring the bond is a member of.
getBonds() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
The bond list is preprocessed such that all bonds leading to a plain hydrogen atom (natural abundance, no custom labels) are at the end of the list.
getBonds() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getBondsAtMaxFrag() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
getBondsBetweenFragments(int, int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
getBondsFragment() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getBondStdDev(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
getBondTorsion(int) - Method in class com.actelion.research.chem.conf.Conformer
Returns the current bond torsion angle in degrees, it is was set before.
getBondType() - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
getBondType() - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
 
getBondType() - Method in class com.actelion.research.share.gui.editor.actions.NewBondAction
 
getBondType() - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
 
getBondType(int) - Method in class com.actelion.research.chem.Molecule
Returns bond type combining bond order and stereo orientation.
getBondType(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getBondTypeSimple(int) - Method in class com.actelion.research.chem.Molecule
This is the bond type without stereo information.
getBorderColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
getBordersMostFreqOccBin(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
Gets the upper and lower limit of the most occupied bin.
getBoundingBox() - Method in class com.actelion.research.share.gui.Polygon
 
getBoundingRect() - Method in class com.actelion.research.chem.AbstractDepictor
 
getBoundingRect() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
getBoundingRect() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
getBoundingRect() - Method in class com.actelion.research.chem.TextDrawingObject
 
getBoundingRect() - Method in class com.actelion.research.share.gui.Arrow
 
getBoundingRect() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
getBoundingRect() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
getBoundingRect(ExtendedMolecule) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getBoundingRect(ExtendedMolecule[]) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getBoundingRect(Reaction, boolean) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getBoundingRect(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getBounds() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
 
getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
Gets the Bounds of a molecule
getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getBounds(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
Gets the Bounds of a molecule
getBounds(Rectangle2D.Double) - Method in class com.actelion.research.chem.Molecule
 
getBounds(String) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
getBounds(String) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
getBrushFillStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getBufferedReader(String) - Static method in class com.actelion.research.util.IO
Do not forget to close BufferedReader
getBuffWrite(String, boolean) - Static method in class com.actelion.research.util.IO
 
getBumpTerm() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
getButtonImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
 
getByte(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
getByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getByteVec() - Method in class com.actelion.research.util.datamodel.IntVec
 
getByteVec(int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getByteVec(int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
 
getCandidatePose() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
getCanMolecule() - Method in class com.actelion.research.chem.Canonizer
 
getCanMolecule(boolean) - Method in class com.actelion.research.chem.Canonizer
 
getCanonizer() - Method in class com.actelion.research.chem.StereoMolecule
This is a convenience method returning the StereoMolecule's Canonizer object after calling internally ensureHelperArrays(cHelperParities) and, thus, effectively running the canonicalization and validating the Canonizer itself.
getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
Is increased by one if more than the the allowed number of fragments was generated.
getCartCoordinates(int[]) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getCartesianTorsionGradient(int[], Conformer, double[], double, Coordinates[], int[][]) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
 
getCatalyst(int) - Method in class com.actelion.research.chem.reaction.Reaction
 
getCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
 
getcAtomColor2String(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getCaveat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getCcMissedMinRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
 
getCcViolatedMaxRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
 
getCcViolatedMinDiffInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
 
getCenter() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getCenter() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getCentered(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCenteredMatrix() - Method in class com.actelion.research.calc.Matrix
 
getCenteredMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
 
getCenterGravity(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMolecule
 
getCenterGravity(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMolecule
 
getCenterGravity(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
Gets the center of Gravity of a molecule
getCenterGravity(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
Gets the center of Gravity of a molecule
getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getCenterID() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getCentralAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
Returns one of the atoms of the torsion fragment's central rotatable bond.
getCEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
getChainLength() - Method in class com.actelion.research.chem.coords.InventorChain
 
getCharge() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getChargeAtom() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getCharges(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
Computes the partial MMFF charges.
getChargeType(int) - Static method in class com.actelion.research.chem.io.Mol2FileParser
 
getCheckerArray() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
getChemDrawBuffer(Reaction) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
getChemDrawBuffer(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
getChemistryBounds() - Method in class com.actelion.research.gui.JChemistryView
 
getChemistryType() - Method in class com.actelion.research.gui.JChemistryView
 
getChildFieldIndex(String, String) - Method in class com.actelion.research.chem.io.DWARFileParser
 
getChirality() - Method in class com.actelion.research.chem.Molecule
Gets the overall chirality of the molecule, which is a calculated information considering: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
getChiralText() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getChiralText() - Method in class com.actelion.research.chem.StereoMolecule
 
getCisPep() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getClassification() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getClipboardData(String) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
getClipboardHandler() - Method in class com.actelion.research.gui.CompoundCollectionPane
 
getClipboardHandler() - Method in class com.actelion.research.gui.JStructureView
 
getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getCLogPIncrements(StereoMolecule, float[]) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
Normalizes ambiguous bonds and assigns cLogP increments to every atom based on its enhanced atom type.
getClosestNeighbour(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
Returns the closest neighbour.
getClusterCenter(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
getClusterMember() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
getCode() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
 
getCoefficients() - Method in class com.actelion.research.util.FastSpline.Polynome
 
getCoefficientVariation() - Method in class com.actelion.research.calc.Matrix
Coefficient of variation (CV) is a normalized measure of dispersion of a probability distribution.
getCol(int) - Method in class com.actelion.research.calc.Matrix
 
getColAsDouble(int) - Method in class com.actelion.research.calc.Matrix
 
getColAsFloat(int) - Method in class com.actelion.research.calc.Matrix
 
getColAsList(int) - Method in class com.actelion.research.calc.Matrix
 
getColDim() - Method in class com.actelion.research.calc.Matrix
 
getColIndexContainingMaxVal(int) - Method in class com.actelion.research.calc.Matrix
 
getColIndexContainingMaxVal(int, int) - Method in class com.actelion.research.calc.Matrix
 
getCollisionIntensity() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
 
getCollisionIntensityMatrix() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
getCollisionIntensitySum() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
getCollisionList() - Method in class com.actelion.research.chem.coords.InventorFragment
 
getCollisionPanalty() - Method in class com.actelion.research.chem.coords.InventorFragment
 
getColName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getColorRecord(Molecule, Collection<Integer>, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getColorVal2String(Molecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getColorVectorSubstructure(StereoMolecule, StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Returns the colors vector for the substructure in mol.
getCols() - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
getColumnProperties(String) - Method in class com.actelion.research.chem.io.DWARFileParser
Returns the original column properties of any source column by column name.
getColumns(List<Integer>) - Method in class com.actelion.research.calc.Matrix
 
getColumns(Vector<Integer>) - Method in class com.actelion.research.calc.Matrix
Deprecated.
use getColumns(List vecIndices) instead
getCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getCOM(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
getCOM(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
getCombinations(List<int[]>) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
 
getComment() - Method in class com.actelion.research.chem.StructureInfo
 
getCompactCopy() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getCompactCopy() - Method in class com.actelion.research.chem.StereoMolecule
 
getCompactMolecule(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
getCompactMolecule(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
getCompactMolecule(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getCompactMolecule(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getCompactMolecule(BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
 
getCompactMolecule(File) - Method in class com.actelion.research.chem.MolfileParser
 
getCompactMolecule(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
getCompactMolecule(String) - Method in class com.actelion.research.chem.MolfileParser
 
getCompactMolecule(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
getComparatorArea() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getComparatorAtomsBonds() - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getComparatorBonds() - Static method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
getComparatorCoverage() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
getComparatorDouble() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
 
getComparatorId() - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
 
getComparatorInt() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
 
getComparatorLength() - Static method in class com.actelion.research.util.StringFunctions
 
getComparatorNumBonds() - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getComparatorNumIndices() - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
getComparatorOrderNumber() - Static method in class com.actelion.research.chem.Element
 
getComparatorScore() - Static method in class com.actelion.research.util.datamodel.ScorePoint
 
getComparatorX() - Static method in class com.actelion.research.util.datamodel.ScorePoint
 
getComparatorX() - Static method in class com.actelion.research.util.PointUtils
 
getComparatorY() - Static method in class com.actelion.research.util.datamodel.ScorePoint
 
getCompatibleFileList(File, int) - Static method in class com.actelion.research.gui.FileHelper
 
getComplexityScore() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getComposite() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getCompound() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getCompound(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
getCompound(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
getConformer(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAMolecule
Returns the corresponding conformer of a molecular volume
getConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
getConformerCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getConformerIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
 
getConformerIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
getConformerLikelihood(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getConnAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
Returns the preferred angle between to three atoms in a row as positive value <= pi.
getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getConnAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getConnBond(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getConnBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getConnBondOrder(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
The neighbours (connected atoms) of any atom are sorted by their relevance:
1.
getConnectionPointCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getConnectionTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
 
getConnexComponents(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Returns a List of all Connex Components of the graph (List of List of Integer)
getContainer() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
getContent(MouseEvent) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
getContext() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
getContrastColor(Color, Color) - Static method in class com.actelion.research.util.ColorHelper
Based on the differences of hue and perceived brightness of foreground color fg and background color bg, this method checks and possibly adjusts the given foreground color fg such that its hue stays unchanged, but its brightness is adapted to make it better perceivable on the background.
getContribution(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
getConverted2CarbonSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Replaces all hetero-atoms, except hydrogen, with carbon.
getCoord() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
getCoordinates() - Method in class com.actelion.research.chem.conf.Conformer
 
getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
 
getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getCoordinates() - Method in class com.actelion.research.chem.io.CompoundFileParser
Either getIDCode and this method or getMolecule() must be overwritten!!!
getCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
This returns encoded atom coordinates according to the defined mode.
getCoordinates() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getCoordinates() - Method in class com.actelion.research.chem.Molecule3D
 
getCoordinates() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
 
getCoordinates(int) - Method in class com.actelion.research.chem.conf.Conformer
 
getCoordinates(int) - Method in class com.actelion.research.chem.Molecule
 
getCoordinates(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns the encoded reaction coordinates.
getCoordinates(Molecule, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
 
getCoordinates(StereoMolecule, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
 
getCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getCoordinatesA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getCoordinatesB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getCoordinatesC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
node deep copy.
getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getCoreCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getCoreCount() - Method in class com.actelion.research.chem.MarkushStructure
 
getCoreSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getCoreStructure(int) - Method in class com.actelion.research.chem.MarkushStructure
 
getCorrPearson(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCorrPearson(Matrix, Matrix) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCorrPearson(List<PointDouble>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCorrPearsonStandardized(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCosine(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
 
getCosine(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getCosine(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Vectors have to be normed!
getCount() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
 
getCountFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
 
getCovalentRadius() - Method in class com.actelion.research.chem.Element
 
getCovalentRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
 
getCovarianceCentered(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getCreatedSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
getCRingClosureName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getCRingOpeningName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getCRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getCryst1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getCurrentDirectory() - Static method in class com.actelion.research.chem.io.CompoundFileHelper
 
getCurrentPositions() - Method in interface com.actelion.research.chem.forcefield.ForceField
 
getCurrentPositions() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
getCursor() - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
getCursor() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
getCursor(int) - Static method in class com.actelion.research.util.CursorHelper
 
getCustomTemplateAtomMask() - Method in class com.actelion.research.chem.coords.CoordinateInventor
 
getData() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
getData() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
 
getData() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
 
getData(String) - Method in class com.actelion.research.chem.StructureInfo
 
getDateDeposition() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getDateFloat(String) - Method in class com.actelion.research.util.DateAnalysis
 
getDateMillis(String) - Method in class com.actelion.research.util.DateAnalysis
 
getDBRef() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getDBRef1DBRef2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getDConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getDecimalFormat(int) - Static method in class com.actelion.research.util.StringFunctions
 
getDefaultAverageBondLength() - Static method in class com.actelion.research.chem.Molecule
 
getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
 
getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
 
getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
 
getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
getDefaultInstance() - Static method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getDefaultInstance() - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
getDefaultMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
This is the default maximum valence of the atom neglecting atom charge or radical influences, e.g.
getDeleteAtomsBondMap(boolean[]) - Method in class com.actelion.research.chem.Molecule
 
getDeleteAtomsBondMap(int[]) - Method in class com.actelion.research.chem.Molecule
 
getDeleteColsZeroVar(List<Integer>) - Method in class com.actelion.research.calc.Matrix
Deletes columns with zero variance.
getDeleteKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getDensity() - Method in class com.actelion.research.chem.StructureInfo
 
getDEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getDepictor() - Method in class com.actelion.research.gui.JStructureView
 
getDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
Returns the human readable description of this filter.
getDescriptor() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
getDescriptor(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
Depending on the mode isLargestFragmentOnly() the descriptor is expected to be represent the whole structure or the largest fragment.
getDescriptor(int, int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
 
getDescriptor(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
getDescriptor(String) - Method in class com.actelion.research.chem.io.DWARFileParser
 
getDescriptorColumn(String) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns a number to be used in getDescriptor() to address the the descriptor with the given short name.
getDescriptorDetail() - Method in class com.actelion.research.chem.AbstractDrawingObject
Creates a string encoding all properties specific to this drawing object.
getDescriptorDetail() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
getDescriptorDetail() - Method in class com.actelion.research.chem.TextDrawingObject
 
getDescriptorHandlerFactory() - Method in class com.actelion.research.chem.io.CompoundFileParser
 
getDescriptorInfo(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
getDescriptorShortName() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
getDescriptorType(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
getDetail() - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
If assessDruglikeness() was called multiple times in multiple threads, then getDetail() won't retrieve the expected detail.
getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
 
getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
 
getDetail(StereoMolecule, int) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
 
getDetails() - Method in class com.actelion.research.chem.io.DWARFileParser
Provided that the mode contains MODE_EXTRACT_DETAILS, then this method returns a map of all embedded detail objects of the DWAR file.
getDeviceConfiguration() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getDFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getDiagonal() - Method in class com.actelion.research.calc.Matrix
Matrix diagonal extraction.
getDiffRect(Rectangle2D, Rectangle2D) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getDihedral(Coordinates, Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
getDihedral(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space.
getDihedral(Molecule3D, int, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
Gets the Dihedral Angle between 4 atoms
getDihedral(StereoMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
Gets the Dihedral Angle between 4 atoms
getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getDirectionality() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getDirectSim(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getDiscreteValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
getDisplayMode() - Method in class com.actelion.research.gui.JDrawArea
 
getDisplayMode() - Method in class com.actelion.research.share.gui.editor.Model
 
getDisplayMolecule() - Method in class com.actelion.research.gui.JStructureView
 
getDisplaySize() - Method in class com.actelion.research.share.gui.editor.Model
 
getDissimilarity(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
D(LigandType_1, LigandType_2) = Sum( d( F(ProteinType_i, LigandType_1), F(ProteinType_i, LigandType_2)), i)
getDissimilarity(TorsionDescriptor, float[]) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
Calculates a similarity value between td and this considering individual torsion values, the importance of the rotatable bond, and the ratio of rotatable/non-rotatable bonds.
getDistance(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
 
getDistanceArray(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getDistanceHistogram() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getDistanceMatrix(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getDistanceTables() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getDistHist(int, int, byte[]) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
 
getDistHist(MultCoordFragIndex, MultCoordFragIndex) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
 
getDistHists() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getDonorCount() - Method in class com.actelion.research.chem.PropertyCalculator
 
getDouble() - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
getDoublePivot() - Method in class com.actelion.research.calc.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDrawArea() - Method in class com.actelion.research.gui.JDrawDialog
 
getDrawArea() - Method in class com.actelion.research.gui.JDrawPanel
 
getDrawConfig() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
 
getDrawingObjects() - Method in class com.actelion.research.gui.JDrawArea
 
getDrawingObjects() - Method in class com.actelion.research.share.gui.editor.Model
 
getDruglikenessString(StereoMolecule) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
 
getDRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getDummy() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getEdgeLengths() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
getEdges() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getEEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getEFGName(int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getEigenvector(Matrix, int, Matrix, Matrix) - Static method in class com.actelion.research.calc.Matrix
Householder reduction according num rec 11.2.
getElectronegativity() - Method in class com.actelion.research.chem.Element
 
getElectronValenceCorrection(int, int) - Method in class com.actelion.research.chem.Molecule
This is the maximum valence correction caused by atom charge or radical status, e.g.
getElement(int) - Static method in class com.actelion.research.chem.PeriodicTable
 
getEliminationRuleList() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
getEncodedCoordinates() - Method in class com.actelion.research.chem.Canonizer
Encodes the molecule's atom coordinates into a compact String.
getEncodedCoordinates() - Method in class com.actelion.research.chem.SimpleCanonizer
 
getEncodedCoordinates(boolean) - Method in class com.actelion.research.chem.Canonizer
Encodes the molecule's atom coordinates into a compact String.
getEncodedCoordinates(boolean, Coordinates[]) - Method in class com.actelion.research.chem.Canonizer
Encodes the molecule's atom coordinates into a compact String.
getEncodedMapping() - Method in class com.actelion.research.chem.Canonizer
 
getEncodedQuery(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
Returns the (or one of the) query structures encodes as idcode.
getEnd() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
getEnd() - Method in class com.actelion.research.util.IntQueue
 
getEnergy() - Method in class com.actelion.research.chem.conf.Conformer
 
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
Calculates the angle energy.
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
Calculates the bond stretch energy.
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
Calculates the electrostatic energy.
getEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
 
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Calculates the out of plane energy.
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.PositionConstraint
 
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
Calculates the stretch bend energy.
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
Calculates the torsional energy.
getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
Calculates the van der Waals energy.
getEnterKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getEquivalentTypes(int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
Compare similarity values of 2 types (across all lines)
getERearrangementName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getERegNo() - Method in class com.actelion.research.chem.io.RDFileParser
 
getErrorCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
getErrors() - Method in class com.actelion.research.chem.io.AbstractParser
 
getERSGroupMemberCounts() - Method in class com.actelion.research.chem.StereoMolecule
 
getERxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getEscapeKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getESRImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
 
getESRImageRows() - Method in class com.actelion.research.share.gui.editor.ImageProvider
 
getESRType() - Method in class com.actelion.research.share.gui.editor.Model
 
getEuclidDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Euclidean distance
getEuclidDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getEuclidDistFast(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Euclidean distance without sqrt
getEuclideanDistanceFast(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Euclidean distance without sqrt
getEuclideanDistanceFastRows(int, int) - Method in class com.actelion.research.calc.Matrix
Skipping the sqrt.
getEuclideanDistanceFastRows(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
Skipping the sqrt.
getExactHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns a hash code representing the exact reaction.
getExcludedNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
This method returns the count of atom neighbours which are marked as being an exclude group.
getExhaustiveStatistics() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getExitAtoms() - Method in class com.actelion.research.chem.shredder.Fragment3D
 
getExitVectorGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getExpdata() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getExplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getExplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getExtendedAtomSequence(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
getExtendedCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getExtendedSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
getExtension(int) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
 
getExtension(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
Return the extension portion of the file's name .
getExtension(File) - Static method in class com.actelion.research.util.IO
 
getExtensionCuts(List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
get a list of int[] arrays that define an extension cut: Given a subtree with a designated head-node, an extension cut separates an extension match from the remaining subtrees.
getExtensionList(int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
getEZParity(int) - Method in class com.actelion.research.chem.Canonizer
Returns the absolute bond parity, which is based on priority ranks.
getFactorial(int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
 
getFactorIsomorphSymmetric() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
 
getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
 
getFailureCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
getFcadj(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
Returns the formal charge adjustment for a given atom type.
getFFP() - Method in class com.actelion.research.chem.coords.InventorTemplate
 
getFGValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
getFGValue(double[]) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
 
getFGValue(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
 
getFGValue(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
getFGValue(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.AngleConstraint
 
getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.BondConstraint
 
getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
 
getFGValue(double[]) - Method in interface com.actelion.research.chem.potentialenergy.PotentialEnergyTerm
 
getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.TorsionConstraint
 
getFGValuePP(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getFGValueSelfPP(double[], MolecularVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getFGValueShape(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms
getFGValueShapeSelf(double[], MolecularVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getFieldData() - Method in class com.actelion.research.chem.io.RDFileParser
 
getFieldData(int) - Method in class com.actelion.research.chem.io.CompoundFileParser
Returns the cell content of the current row.
getFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
 
getFieldData(int) - Method in class com.actelion.research.chem.io.ODEFileParser
 
getFieldData(int) - Method in class com.actelion.research.chem.io.SDFileParser
 
getFieldData(String) - Method in class com.actelion.research.chem.io.RDFileParser
 
getFieldData(String) - Method in class com.actelion.research.chem.SDFileMolecule
 
getFieldIndex(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
 
getFieldNames() - Method in class com.actelion.research.chem.io.CompoundFileParser
Compiles all column names that contain alpha-numerical information.
getFieldNames() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getFieldNames() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getFieldNames() - Method in class com.actelion.research.chem.io.RDFileParser
Returns a list of field names.
getFieldNames() - Method in class com.actelion.research.chem.io.SDFileParser
Returns a list of field names.
getFieldNames(int) - Method in class com.actelion.research.chem.io.SDFileParser
Returns a list of field names.
getFields() - Method in class com.actelion.research.chem.SDFileMolecule
 
getFile() - Method in class com.actelion.research.gui.JFileChooserOverwrite
 
getFile(Component, String, int) - Static method in class com.actelion.research.gui.FileHelper
For compatibility reasons...
getFileType(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
 
getFinalRank() - Method in class com.actelion.research.chem.Canonizer
 
getFingerprint(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
Generates a fingerprint of the default size for the given ExtendedMolecule
getFingerprint(StereoMolecule, int) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
Generates the fingerprint of a molecule
getFirstHittingLongIndexBlockNo() - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
getFisherProjectionParity(int, int[], double[], int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
If the atom is a stereo center in fisher projection, then its tetrahedral parity is returned.
getFitMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
 
getFlatness() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
getFlavors() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
getFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
 
getFlipped() - Method in class com.actelion.research.calc.Matrix
Opposite direction to transpose.
getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getFont() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
getFont() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
getFont(AttributeSet) - Method in class com.actelion.research.gui.hidpi.ScaledStyleSheet
 
getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getFontRenderContext() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getFontScaleFactor() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
 
getForceConstants(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
Gets the force constants associated with a torsion angle.
getForegroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
 
getForegroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getFormalCharges(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
Computes the MMFF formal charges for a molecules atoms.
getFormula() - Method in class com.actelion.research.chem.MolecularFormula
 
getFormula(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getFormulaIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getFractalDimension() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
getFractionCarbonInteractions() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getFragment() - Method in class com.actelion.research.chem.conf.TorsionDetail
Returns the direct surrounding of the previously classified rotatable bond.
getFragment() - Method in class com.actelion.research.chem.coords.InventorTemplate
 
getFragment(int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
 
getFragment(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
 
getFragment(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getFragment(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
 
getFragment(IBitArray, boolean) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
 
getFragmentAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
getFragmentAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Returns an array of all atoms for which a path of bonds leads to rootAtom not considering metal ligand bonds.
getFragmentAtoms(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Returns an array of all atoms for which a path of bonds leads to rootAtom.
getFragmentIdCode(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
 
getFragmentIdCodeCarbonSkeleton(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
 
getFragmentList() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
 
getFragmentMatches(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Find all fragment occurences in mol (only the movable atoms are considered).
getFragmentNo(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getFragmentNumbers(int[], boolean[], boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Locates all disconnected fragments in the molecule and assigns fragment numbers (starting from 0) to all atoms.
getFragmentNumbers(int[], boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Locates all unconnected fragments in the Molecule and assigns fragment indexes for every atom starting with 0.
getFragments() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getFragments() - Method in class com.actelion.research.chem.StereoMolecule
Separates all disconnected fragments of this Molecule into individual Molecule objects.
getFragments() - Method in class com.actelion.research.gui.JDrawArea
 
getFragments() - Method in class com.actelion.research.share.gui.editor.Model
 
getFragments(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
Returns list with indices for fragments with size bonds.
getFragments(int[], int) - Method in class com.actelion.research.chem.StereoMolecule
Separates all disconnected fragments of this Molecule into individual molecule objects.
getFragments(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragmenter3D
Applying the constraints passed to the Fragmenter3D constructor, this method shredders the given 3D-molecule and returns all generated 3D-fragments as an ArrayList.
getFragmentsForSingleAtom(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
 
getFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The free valence is the number of potential additional single bonded neighbours to reach the atom's maximum valence.
getFrequencies() - Method in class com.actelion.research.calc.histogram.Histogram
 
getFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
getFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
getFrequency(int) - Method in class com.actelion.research.calc.histogram.Histogram
 
getFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
 
getFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
 
getFromQuadraticMatrix(Matrix, double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getFullyMappedReactions() - Method in class com.actelion.research.chem.reaction.Reactor
After instantiating the Reactor with MODE_FULLY_MAP_REACTIONS and after supplying real reactants, this method may be used to construct the fully mapped reaction.
getFunction(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getFunction(long) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
getFunction(long) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getFunction(String) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
getFunctionalGroupEquivalenceLevel(int, int) - Static method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
Determines the similarity of two functional groups based on their location in the binary functional group similarity tree.
getFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getFunctionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getFunctionalityIndex() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getFunctionGroupCountMap() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
Applying a predefined dictionary of logically arranged 1024 functional groups this method determines all functional groups present in the molecule, counts how often they occurr in the molecule.
getGenericAcceptor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getGenericDonor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getGenericNegCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getGenericPosCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getGeomFactory() - Method in class com.actelion.research.share.gui.editor.Model
 
getGlobalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
 
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.PositionConstraint
 
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
Calculates the gradient and adds it to the gradients array.
getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
Calculates the gradient and adds it to the gradients array.
getGradientContribution(Gaussian3D, Gaussian3D, double[], boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getGraphAtoms() - Method in class com.actelion.research.chem.Canonizer
 
getGraphIndexes() - Method in class com.actelion.research.chem.Canonizer
 
getGridCoordinates(Coordinates) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getGridSize() - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getGyrationRadius() - Method in class com.actelion.research.chem.docking.LigandPose
 
getHalignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
Gets the Halignment attribute of the VerticalFlowLayout object
getHandleHydrogenAtomMap(boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
getHandleHydrogenBondMap() - Method in class com.actelion.research.chem.ExtendedMolecule
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current bond indexes to those new bond indexes that would result from a call to handleHydrogens.
getHandleHydrogenMap() - Method in class com.actelion.research.chem.ExtendedMolecule
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
getHandleHydrogenMap() - Method in class com.actelion.research.chem.MolfileParser
If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP
getHash() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
getHash(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
 
getHashCode(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
getHashMap(List<IdentifiedObject<T>>) - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
 
getHashSetIndexInevitablePPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getHConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getHDonorsAcceptors(ExtendedMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Returns a array of 2 elements [number of donors, number of acceptors]
getHeaderString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getHeaderTags() - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getHeadOrTail() - Method in class com.actelion.research.chem.io.DWARFileParser
Provided that the mode contains MODE_BUFFER_HEAD_AND_TAIL, then this method returns a list of all header/footer rows of the DWAR file.
getHeight() - Method in class com.actelion.research.chem.coords.InventorFragment
 
getHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getHeight() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getHelix() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getHelperArrayStatus() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getHEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getHet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getHetAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getHeteroOnlyNode(PPNode) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getHeteroPosition(int) - Method in class com.actelion.research.chem.RingCollection
Returns the position of the electron pair providing hetero atom or carbenium atom in case of 5-membered, respective 7-membered aromatic ring.
getHexStringFromIndex(int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getHFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getHgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
Gets the Hgap attribute of the VerticalFlowLayout object
getHighestAtomStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
getHighestMapNo() - Method in class com.actelion.research.chem.reaction.Reaction
 
getHighLightColor() - Method in class com.actelion.research.share.gui.DrawConfig
 
getHighLightColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getHiliteAtom() - Method in class com.actelion.research.gui.JDrawArea
 
getHiliteBond() - Method in class com.actelion.research.gui.JDrawArea
 
getHistogram() - Method in class com.actelion.research.calc.histogram.Histogram
 
getHistogram(double[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogram(float[][], int, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogram(float[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogram(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogram(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogram(Matrix, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHistogramBins(double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
getHitQuote() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
getHMId_Formula() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
 
getHmId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getHMId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
 
getHMId_Site() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
 
getHMId_Synonyms() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
 
getHmNo_Remark() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
 
getHorizontalFill() - Method in class com.actelion.research.gui.VerticalFlowLayout
Gets the Hfill attribute of the VerticalFlowLayout object
getHoseCodes(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
This descriptor requires proper up/down bonds, because it encodes stereo parities.
getHoseCodesFromDiaID(String, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
 
getHRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getHRxnGroupDef(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getHydrogenMap() - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
 
getHydrogens() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getIconScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
 
getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getId() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
getId() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
 
getId() - Method in class com.actelion.research.chem.StructureInfo
 
getId() - Method in class com.actelion.research.chem.SVGDepictor
 
getId() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
getId() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
 
getID() - Method in class com.actelion.research.calc.Matrix
 
getID() - Method in class com.actelion.research.chem.conf.TorsionDetail
Returns the torsion identifier that resulted from the most previous classification.
getID() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getIdcode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
 
getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
getIdCode() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
getIdCode() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
getIDCode() - Method in class com.actelion.research.chem.Canonizer
 
getIDCode() - Method in class com.actelion.research.chem.io.CompoundFileParser
Either this method and getCoordinates() or getMolecule() must be overwritten!!!
getIDCode() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getIDCode() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getIDCode() - Method in class com.actelion.research.chem.shredder.Fragment3D
 
getIDCode() - Method in class com.actelion.research.chem.SimpleCanonizer
 
getIDCode() - Method in class com.actelion.research.chem.StereoMolecule
This is a convenience method that creates the molecule's idcode without explicitly creating a Canonizer object for this purpose.
getIDCode() - Method in class com.actelion.research.share.gui.editor.Model
 
getIDCode(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
Returns the (or one of the) query structures encodes as idcode.
getIDCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns the idcode of the structure or largest fragment.
getIDCode(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
Generates an IDCODE for a defined and simplified state of a given molecule.
getIdCodeFromFragment(StereoMolecule, ListWithIntVec) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
 
getIDCodeVersion(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getIDCodeVersion(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
getIDCoordinates() - Method in class com.actelion.research.chem.shredder.Fragment3D
 
getIDCoordinates() - Method in class com.actelion.research.chem.StereoMolecule
This is a convenience method that creates the molecule's id-coordinates matching the idcode available with getIDCode().
getIdentifier() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getIdFlexophorePoint1() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getIdFlexophorePoint2() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getImage() - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
Deprecated.
Use ImageClipboardHandler.pasteImage for consistency reasons
getImageProvider() - Method in class com.actelion.research.share.gui.editor.Model
 
getImplicitHigherValence(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
If the explicitly attached neighbors cause an atom valence to exceed the lowest allowed valence for this atomic no, then this method returns the next higher allowed valence, e.g.
getImplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates and return the number of implicit hydrogens at atom.
getImplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return the number of implicit hydrogens, ie.
getIncrement(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
 
getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getIndex() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getIndex() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getIndex() - Method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
getIndex() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
getIndex() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
 
getIndex() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
 
getIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
 
getIndex(int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getIndex(T) - Method in class com.actelion.research.util.SortedList
Returns the position index of object in the sorted list.
getIndex(T) - Method in class com.actelion.research.util.UniqueList
When objects were added after the last getIndex() call, then the original-index-map needs to be re-created.
getIndexAboveEqual(T) - Method in class com.actelion.research.util.SortedList
If object is not member of this list, returns potential insert index.
getIndexBaseFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getIndexBelowEqual(T) - Method in class com.actelion.research.util.SortedList
If object is not member of this list, returns potential insert index.
getIndexCenter() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
getIndexCorrespondingBaseNode(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getIndexFromCoord(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
 
getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
 
getIndexMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
getIndexOriginalAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
getIndexOrInsertIndex(T) - Method in class com.actelion.research.util.SortedList
Returns the position index of object in the sorted list.
getIndexPosStartForDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getIndexQueryFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getIndexSphereVisualization() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getIndicesBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
 
getInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getInfo() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
getInfo() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
 
getInfo() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
getInfo() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getInfo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getInitialRot() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
getInitialTranslate() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
getInstance() - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
 
getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
 
getInstance() - Static method in class com.actelion.research.chem.name.StructureNameResolver
 
getInstance() - Static method in class com.actelion.research.chem.phesa.QuickMathCalculator
 
getInstance() - Static method in class com.actelion.research.chem.reaction.ClassificationData
 
getInstance(int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
Use this as constructor for serial mode.
getInt() - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
getInt(byte[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getIntegratedAreaWeighted(int[], double[], int) - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
Takes the natural logarithm for each area fraction.
getInteractionAtomType(int) - Method in class com.actelion.research.chem.Molecule3D
 
getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getInteractionClasses() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getInteractionSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getInteractionType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getInteractionTypeCount() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
realize() may be called first.
getInteractionTypeFromByteArray(byte, byte, byte) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
getIntercept() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getInterMolecularInteractions(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
getInverseTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
 
getIonizableGroups() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
 
getIRegNo() - Method in class com.actelion.research.chem.io.RDFileParser
 
getIsotopeList(int) - Static method in class com.actelion.research.chem.IsotopeHelper
 
getJrnl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getKey(int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getKeyFragment(int) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getKeyStrokeBuffer() - Method in class com.actelion.research.share.gui.editor.Model
 
getKeywords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getKoop() - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
 
getKoop(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
 
getKoop(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
Returns the Koop parameters from the OutOfPlane table.
getL() - Method in class com.actelion.research.calc.LUDecomposition
Return lower triangular factor
getL1() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
getL2() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
getLambda() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
getLength() - Method in class com.actelion.research.chem.Coordinates
 
getLength() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
getLength() - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
 
getLength(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
 
getLengthIntVec() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
getLi() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
 
getLiConnect() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getLigandBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getLigandCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getLigandRMSD(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Gets the root mean square deviation between 2 positions.
getLigConf() - Method in class com.actelion.research.chem.docking.LigandPose
 
getLikelihood() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
getLikelyhood() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.
getLikelyRandomConformerIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
Calculates a random conformer index giving conformers with lower strains a higher chance to be selected.
getLikelyRandomTorsionIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
Calculates a random torsion index giving torsions with higher likelyhoods (i.e.
getLiLiIdCode() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
getLinedCol() - Method in class com.actelion.research.calc.Matrix
 
getLineWidth() - Method in class com.actelion.research.chem.AbstractDepictor
 
getLineWidth() - Method in class com.actelion.research.chem.Depictor
 
getLineWidth() - Method in class com.actelion.research.chem.Depictor2D
 
getLineWidth() - Method in class com.actelion.research.chem.SVGDepictor
 
getLineWidth() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
getLink() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
getLinkNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getLiNonOverLappingIsomorphSubstruct() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
getList() - Method in class com.actelion.research.calc.Matrix
 
getList(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getListIndex(String) - Method in class com.actelion.research.chem.SortedStringList
 
getListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
 
getListIndexOriginalAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getLocalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
getLocaleDateFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
 
getLocaleFormat() - Method in class com.actelion.research.util.Formatter
 
getLocaleTimeFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
 
getLogP() - Method in class com.actelion.research.chem.PropertyCalculator
 
getLogPDetail() - Method in class com.actelion.research.chem.PropertyCalculator
 
getLogS() - Method in class com.actelion.research.chem.PropertyCalculator
 
getLogSDetail() - Method in class com.actelion.research.chem.PropertyCalculator
 
getLongestChain(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Return the longest molecular chain starting at atm
getLongIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getLongIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getLowestFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The lowest free valence is the number of potential additional single bonded neighbours to reach the atom's lowest valence above or equal its current occupied valence.
getManhattanBlockDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
getMapping(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns the encoded reaction mapping.
getMappingIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getMapToolColor() - Method in class com.actelion.research.share.gui.DrawConfig
 
getMapToolColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getMarkushCount() - Method in class com.actelion.research.share.gui.editor.Model
 
getMarkushStructure() - Method in class com.actelion.research.gui.JDrawArea
 
getMarkushStructure() - Method in class com.actelion.research.share.gui.editor.Model
 
getMask() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
getMask() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
 
getMaster() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMatch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
getMatches() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
getMatches() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
 
getMatchingTransform(PPTriangle, double[][]) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
getMatchingTransforms(Map<Integer, ArrayList<PPTriangle>>, Map<Integer, ArrayList<PPTriangle>>, int, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher
 
getMatchList() - Method in class com.actelion.research.chem.SSSearcher
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
getMatchList() - Method in class com.actelion.research.chem.SSSearcherWithIndex
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
getMatrix(int[], int[]) - Method in class com.actelion.research.calc.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class com.actelion.research.calc.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class com.actelion.research.calc.Matrix
Get a submatrix.
getMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
 
getMatrixFromString(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
getMax() - Method in class com.actelion.research.calc.Matrix
 
getMax(int) - Method in class com.actelion.research.calc.Matrix
get max value for that col.
getMaxAtoms() - Method in class com.actelion.research.chem.Molecule
The currently defined maximum of atoms, which increases automatically when using high level construction methods and new atoms exceed the current maximum.
getMaxBonds() - Method in class com.actelion.research.chem.Molecule
The currently defined maximum of bonds, which increases automatically when using high level construction methods and new bonds exceed the current maximum.
getMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getMaxFreeValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getMaximumCommonSubstructure(List<StereoMolecule>) - Method in class com.actelion.research.chem.mcs.MCSFunctions
 
getMaximumDistanceInPPPoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getMaximumIonCharge(Molecule3D, int) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
 
getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
getMaximumOverlap(List<String>, int) - Static method in class com.actelion.research.util.StringFunctions
Finds the maximum common String in all Strings.
getMaximumSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getMaximumValue() - Method in class com.actelion.research.calc.Matrix
 
getMaximumX() - Method in class com.actelion.research.calc.histogram.Histogram
 
getMaximumY() - Method in class com.actelion.research.calc.histogram.Histogram
 
getMaxIndex() - Method in class com.actelion.research.calc.Matrix
 
getMaxMin() - Method in class com.actelion.research.calc.Matrix
max and min vals for all cols
getMaxNumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
getMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
getMaxOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getMaxRow(int) - Method in class com.actelion.research.calc.Matrix
 
getMaxRowIndex(int) - Method in class com.actelion.research.calc.Matrix
 
getMaxRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
Shuffles the indices before searching the minimum.
getMaxValence(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getMaxValence(int) - Method in class com.actelion.research.chem.Molecule
This is the defined maximum valence (or set abnormal valence) corrected by atom charge or radical influences, e.g.
getMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
This is the defined maximum valence (or set abnormal valence) neglecting atom charge or radical influences, e.g.
getMaxX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getMaxY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getMCS() - Method in class com.actelion.research.chem.mcs.MCS
 
getMCS() - Method in class com.actelion.research.chem.mcs.MCSFast
 
getMCS(Reaction, boolean[], SSSearcher) - Static method in class com.actelion.research.chem.reaction.CommonSubGraphHelper
 
getMCSBondArray(boolean[], boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
Calculates the bond arrays for molecule and fragment for their maximum common substructure.
getMdltyp() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMean() - Method in class com.actelion.research.calc.Matrix
 
getMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getMean(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getMeanAngle(InventorAngle[], int) - Static method in class com.actelion.research.chem.coords.CoordinateInventor
 
getMeanCol(int) - Method in class com.actelion.research.calc.Matrix
 
getMeanCol(int, int[]) - Method in class com.actelion.research.calc.Matrix
 
getMeanCols() - Method in class com.actelion.research.calc.Matrix
 
getMeanCols(int[]) - Method in class com.actelion.research.calc.Matrix
 
getMeanRow(int) - Method in class com.actelion.research.calc.Matrix
 
getMeanRows() - Method in class com.actelion.research.calc.Matrix
 
getMedian() - Method in class com.actelion.research.calc.Matrix
 
getMedian(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getMedian(int) - Method in class com.actelion.research.calc.Matrix
 
getMedian(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getMedianBin(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
 
getMedianCols() - Method in class com.actelion.research.calc.Matrix
 
getMedianForDouble(List<Double>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getMedianForInteger(List<Integer>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getMedianForLong(List<Long>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getMergedCopy() - Method in class com.actelion.research.chem.reaction.Reaction
Merges all reactants into one molecule and all products into another ad creates a new Reaction object from those.
getMergeRows(Matrix) - Method in class com.actelion.research.calc.Matrix
 
getMessage() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
getMetalBondedConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getMin() - Method in class com.actelion.research.calc.Matrix
 
getMin(int) - Method in class com.actelion.research.calc.Matrix
 
getMinColIndex(int) - Method in class com.actelion.research.calc.Matrix
 
getMinDist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getMinimumX() - Method in class com.actelion.research.calc.histogram.Histogram
 
getMinMaxSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
 
getMinOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
getMinPos() - Method in class com.actelion.research.calc.Matrix
 
getMinRow(int) - Method in class com.actelion.research.calc.Matrix
 
getMinRowIndex(int) - Method in class com.actelion.research.calc.Matrix
 
getMinRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
03.10.04 MvK Shuffles the indices before searching the minimum.
getMinRows() - Method in class com.actelion.research.calc.Matrix
 
getMinRowsPosCol() - Method in class com.actelion.research.calc.Matrix
 
getMinX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getMinY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getMirror(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
Get the mirror image of p through the plane defined by c1, c2, c3
getMMFFMolecule() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
getMode() - Method in class com.actelion.research.gui.JDrawArea
 
getMode() - Method in class com.actelion.research.share.gui.editor.Model
 
getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getModel() - Method in class com.actelion.research.gui.CompoundCollectionPane
 
getModRes() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMol() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getMol() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getMol() - Method in class com.actelion.research.chem.shredder.Fragment
 
getMolDistHist() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getMolecularPathCount(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Returns the number of paths of the given length (gives an idea of the number of branches)
getMolecule() - Method in class com.actelion.research.chem.conf.Conformer
 
getMolecule() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
getMolecule() - Method in class com.actelion.research.chem.io.CompoundFileParser
Either this method or getIDCode() and getCoordinates() must be overwritten!!!
getMolecule() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
getMolecule() - Method in class com.actelion.research.chem.io.SDFileParser
 
getMolecule() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
 
getMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
Returns the most recently defined molecule.
getMolecule() - Method in class com.actelion.research.chem.StructureTransferData
 
getMolecule() - Method in class com.actelion.research.gui.JDrawArea
 
getMolecule() - Method in class com.actelion.research.gui.JStructureView
 
getMolecule() - Method in class com.actelion.research.share.gui.editor.Model
 
getMolecule() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
getMolecule(int) - Method in class com.actelion.research.chem.ExtendedDepictor
 
getMolecule(int) - Method in class com.actelion.research.chem.reaction.Reaction
 
getMolecule(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
 
getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
 
getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
 
getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
 
getMolecule(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
getMoleculeAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
getMoleculeBounds(int) - Method in class com.actelion.research.gui.JChemistryView
Returns the bounding rectangle of the indicated molecule, if multiple molecules are shown, e.g.
getMoleculeColor() - Method in class com.actelion.research.chem.Molecule
cMoleculeColorDefault: atom coloring depends on atomic number.
getMoleculeCount() - Method in class com.actelion.research.chem.ExtendedDepictor
 
getMoleculeCount() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
getMoleculeDepictor(int) - Method in class com.actelion.research.chem.ExtendedDepictor
 
getMoleculeDepictor(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
getMoleculeForDisplay(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
getMoleculeForDisplay(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
getMoleculeName() - Method in class com.actelion.research.chem.io.CompoundFileParser
 
getMoleculeName() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getMoleculeName() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getMoleculeName() - Method in class com.actelion.research.chem.io.SDFileParser
 
getMoleculeRemovedUnrelatedAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getMolecules() - Method in class com.actelion.research.chem.reaction.Reaction
 
getMoleculeTransferable() - Method in class com.actelion.research.gui.JChemistryView
 
getMoleculeTransferable(Point) - Method in class com.actelion.research.gui.JStructureView
 
getMolfile() - Method in class com.actelion.research.chem.MolfileCreator
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
getMolfile() - Method in class com.actelion.research.chem.MolfileV3Creator
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
getMolFile(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
getMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getMolweight() - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates a rounded mass of the molecule
getMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
Creates most central ring system as new StereoMolecule from mol without touching mol.
getMST() - Method in class com.actelion.research.calc.graph.MinimumSpanningTree
 
getmTransformation() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
getMtrix1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMtrix2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMtrix3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
getMutatedSet(StereoMolecule, int, boolean, int) - Method in class com.actelion.research.chem.Mutator
 
getName() - Method in class com.actelion.research.chem.conf.Conformer
 
getName() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getName() - Method in class com.actelion.research.chem.Element
 
getName() - Method in class com.actelion.research.chem.Molecule
Allows to set a molecule name or identifier, that is, for instance, written to or read from molfiles.
getName() - Method in class com.actelion.research.chem.Molecule3D
 
getName() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getName() - Method in class com.actelion.research.chem.reaction.Reaction
 
getName() - Method in class com.actelion.research.chem.StructureInfo
 
getName(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getNameIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getNative() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
getNative() - Method in class com.actelion.research.share.gui.Delegator
 
getNative() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
getNative() - Method in interface com.actelion.research.share.gui.editor.geom.StrokeLineCap
 
getNaturalPercentage(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
 
getNeededNumberOfBondsInFragment(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
getNegativeNeighbourCount(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
getNegIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
 
getNeighbours() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getNeighbours(Coordinates[], double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
Gets a Set of all neigbouring atoms.
getNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
Gets a Set of all neigbouring atoms.
getNeighbours(Coordinates, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getNeighbours(Coordinates, double, boolean, int) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
Gets a Set of all neigbouring atoms.
getNeighbours(Molecule, int, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getNeighbours(Molecule, int, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
getNew(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
 
getNew(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
 
getNext4NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
 
getNext8NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
 
getNextColor() - Static method in class com.actelion.research.chem.reaction.MCSReactionMapper
 
getNextConformer() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
getNextConformer() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
Picks a new conformer from the conformer pool created by initializeConformers().
getNextConformer(TorsionSet[]) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
getNextConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
getNextEnumeration() - Method in class com.actelion.research.chem.MarkushStructure
After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.
getNextFieldData() - Method in class com.actelion.research.chem.io.SDFileParser
Returns the field data of the current record as one big String as it was read from the input file.
getNextFileName(String) - Static method in class com.actelion.research.util.IO
Has to be the total path of the file or there will be errors.
getNextMapNo() - Method in class com.actelion.research.share.gui.editor.Model
*********************************************************************************************************
getNextMolecule() - Method in class com.actelion.research.chem.io.RDFileParser
RD-files may contains lists of molecules or lists of reactions.
getNextMolFile() - Method in class com.actelion.research.chem.io.SDFileParser
Returns the molfile of the current record as one big String as it was read from the input file.
getNextReaction() - Method in class com.actelion.research.chem.io.RDFileParser
RD-files may contains lists of molecules or lists of reactions.
getNextTautomer(StereoMolecule) - Method in class com.actelion.research.chem.TautomerHelper
 
getNextTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
Creates the next set of torsion indexes to be tried by the ConformerGenerator.
getNMovables() - Method in class com.actelion.research.chem.Molecule3D
 
getNode() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
getNode(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
 
getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
!Slow method, it has to iterate through a loop to find the node in the array!
getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getNodeA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getNodeB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getNodeC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
getNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getNodes(Collection<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getNodesFromEdges(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getNodesQuery() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
getNonHydrogenNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
This method returns the non-hydrogen neighbour count of atom.
getNoOfKeys() - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getNorm() - Method in class com.actelion.research.util.datamodel.ByteVec
 
getNorm() - Method in class com.actelion.research.util.datamodel.IntVec
 
getNorm() - Method in class com.actelion.research.util.DoubleVec
 
getNorm(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
 
getNormalized(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getNormalizedAtomX(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
 
getNormalizedAtomY(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
 
getNormalizedMatrix() - Method in class com.actelion.research.calc.Matrix
 
getNormalizedMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
 
getNormalizedTorsionIndex(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
Normalizes a torsion angle considering the fragments symmetry type by returning the lowest symmetrically equivalent torsion that is >= 0.
getNormSq(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
 
getNoStereoCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns a hash code representing the structure or its largest fragment without any stereo information.
getNoStereoHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns a hash code representing the reaction without any stereo information.
getNoStereoHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
 
getNoStereoTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns a hash code representing the generic tautomer of the structure or its largest fragment with the stereo information removed before creating the generic tautomer.
getNoStereoTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
 
getNumAcidicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumAlcoholicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumAliphaticRingAtoms(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumAmide(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumArguments() - Method in class com.actelion.research.util.CommandLineParser
 
getNumAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumArylAmine(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumBasicNitrogen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumberAbove(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getNumberOfAtomsBetweenBonds(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Computes a matrix of distances between all the bonds in the graph.
getNumberOfBondsBetweenAtoms(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Computes a matrix of distances between all the atoms in the graph.
getNumberOfBondsBetweenAtoms(StereoMolecule, int, int[][]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
From Joel Freyss developed for the FFMolecule Computes a matrix of distances between all the atoms in the graph.
getNumberOfHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
 
getNumBins() - Method in class com.actelion.research.calc.histogram.Histogram
 
getNumBondsAtMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getNumBondsAtMaxSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getNumBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
getNumCarbonAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumCarboxy(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumCExclusiveNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getNumCyanoGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Counts cyano and iso-cyano
getNumElements() - Method in class com.actelion.research.calc.Matrix
 
getNumElementsEqual(double) - Method in class com.actelion.research.calc.Matrix
 
getNumElementsLarger(double) - Method in class com.actelion.research.calc.Matrix
 
getNumHeavyAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumHeteroAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumHeteroAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumHeteroNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getNumIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
getNumInevitablePharmacophorePoints() - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
 
getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
Only for interface compliance needed.
getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
getNumIsopropyl(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNummdl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getNumNitroGroupN(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumOverlappingIndices(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
getNumPPNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getNumPPNodes() - Method in interface com.actelion.research.util.graph.complete.ICompleteGraph
 
getNumQueryAtoms(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumRegressionPoints() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getNumSubstructure(StereoMolecule, String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumSulfOxyGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumThioEther(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getNumWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getObjectiveCompleteGraphHard() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getObsolete() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getOccupiedValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
The sum of bond orders of explicitly connected neighbour atoms including explicit hydrogen.
getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule
The sum of bond orders of explicitly connected neighbour atoms.
getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule3D
 
getOccurencesArray() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
getOffsetX() - Method in class com.actelion.research.chem.DepictorTransformation
 
getOffsetY() - Method in class com.actelion.research.chem.DepictorTransformation
 
getOneConformer(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
getOneConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
getOrderNumber() - Method in class com.actelion.research.chem.Element
 
getOrganicFunctionalGroupCounts() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
 
getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
getOrigX1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getOrigX2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getOrigX3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getOverlap(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getOverlap(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getOverlap(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getPaint() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getPairPotentials() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
getParsed(Vector<String>) - Static method in class com.actelion.research.calc.Matrix
Parses an vector with Strings and converts it to a Matrix.
getPartial(int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
Gets the partial charge of a bond type and its two atom types.
getPartialCharge(int) - Method in class com.actelion.research.chem.Molecule3D
 
getPath(int[], int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Locates and returns the shortest path between atoms atom1 and atom2
getPathBonds(int[], int[], int) - Method in class com.actelion.research.chem.ExtendedMolecule
Finds bonds of a path that is defined by an atom sequence.
getPathLength(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates the length of the shortest path between atoms atom1 and atom2
getPathLength(int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Calculates the length of the shortest path between atoms atom1 and atom2, which is not larger than maxLength and avoids atoms indicated by neglectAtom.
getPathsFromHeadNode(int, List<Set<Integer>>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getPbci(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
 
getPenStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSorted(double[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSorted(float[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSorted(float[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSorted(int[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getPercentileFromSorted(List<Double>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSortedInt(List<Integer>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPercentileFromSortedLong(List<Long>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
getPeripherySimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getPeripherySimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getPermutationCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
getPermutations(int[], int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
 
getPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getPharmacophorePoints(StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
getPivot() - Method in class com.actelion.research.calc.LUDecomposition
Return pivot permutation vector
getPlainHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
getPointsBetween(Point, Point) - Static method in class com.actelion.research.util.PointUtils
 
getPolarAtomTypeCount() - Static method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
getPolarAtomTypeCounts(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
getPolarSurfaceArea() - Method in class com.actelion.research.chem.PropertyCalculator
 
getPolarSurfaceAreaDetail() - Method in class com.actelion.research.chem.PropertyCalculator
 
getPolled() - Method in class com.actelion.research.util.Pipeline
 
getPose() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
 
getPosIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
 
getPositionInContainer() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
getPositionInContainer() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
 
getPositions(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
Parses a SDF file to extract the positions of each atom.
getPotentialConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Calculates the potential count of conformers by multiplying degrees of freedom (torsions per rotatable bond & rigid fragment multiplicities).
getPPGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getPPP(int) - Method in class com.actelion.research.chem.Molecule3D
 
getPPPoints(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getPpWeight() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getPrefactor(int, int) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
 
getPreviousAlignment() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getPreviousConformerContribution() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
getPreviousPheSAResult() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
additional output: element 0: total similarity (identical to getSimilarity(...)) element 1: pharmacophore similarity element 2: contribution to similarity that originates from additional volumes (incl/excl)
getPriority() - Method in class com.actelion.research.chem.coords.FragmentAssociation
 
getProbabilityFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
 
getProduct(int) - Method in class com.actelion.research.chem.reaction.Reaction
 
getProductDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
 
getProductDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getProductIDCodes() - Method in class com.actelion.research.chem.reaction.Reactor
 
getProducts() - Method in class com.actelion.research.chem.reaction.Reaction
 
getProducts() - Method in class com.actelion.research.chem.reaction.Reactor
 
getProducts(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getProductsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getProtAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getPseudoEZGroup(int) - Method in class com.actelion.research.chem.Canonizer
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this bond's relative stereo feature group number provided this bond is a pseudo stereo bond, i.e.
getPseudoStereoGroupCount() - Method in class com.actelion.research.chem.Canonizer
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns the number of independent relative stereo feature groups.
getPseudoTHGroup(int) - Method in class com.actelion.research.chem.Canonizer
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this atom's relative stereo feature group number provided this atom is a pseudo stereo center, i.e.
getPurity() - Method in class com.actelion.research.chem.StructureInfo
 
getPythag(double, double) - Static method in class com.actelion.research.calc.Matrix
pythag computes sqrt(a^2 + b^2) without destructive underflow or overflow.
getPythag2(double, double) - Static method in class com.actelion.research.calc.Matrix
 
getQ0() - Method in class com.actelion.research.chem.phesa.Quaternion
 
getQ1() - Method in class com.actelion.research.chem.phesa.Quaternion
 
getQ2() - Method in class com.actelion.research.chem.phesa.Quaternion
 
getQ3() - Method in class com.actelion.research.chem.phesa.Quaternion
 
getQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
getQuery() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
getRandom() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
 
getRandom(int, int) - Static method in class com.actelion.research.util.StringFunctions
 
getRandomRotation() - Static method in class com.actelion.research.chem.phesa.Quaternion
get a random quaternion, from: https://stackoverflow.com/questions/31600717/how-to-generate-a-random-quaternion-quickly
getRangeStatistics(MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
 
getRatioCoveredBonds() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getRatioNonSymmetricAtoms() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getRatioSymmetricAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.SymmetryCalculator
 
getRatioUsedBondsUpToMaxFreq() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getReactant(int) - Method in class com.actelion.research.chem.reaction.Reaction
 
getReactantCount() - Method in class com.actelion.research.share.gui.editor.Model
 
getReactantDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
 
getReactantDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getReactants() - Method in class com.actelion.research.chem.reaction.Reaction
 
getReactants(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getReactantsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getReaction() - Method in class com.actelion.research.chem.ExtendedDepictor
 
getReaction() - Method in class com.actelion.research.gui.JDrawArea
 
getReaction() - Method in class com.actelion.research.gui.JDrawDialog
 
getReaction() - Method in class com.actelion.research.gui.JEditableChemistryView
 
getReaction() - Method in class com.actelion.research.share.gui.editor.Model
 
getReaction(File) - Method in class com.actelion.research.chem.io.RXNFileParser
 
getReaction(File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
 
getReaction(String) - Method in class com.actelion.research.chem.io.RXNFileParser
 
getReaction(String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
 
getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawArea
 
getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawDialog
 
getReactionCenterAtoms(int, boolean[], boolean[], int[]) - Method in class com.actelion.research.chem.reaction.Reaction
Fills an array mapping on the atoms for the given molecule of this reaction.
getReactionCenterMapNos() - Method in class com.actelion.research.chem.reaction.Reaction
This method determines the largest mapping number in use (maxMapNo), creates a boolean array[maxMapNo+1], and within this array flags every mapping number that refers to atoms, which change bonds in the course of the reaction.
getReactionCenterSimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getReactionCenterSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getReactionCode(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns the reaction idcode.
getReactionCount() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
Returns the search type as integer including mode flags.
getReactionDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
 
getReactionDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getReactionTransferable() - Method in class com.actelion.research.gui.JChemistryView
 
getReactionType(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
 
getRearAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
Returns that neighbor atom of a central atom that lies in the rotatable bond axis.
getRearAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getRecentException() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getReceptorAtomTypes(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingEngine
 
getRecordCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
getRefConformerIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
 
getReferenceAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
Returns the reference atom of one part of the torsion fragment.
getReferenceVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
getRefMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
 
getRefMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getRelativeWeight() - Method in class com.actelion.research.chem.MolecularFormula
 
getRelevance() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
getRelevance(StereoMolecule, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
getRelevance(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
getRelMaxDistInHist() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
getRelMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
getRelMaxDistInHist(int, int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
 
getRemainingStructure(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
 
getRemark(int) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRemark0() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRemark1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRemark2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRemark3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRemarks() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRenderingHint(RenderingHints.Key) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getRenderingHints() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getREntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRequestCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
getResiduals() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getResiduals() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
getResname() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
getResName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getResnum() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
getResNum() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getResolution() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
getResSequence(int) - Method in class com.actelion.research.chem.Molecule3D
 
getRetinaScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
Macintosh retina display support for Java 7 and newer.
getRetronDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
getRevdat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getRGroup(int) - Method in class com.actelion.research.chem.MarkushStructure
 
getRGroupCount() - Method in class com.actelion.research.chem.MarkushStructure
 
getRingAtoms() - Method in class com.actelion.research.chem.coords.InventorChain
 
getRingAtoms(int) - Method in class com.actelion.research.chem.RingCollection
 
getRingBonds() - Method in class com.actelion.research.chem.coords.InventorChain
 
getRingBonds(int) - Method in class com.actelion.research.chem.RingCollection
 
getRings(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getRingsAccurate(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Find the smallest covering set of rings for the Molecule.
getRingSet() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getRingSetSimple() - Method in class com.actelion.research.chem.ExtendedMolecule
 
getRingsFast(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Find the list of rings for the Molecule.
getRingSize(int) - Method in class com.actelion.research.chem.RingCollection
 
getRingSizeAdjust(int) - Method in class com.actelion.research.chem.AtomTypeList
 
getRMS(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
 
getRmsd(Coordinates[], Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
 
getRmsd(Coordinates[], Coordinates[], int) - Static method in class com.actelion.research.chem.Coordinates
 
getRMSD() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
getRMSD(ClusterNode, DistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
getRND(int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getRND(int, int) - Static method in class com.actelion.research.calc.Matrix
 
getRole() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
getRotatableBondCount() - Method in class com.actelion.research.chem.ExtendedMolecule
Simple method to calculate rotatable bonds.
getRotatableBondCount() - Method in class com.actelion.research.chem.PropertyCalculator
 
getRotatableBondCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
After calling initializeConformers() this method returns the number of rotatable bonds, which are used to separate the molecule into rigid fragments.
getRotatableBonds() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getRotatableBondWeights(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDescriptor
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
getRotatedCenter(double[][], double, double[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getRotationCenters() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getRotationMatrix(double, Coordinates, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getRotMatrix() - Method in class com.actelion.research.chem.phesa.Quaternion
 
getRotMatrix(Coordinates, double, double[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
 
getRotMatrixDerivative(Coordinates, double, Coordinates[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
 
getRow() - Method in class com.actelion.research.chem.io.DWARFileParser
Returns the entire line containing all row data
getRow(int) - Method in class com.actelion.research.calc.Matrix
Flat copy.
getRowAsFloat(int) - Method in class com.actelion.research.calc.Matrix
 
getRowAsList(int) - Method in class com.actelion.research.calc.Matrix
 
getRowCopy(int) - Method in class com.actelion.research.calc.Matrix
 
getRowCount() - Method in class com.actelion.research.chem.io.CompoundFileParser
Depending on data source returns the total row count or -1 if unknown
getRowCount() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getRowCount() - Method in class com.actelion.research.chem.io.ODEFileParser
 
getRowCount() - Method in class com.actelion.research.chem.io.RDFileParser
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
getRowCount() - Method in class com.actelion.research.chem.io.SDFileParser
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
getRowCount() - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
This is the total number of records, whether they qualify for a structure search or not.
getRowCount() - Method in interface com.actelion.research.chem.StructureSearchDataSource
This is the total number of records, whether they qualify for a structure search or not.
getRowDim() - Method in class com.actelion.research.calc.Matrix
 
getRowName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
getRows() - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
getRRefuncName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRRxnDef(int, int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRRxnFGroups(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRRxnMasks(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRRxnSymmetric(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
 
getRuleList() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
getRuleStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.DistanceRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.PlaneRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
getRuleType() - Method in class org.openmolecules.chem.conf.so.TorsionRule
 
getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileCreator
 
getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileV3Creator
 
getScale1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getScale2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getScale3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
 
getScaleFactor(Graphics2D) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
 
getScaling() - Method in class com.actelion.research.chem.DepictorTransformation
 
getScalingFactor() - Method in class com.actelion.research.chem.MolfileV3Creator
 
getScore() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
 
getScore() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
getScore() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
 
getScore() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
 
getScore() - Method in class com.actelion.research.chem.mcs.MCS
Calculates the score by bonds_mcs/Max(bonds_mol, bonds_frag)
getScore() - Method in class com.actelion.research.chem.mcs.MCSFast
 
getScore() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getScore() - Method in class com.actelion.research.util.datamodel.ScorePoint
 
getScore(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
 
getScoreFracBitsCommonQuery(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
(sum bits set common) / (sum bits set in query)
getScoreFracBitsInCommonBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
(sum bits set common) / (sum bits set in both)
getScoreQueryInBase(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getScoreQueryInBaseBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
(sum bits set only in query) / (sum bits set in query)
getScoreQueryInBaseBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getScoreQueryInBaseByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getSelectedAtom() - Method in class com.actelion.research.share.gui.editor.Model
 
getSelectedBond() - Method in class com.actelion.research.share.gui.editor.Model
 
getSelectedCopy(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
 
getSelectedDrawingObject() - Method in class com.actelion.research.share.gui.editor.Model
 
getSelectedReaction() - Method in class com.actelion.research.share.gui.editor.Model
 
getSelectionColor() - Method in class com.actelion.research.share.gui.DrawConfig
 
getSelectionColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
 
getSelfAtomOverlap(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
calculate the self-overlap of the base molecule
getSelfAtomOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getSelfAtomOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getSelfPPOverlap(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getSelfPPOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getSelfPPOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getSEQADV() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSEQRES() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSerialId() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getSharedRing(int, int) - Method in class com.actelion.research.chem.RingCollection
brute force method to check, whether and which ring is shared by two bonds
getSheet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getShift() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
 
getShiftVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
getShortName() - Method in class com.actelion.research.chem.Molecule3D
 
getSigma() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
getSim() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
 
getSimilarity() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
 
getSimilarity() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getSimilarity(byte[], byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
getSimilarity(int[][], int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
 
getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
 
getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getSimilarity(DistHist, int, int, DistHist, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
 
getSimilarity(PPNode, PPNode) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
 
getSimilarity(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarity(PharmacophoreTree, PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
getSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getSimilarity(PheSAMolecule, PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
calculates the Shape- and/or Pharmacophore similarity of a query molecule with a base molecule
getSimilarity(StereoMolecule, StereoMolecule, DescriptorHandler) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getSimilarity(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
getSimilarity(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
getSimilarity(Object, Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getSimilarity(Collection<PharmacophoreNode>, Collection<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getSimilarity(Collection<Integer>, Collection<Integer>, List<PharmacophoreNode>, List<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getSimilarity(T, T) - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
 
getSimilarityAngleCosine(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getSimilarityBytewiseOverlap(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getSimilarityExtraCarbonConsideration(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityHardMatchAverage(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityHardMatchMultiplicative(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityHardMatchOptimistic(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityList(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityMappingNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getSimilarityNodes(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getSimilarityNodes(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
getSimilaritySimple(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
getSimilarityTanimoto(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getSimilarityTanimoto(long[], long[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
 
getSimilarityTanimoto(long[], long[], int, int) - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getSimilarityThreshold() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
getSimilars(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
 
getSimpleAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getSingularValues() - Method in class com.actelion.research.calc.SingularValueDecomposition
Return the one-dimensional array of singular values
getSite(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSiteIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSize() - Method in class com.actelion.research.chem.conf.Conformer
 
getSize() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getSize() - Method in class com.actelion.research.chem.prediction.IncrementTable
 
getSize() - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
 
getSize() - Method in class com.actelion.research.chem.RingCollection
 
getSize() - Method in class com.actelion.research.chem.shredder.Fragment
 
getSize() - Method in class com.actelion.research.chem.SortedStringList
 
getSize() - Method in class com.actelion.research.chem.TextDrawingObject
 
getSize() - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
getSize() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
getSize() - Method in class com.actelion.research.util.ErrorHashMap
 
getSize() - Method in class com.actelion.research.util.IntQueue
 
getSize1() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
getSize2() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
getSizeAfterLastBitSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
getSizeAfterLastBitSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
getSizeArrayLIV() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
getSizeArrayLIV() - Static method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
 
getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
getSizeForBits(int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getSizeHeap() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getSizes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
getSkinnable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
getSlope() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getSlope() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getSlopeFragments() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getSlopeR2() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
getSmallerSideAtomCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getSmallerSideAtomLists() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getSmiles() - Method in class com.actelion.research.chem.IsomericSmilesCreator
 
getSmiles() - Method in class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
 
getSmiles() - Method in class com.actelion.research.share.gui.editor.Model
 
getSmoothing() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
getSolution() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
getSorted() - Method in class com.actelion.research.calc.Matrix
Sorts the row of the matrix according the compareTo(...) function in DoubleVec
getSorted(int) - Method in class com.actelion.research.util.UniqueList
 
getSortedIndex(T) - Method in class com.actelion.research.util.UniqueList
 
getSortedListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
 
getSortedStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
 
getSource() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSpecialFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
 
getSpecialFieldIndex(String) - Method in class com.actelion.research.chem.io.DWARFileParser
 
getSpecialFieldMap() - Method in class com.actelion.research.chem.io.DWARFileParser
Returns a columnName->SpecialField map of all non-alphanumerical columns.
getSpline() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
getSplit() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSplittedOverlappingText(List<String>, int, int) - Static method in class com.actelion.research.util.StringFunctions
Generates a list with overlap
getSprsde() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSQRT() - Method in class com.actelion.research.calc.Matrix
 
getSSBond() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getStandardDeviation() - Method in class com.actelion.research.calc.Matrix
 
getStandardDeviation(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getStandardDeviationCols() - Method in class com.actelion.research.calc.Matrix
 
getStandardized() - Method in class com.actelion.research.calc.Matrix
Get the standard scores, also known as z-scores.
getStandardized(String, String, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
Under normal circumstances, one should never need to standardize a molecule from an idcode, because molecules should be standardized before generating the canonical encoding.
getState() - Method in class com.actelion.research.chem.docking.LigandPose
 
getState() - Method in interface com.actelion.research.chem.optimization.Evaluable
 
getState() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
getState() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
 
getState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
getState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
getState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
getStbnType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
getStdDev(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
 
getStdDevFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
getStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Checks whether at least one of the connected bonds is a stereo bond.
getStereoCenterCount() - Method in class com.actelion.research.chem.PropertyCalculator
 
getStereoCenterCount() - Method in class com.actelion.research.chem.StereoMolecule
 
getStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
getStrain(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
 
getString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
getString() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getString(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
getString(String, String, String) - Static method in class com.actelion.research.util.StringFunctions
 
getString(String, String, String, int) - Static method in class com.actelion.research.util.StringFunctions
 
getStringAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
 
getStringAt(int) - Method in class com.actelion.research.chem.SortedStringList
 
getStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
 
getStringFromRegEx(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
getStringTypeAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
 
getStringWidth(String) - Method in class com.actelion.research.chem.AbstractDepictor
 
getStringWidth(String) - Method in class com.actelion.research.chem.Depictor
 
getStringWidth(String) - Method in class com.actelion.research.chem.Depictor2D
 
getStringWidth(String) - Method in class com.actelion.research.chem.SVGDepictor
 
getStringWidth(String) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
getStroke() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getStructure() - Method in class com.actelion.research.gui.JDrawDialog
 
getStructureCenter(Molecule3D, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getStructureCenter(Molecule3D, int, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
The Structure Center Atom is defined as the atom with the biggest no of rotatables bonds and the closest to the center
getStructureCoordinates3DColumnName() - Method in class com.actelion.research.chem.io.DWARFileParser
 
getStructureCount() - Method in class com.actelion.research.chem.StructureSearchSpecification
Returns the search type as integer including mode flags.
getStructureInfo() - Method in class com.actelion.research.chem.StructureTransferData
 
getStructures() - Method in class com.actelion.research.gui.JEditableChemistryView
If chemistryType is
getStyle() - Method in class com.actelion.research.chem.TextDrawingObject
 
getStyleSheet() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
Overriden to return our own slimmed down style sheet.
getSubFragment(MolDistHist, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
getSubFragment(MolDistHistViz, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
getSubFragmentCheckedRange(MolDistHist, int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
getSubFragments(MolDistHistViz, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
Inevitable pharmacophore points are considered (01.11.2012)
getSubMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
 
getSubMatrix(List<Integer>) - Method in class com.actelion.research.calc.Matrix
 
getSubset(int) - Method in class com.actelion.research.chem.conf.ConformerSet
 
getSubstituent(int, int, boolean[], ExtendedMolecule, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
Determines all atoms of the substituent attached to coreAtom and starting with firstAtom.
getSubstituent(String) - Static method in class com.actelion.research.chem.NamedSubstituents
 
getSubstituentIDCode(String) - Static method in class com.actelion.research.chem.NamedSubstituents
 
getSubstituentSize(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
Counts the number of atoms of the substituent connected to coreAtom defined by firstAtom and not including the coreAtom.
getSubTreeSize(List<Integer>, int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
getSum() - Method in class com.actelion.research.calc.Matrix
 
getSumCol(int) - Method in class com.actelion.research.calc.Matrix
 
getSumCols() - Method in class com.actelion.research.calc.Matrix
 
getSumFragsUntilMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
getSumFromRange(double, double) - Method in class com.actelion.research.calc.histogram.Histogram
Parts of the range outside the bins are not considered.
getSumRow(int) - Method in class com.actelion.research.calc.Matrix
 
getSumRows() - Method in class com.actelion.research.calc.Matrix
 
getSumSquared() - Method in class com.actelion.research.calc.Matrix
 
getSumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
getSumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
getSumUpperTriangle() - Method in class com.actelion.research.calc.Matrix
Matrix has to be quadratic.
getSumY() - Method in class com.actelion.research.calc.histogram.Histogram
 
getSymbol() - Method in class com.actelion.research.chem.Element
 
getSymmetryRank(int) - Method in class com.actelion.research.chem.Canonizer
Returned symmetry rank before tie breaking.
getSymmetryRank(int) - Method in class com.actelion.research.chem.StereoMolecule
This returns atom symmetry numbers from within the molecule canonicalization procedure.
getSymmetryType(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
A fragment's symmetry type defines whether one part of a full 360 degree matches symmetrically another range.
getSynonymIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSynonyms(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getSystemProperty(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
Tries to look up the System property for the given key.
getTagDescriptorSimilarity(DescriptorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
getTagDescriptorSimilarity(ISimilarityCalculator<?>) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
Creates a header tag name from the descriptor short name.
getTagDescriptorSimilarity(SimilarityCalculatorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
getTagDescriptorSimilarity(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
getTanimotoDist(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
getTanimotoDist(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Calculates the Tanimoto coefficient
getTanimotoDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Calculates the Inverse Tanimoto coefficient
getTanimotoDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
 
getTanimotoDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Calculates the Inverse Tanimoto coefficient
getTanimotoDistanceDotProd(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
getTanimotoDistBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getTanimotoDistBitWise(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Calculates the Tanimoto coefficient
getTanimotoDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Calculates the Tanimoto coefficient
getTanimotoDistInv(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Byte wise inverse Tanimoto distance.
getTanimotoDistInv(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getTanimotoDistInvBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getTanimotoDistInvBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Calculates the Inverse Tanimoto coefficient
getTanimotoDistInvByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getTanimotoDistInvByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.calc.VectorSimilarity
 
getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
 
getTanimotoSimilarity(float[], float[]) - Static method in class com.actelion.research.calc.VectorSimilarity
 
getTanimotoSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
 
getTanimotoSimilarity(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Calculates the Tanimoto coefficient according broken link 22.01.2019 http://www.pnylab.com/pny/papers/nmet/nmet/
getTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns a hash code representing the generic tautomer of the structure or its largest fragment.
getTautomerCount() - Method in class com.actelion.research.chem.TautomerHelper
 
getTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
 
getText() - Method in class com.actelion.research.chem.TextDrawingObject
 
getText() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
 
getTextSize() - Method in class com.actelion.research.chem.AbstractDepictor
 
getTextSize() - Method in class com.actelion.research.chem.Depictor
 
getTextSize() - Method in class com.actelion.research.chem.Depictor2D
 
getTextSize() - Method in class com.actelion.research.chem.SVGDepictor
 
getTextSize() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
getThemeColor(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
 
getTHParity(int) - Method in class com.actelion.research.chem.Canonizer
Returns the absolute tetrahedral parity, which is based on priority ranks.
getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
 
getTitle() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
getTokenized(String, String) - Static method in class com.actelion.research.util.StringFunctions
Returns the tokenized and trimmed values.
getTokenizedBySeperatorRegex(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
getTokenizedQuoted(String) - Static method in class com.actelion.research.util.StringFunctions
Get a list from quoted and comma or otherwise separated phrases.
getToleratedVDWRadius(int) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
getTopologicalDistance(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getTopologicalDistanceMatrix(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
getTorsion(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getTorsionAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getTorsionBinCounts(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
Returns the full circle histogram of torsion angles.
getTorsionCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getTorsionDescriptor() - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds.
getTorsionDescriptor(Conformer) - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor.
getTorsionFrequencies() - Method in class com.actelion.research.chem.conf.TorsionPrediction
 
getTorsionFrequencies(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
Returns an array of frequencies in rounded percent.
getTorsionID(StereoMolecule, int, int[], TorsionDetail) - Static method in class com.actelion.research.chem.conf.TorsionDB
Determines uniquely an identifying name for the rotatable bond and its vicinity.
getTorsionIDs() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
getTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
getTorsionLikelyhood(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
 
getTorsionRanges() - Method in class com.actelion.research.chem.conf.TorsionPrediction
 
getTorsionRanges(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
Returns an array containing left and right limits of the torsion curves, of which the maxima are returned by getTorsions().
getTorsions() - Method in class com.actelion.research.chem.conf.TorsionPrediction
 
getTorsions(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
Returns an array of maxima of the smoothened torsion histogram as short values in the range: 0 <= v < 360.
getTorsionSetCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
getTorsionStrainClass(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
Checks, whether the torsion angle lies within statistical limits.
getTorus(int, int) - Method in class com.actelion.research.calc.Matrix
 
getTotalAtomOverlap(double[]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)
getTotalEnergy() - Method in interface com.actelion.research.chem.forcefield.ForceField
 
getTotalEnergy() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Gets the total energy of the molecule as the sum of the energy terms.
getTotalEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
 
getTotalEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Gets the total energy of the molecule as the sum of the energy terms.Requires the atomic positions to be in the correct order.
getTotalOccurences() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
getTotalPPOverlap(double[]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
 
getTotalSizeResults() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getTotalStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
getTrace() - Method in class com.actelion.research.calc.Matrix
Matrix trace.
getTransferable(Point) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
getTransferable(Point) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
getTransferData(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
 
getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
 
getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
 
getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
getTransferDataFlavors() - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
 
getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
 
getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
 
getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
getTransform() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
 
getTransform() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
getTransformation() - Method in class com.actelion.research.chem.AbstractDepictor
 
getTranspose() - Method in class com.actelion.research.calc.Matrix
 
getType() - Method in class com.actelion.research.gui.DrawAreaEvent
 
getType(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns the MMFF type of an atom in a molecule.
getType(Tables, MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
Returns the MMFF bond type of a bond on a molecule.
getType(Tables, MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
Returns the MMFF bond type of a bond on a molecule.
getType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
Gets the angle type of an angle bend.
getType(Tables, MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
Returns the torsion type of a torsion angle.
getTypeString() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
getTypeString() - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
getTypeString() - Method in class com.actelion.research.chem.TextDrawingObject
 
getTypeString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
getU() - Method in class com.actelion.research.calc.LUDecomposition
Return upper triangular factor
getU() - Method in class com.actelion.research.calc.SingularValueDecomposition
Return the left singular vectors
getUIScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
For Windows and Linux this method returns the user defined UI scaling factor.
getUnique() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getUnique(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getUnique(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getUniqueDateDir(File) - Static method in class com.actelion.research.util.IO
 
getUniqueDateDir(File, String) - Static method in class com.actelion.research.util.IO
 
getUniqueDateDir(String) - Static method in class com.actelion.research.util.IO
 
getUniqueDir(File, String) - Static method in class com.actelion.research.util.IO
 
getUniqueFileName(File) - Static method in class com.actelion.research.util.IO
 
getUniqueFileName(File, File) - Static method in class com.actelion.research.util.IO
 
getUniqueFileName(File, File, DecimalFormat) - Static method in class com.actelion.research.util.IO
If the file does not exists the input file is returned.
getUniqueFileName(String) - Static method in class com.actelion.research.util.IO
A number is added to the base name of the file
getUniqueFileName(String, String) - Static method in class com.actelion.research.util.IO
 
getUniqueFragments() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
getUniqueFragmentsEstimated() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
getUniqueUserDir() - Static method in class com.actelion.research.util.IO
 
getUpperTriangle() - Method in class com.actelion.research.calc.Matrix
For a quadratic matrix only.
getUserData() - Method in class com.actelion.research.chem.Molecule
 
getV() - Method in class com.actelion.research.calc.SingularValueDecomposition
Return the right singular vectors
getValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
getValidSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
getValignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
Gets the Valignment attribute of the VerticalFlowLayout object
getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
getValue() - Method in class com.actelion.research.util.Angle
 
getValueAt(int) - Method in interface com.actelion.research.calc.INumericalDataColumn
 
getValueAt(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
 
getValueAtAbsolutePosition(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
getValueCount() - Method in class com.actelion.research.calc.CorrelationCalculator
 
getValueCount() - Method in interface com.actelion.research.calc.INumericalDataColumn
 
getValueCount() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
getValueCountMatrix() - Method in class com.actelion.research.calc.CorrelationCalculator
 
getValues() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getValues() - Method in class com.actelion.research.util.hash.HashSetInt
Deep copy.
getValuesAsArray() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getValuesAsArrayX() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getValuesAsArrayY() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getVariance() - Method in class com.actelion.research.calc.Matrix
 
getVariance(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
getVarianceCentered() - Method in class com.actelion.research.calc.Matrix
 
getVarianceCol(int) - Method in class com.actelion.research.calc.Matrix
 
getVarianceCols() - Method in class com.actelion.research.calc.Matrix
 
getVDWRadius() - Method in class com.actelion.research.chem.Element
 
getVDWRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
 
getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getVectorSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
getVectorSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getVectorSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
getVersion() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
getVersion() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
 
getVersion() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
getVgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
Gets the Vgap attribute of the VerticalFlowLayout object
getViewFactory() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
Returns the ViewFactory that is used to make sure the Views don't load in the background.
getViolatedConditionsCount() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
getVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getVolumeGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
getVolumeOverlap(Gaussian3D) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getVolumeOverlap(Gaussian3D, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getVolumeOverlap(Gaussian3D, Coordinates, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getVolumes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getVolumes() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
 
getWeight() - Method in class com.actelion.research.chem.Element
 
getWeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getWeight(int) - Static method in class com.actelion.research.chem.PeriodicTable
 
getWeights() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
getWidth() - Method in class com.actelion.research.chem.coords.InventorFragment
 
getWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
getWidth() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
getWithCopy(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
 
getWithCopy(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
getWithCopy(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
getWithCopy(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
 
getWordsFormatted(String) - Static method in class com.actelion.research.util.StringFunctions
Removes all non characters and digits.
getWordsFormattedUniqueLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
getX() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getX() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getX() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
 
getX(int) - Method in class com.actelion.research.chem.conf.Conformer
 
getXMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
getY() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getY() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getY() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
 
getY(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getY(int) - Method in class com.actelion.research.chem.conf.Conformer
 
getYMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
getZ() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
getZ() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
getZ(int) - Method in class com.actelion.research.chem.conf.Conformer
 
getZNeighbour(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
Provided that the bond parity of a double bond is available, this method determines, whether connAtom has a counterpart with Z- (cis) configuration at the other end of the double bond.
gfxConfig - Variable in class com.actelion.research.share.gui.Arrow
 
Graph - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
Graph(Map<Integer, List<Integer>>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
 
Graph.Edge - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
GraphicsContextImpl - Class in com.actelion.research.jfx.gui
Project: User: rufenec Date: 11/24/2014 Time: 6:24 PM
GraphicsContextImpl(GraphicsContext) - Constructor for class com.actelion.research.jfx.gui.GraphicsContextImpl
 
GRAY - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
GREEN - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
grid - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
grid - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
GRID_DIMENSION - Static variable in class com.actelion.research.chem.docking.DockingEngine
 
GRID_RESOLUTION - Static variable in class com.actelion.research.chem.docking.DockingEngine
 
gridSize - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
gridWidth - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
GUANIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 

H

HARD_MATCH_OPTIMISTIC_PERCENTILE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
hasCIPParityDistinctionProblem() - Method in class com.actelion.research.chem.Canonizer
 
hascode() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
 
hasErrors() - Method in class com.actelion.research.util.ErrorHashMap
 
hash - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
hash - Variable in class com.actelion.research.chem.properties.complexity.IndexHash
 
hash(String) - Static method in class com.actelion.research.chem.CanonizerUtil.StrongHasher
 
hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
hashCode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
 
hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
Returns the hash code of this sorted pair object.
hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns the hashcode of this vector.
hashCode() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
hashCode() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
hashCode() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
 
hashCode() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
hashCode() - Method in class com.actelion.research.util.datamodel.ByteVec
The hash code has to be calculated before.
hashCode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
Taken from idcode.
hashCode() - Method in class com.actelion.research.util.datamodel.IntArray
 
hashCode() - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
hashCode() - Method in class com.actelion.research.util.datamodel.IntVec
 
hashCode() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
hasHeteroAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
hashlittle(byte[], long) - Static method in class com.actelion.research.util.BurtleHasher
 
hashlittle(byte[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
 
hashlittle(int[], long) - Static method in class com.actelion.research.util.BurtleHasher
MvK 10.02.2010
hashlittle(int[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
 
hashlittle(String, long) - Static method in class com.actelion.research.util.BurtleHasher
 
hashmask(int) - Static method in class com.actelion.research.util.BurtleHasher
 
HashSetInt - Class in com.actelion.research.util.hash
HashSetInt
HashSetInt() - Constructor for class com.actelion.research.util.hash.HashSetInt
 
HashSetInt(int) - Constructor for class com.actelion.research.util.hash.HashSetInt
 
HashSetInt(int[]) - Constructor for class com.actelion.research.util.hash.HashSetInt
 
HashSetInt(List<Integer>) - Constructor for class com.actelion.research.util.hash.HashSetInt
 
hashsize(long) - Static method in class com.actelion.research.util.BurtleHasher
 
hashword(String, long) - Static method in class com.actelion.research.util.BurtleHasher
 
hasMoreLines() - Method in class com.actelion.research.io.StringReadChannel
 
hasNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
hasNext() - Method in class com.actelion.research.chem.io.RDFileParser
 
hasOnlyFinite() - Method in class com.actelion.research.calc.Matrix
 
hasSamePosition(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
hasStructureCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
 
hasStructureCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
 
hasStructureCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
 
hasStructures() - Method in class com.actelion.research.chem.io.DWARFileParser
If you don't read any records after calling this method, don't forget to call close() to close the underlying file.
hasUnbalancedAtomCharge(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
hblaurie - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
HBOND_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
HBTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
 
help() - Method in class com.actelion.research.util.CommandLineParser
 
HELP - Static variable in class com.actelion.research.util.CommandLineParser
 
HerschbachLaurie - Class in com.actelion.research.chem.forcefield.mmff.table
Table for Herschbach-Laurie version of Badger's rule.
HerschbachLaurie(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
 
HetNameParser - Class in com.actelion.research.chem.io.pdb.parser
HetNameParser
HetNameParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetNameParser
 
HetSynonymParser - Class in com.actelion.research.chem.io.pdb.parser
HetSynonymParser
HetSynonymParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
 
hex2String(String) - Static method in class com.actelion.research.util.StringFunctions
 
hg_step1(int, double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hg_step2(int, double[][], int[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hg_step3(int, int[][], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hg_step4(int, double[][], int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hg_step5(int, int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hg_step6(int, double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
hgAlgorithm(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
HiDPIHelper - Class in com.actelion.research.gui.hidpi
 
HiDPIHelper() - Constructor for class com.actelion.research.gui.hidpi.HiDPIHelper
 
HiDPIIcon - Class in com.actelion.research.gui.hidpi
Created by thomas on 07/12/15.
HiDPIIcon(Image, boolean) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIcon
 
HiDPIIconButton - Class in com.actelion.research.gui.hidpi
Created by sandert on 04/12/15.
HiDPIIconButton(String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
HiDPIIconButton(String, String, String, int, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
HiDPIToggleButton - Class in com.actelion.research.gui.hidpi
Created by thomas on 07/12/15.
HiDPIToggleButton(String, String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIToggleButton
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
HiDPIUtil - Class in com.actelion.research.gui.hidpi
 
HiDPIUtil() - Constructor for class com.actelion.research.gui.hidpi.HiDPIUtil
 
HIGHLIGHT_ATOM_RADIUS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
 
highlightAtom(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
hilite(Graphics) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
hilite(Graphics) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
hilite(Graphics) - Method in class com.actelion.research.chem.TextDrawingObject
 
Histogram - Class in com.actelion.research.calc.histogram
Histogram
Histogram(double[], double, double, int) - Constructor for class com.actelion.research.calc.histogram.Histogram
 
Histogram(double[], int) - Constructor for class com.actelion.research.calc.histogram.Histogram
 
histogram2String(Matrix, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
HistogramMatchCalculator - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
HistogramMatchCalculator
HistogramMatchCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
 
hit(Rectangle, Shape, boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
HOSE_CODE_CUT_C_SP3_SP3 - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
 
HoseCodeCreator - Class in com.actelion.research.chem.contrib
 
HoseCodeCreator() - Constructor for class com.actelion.research.chem.contrib.HoseCodeCreator
 
HS_BDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HS_CROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HS_DIAGCROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HS_FDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HS_HORIZONTAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HS_VERTICAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
HungarianAlgorithm - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
HungarianAlgorithm() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
HYBRID - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
HYBRID_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
 
Hydrogen - Static variable in class com.actelion.research.chem.PeriodicTable
 
HydrogenHandler - Class in com.actelion.research.chem.contrib
 
HydrogenHandler() - Constructor for class com.actelion.research.chem.contrib.HydrogenHandler
 
hypot(double, double) - Static method in class com.actelion.research.calc.SingularValueDecomposition
 

I

iAMPAC_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IArrow - Interface in com.actelion.research.share.gui.editor.chem
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
IAtomPropertiesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
Project: User: rufenec Date: 11/24/2014 Time: 5:03 PM
IAtomQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
Project: User: rufenec Date: 11/24/2014 Time: 4:53 PM
IBitArray - Interface in com.actelion.research.chem.properties.complexity
 
IBitArrayFactory<T extends IBitArray> - Interface in com.actelion.research.chem.properties.complexity
 
IBondQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
Project: User: rufenec Date: 11/24/2014 Time: 4:57 PM
IChangeListener - Interface in com.actelion.research.share.gui.editor.listeners
Project: User: rufenec Date: 11/24/2014 Time: 3:25 PM
IClipboardHandler - Interface in com.actelion.research.gui.clipboard
 
IColor - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
ICompleteGraph - Interface in com.actelion.research.util.graph.complete
ICompleteGraph
ICursor - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
id - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
ID_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
 
IDABORT - com.actelion.research.share.gui.DialogResult
 
IDCANCEL - com.actelion.research.share.gui.DialogResult
 
idcode - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
 
IDCode() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
 
IDCodeCoord - Class in com.actelion.research.util.datamodel
IDCodeCoord Apr 12, 2012 MvK: Start implementation
IDCodeCoord(int, String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
 
IDCodeCoord(String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
 
IDCodeCoord(String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
 
IDCodeParser - Class in com.actelion.research.chem
 
IDCodeParser() - Constructor for class com.actelion.research.chem.IDCodeParser
This default constructor creates molecules guaranteed to have 2D-atom-coordinates.
IDCodeParser(boolean) - Constructor for class com.actelion.research.chem.IDCodeParser
 
IDCodeParserWithoutCoordinateInvention - Class in com.actelion.research.chem
Typically you should use IDCodeParser instead of this class.
IDCodeParserWithoutCoordinateInvention() - Constructor for class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
IDCodeWithName() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
 
idColumn - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
iDEL_RE - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IdentifiedObject<T> - Class in com.actelion.research.util.datamodel
IdentifiedObject Nov 2, 2011 MvK: Start implementation
IdentifiedObject() - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
 
IdentifiedObject(T, long) - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
 
IDepictor<T> - Interface in com.actelion.research.share.gui.editor.chem
Project: User: rufenec Date: 11/24/2014 Time: 3:26 PM
IDialog - Interface in com.actelion.research.share.gui.editor.dialogs
 
iDICT_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IDNO - com.actelion.research.share.gui.DialogResult
 
IDOK - com.actelion.research.share.gui.DialogResult
 
IdoScore - Class in com.actelion.research.chem.docking.scoring
 
IdoScore(StereoMolecule, Set<Integer>, int[], MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.IdoScore
 
IDOSCORE - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
 
IDrawContext<T> - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 3:22 PM
IDrawingObject - Interface in com.actelion.research.share.gui.editor.chem
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
IDRETRY - com.actelion.research.share.gui.DialogResult
 
IDYES - com.actelion.research.share.gui.DialogResult
 
IFactory<S extends AMemorizedObject> - Interface in com.actelion.research.util.graph.complete
IFactory
iGAST_HUCK - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
iGASTEIGER - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
iGAUSS80_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
iHUCKEL - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IIdentifiedObject<T> - Interface in com.actelion.research.util.datamodel
IIdentifiedObject Nov 4, 2011 MvK: Start implementation
IKeyCode - Interface in com.actelion.research.share.gui.editor.io
Project: User: rufenec Date: 11/24/2014 Time: 4:17 PM
IKeyEvent - Interface in com.actelion.research.share.gui.editor.io
Project: User: rufenec Date: 11/24/2014 Time: 3:20 PM
ImageClipboardHandler - Class in com.actelion.research.gui.clipboard
 
ImageClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler
 
ImageClipboardHandler.ImageSelection - Class in com.actelion.research.gui.clipboard
 
ImageProvider<T> - Class in com.actelion.research.share.gui.editor
Created by rufenec on 08/05/15.
ImageProvider() - Constructor for class com.actelion.research.share.gui.editor.ImageProvider
 
ImageSelection(Image) - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
 
iMMFF94_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IMolDistHist - Interface in com.actelion.research.chem.descriptor.flexophore
 
IMoleculeView - Interface in com.actelion.research.jfx.gui.chem
 
IMouseEvent - Interface in com.actelion.research.share.gui.editor.io
Project: User: rufenec Date: 11/24/2014 Time: 3:19 PM
IMPORTANT - Static variable in class com.actelion.research.chem.Molecule3D
 
iMULLIKEN_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
in - Variable in class com.actelion.research.util.LittleEndianDataInputStream
 
INCLUDE_ALL - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_CATALYSTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_COORDS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_DEFAULT - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_DRAWING_OBJECTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_MAPPING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUDE_RXN_CODE_ONLY - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
INCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
 
increase(int, int, double) - Method in class com.actelion.research.calc.Matrix
 
increaseNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
INCREMENT - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
 
incrementByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
incrementFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
 
incrementFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
 
incrementHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
 
IncrementTable - Class in com.actelion.research.chem.prediction
 
IncrementTable() - Constructor for class com.actelion.research.chem.prediction.IncrementTable
 
IncrementTable(String) - Constructor for class com.actelion.research.chem.prediction.IncrementTable
 
index - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
 
index(int, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
Returns the index of a row for a given molecule and four connected atoms which form a torsion angle.
index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
Returns the index of a row for a given molecule and three connected atoms which form an angle.
index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
Returns the index that a given set of three atoms have in the Dfsb table.
index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
Returns the index of a row for a given molecule and three connected atoms which form an angle.
IndexCoordinates - Class in com.actelion.research.chem.descriptor.flexophore
 
IndexCoordinates() - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
IndexCoordinates(int, int, Coordinates) - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
IndexHash - Class in com.actelion.research.chem.properties.complexity
 
IndexHash() - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
 
IndexHash(int) - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
 
indexOf(byte[], byte) - Static method in class com.actelion.research.util.ArrayUtils
 
indexOf(byte[], byte, int) - Static method in class com.actelion.research.util.ArrayUtils
 
indexOf(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
indexOf(int) - Method in class com.actelion.research.util.IntQueue
 
indexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
indexOf(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
 
indexOf(int[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
 
indexOf(Object[], Object) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
indexOf(Object[], Object) - Static method in class com.actelion.research.util.ArrayUtils
 
INFO - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
INFO_AMINO - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_ATOMNAME - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_ATOMSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_BFACTOR - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_CHAINID - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_DEFAULT - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
INFO_DESCRIPTION - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_INTERACTION_ATOM_TYPE - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_PPP - Static variable in class com.actelion.research.chem.Molecule3D
 
INFO_RESSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
 
informListeners() - Method in class com.actelion.research.gui.JChemistryView
 
init() - Method in class com.actelion.research.chem.AbstractDepictor
 
init() - Method in class com.actelion.research.chem.Depictor
 
init() - Method in class com.actelion.research.chem.Depictor2D
 
init() - Method in class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
 
init() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
init() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
init(int) - Method in class com.actelion.research.chem.CanonizerBaseValue
 
init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
 
init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
 
init(StereoMolecule) - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
 
initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
INITIAL_SPLITS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
initialCut(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
a cut divides a edge into a target node and a source node: an edge is defined as a tuple of two nodes (a,b), a left cut results in node a being the source node and b being the target node: a-->--b a right cut results in the right node being the source node: a--<--b returns int array with source node as 0th element and target node as 1st element
initialize() - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
initialize(double[], double, double, int) - Method in class com.actelion.research.calc.histogram.Histogram
 
initialize(int) - Static method in class com.actelion.research.chem.conf.TorsionDB
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
initialize(int) - Method in class com.actelion.research.util.BinaryDecoder
 
initialize(int, int) - Static method in class com.actelion.research.chem.conf.TorsionDB
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
initialize(StereoMolecule, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
Don't call this method directly.
initialize(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
initializeConformers(long, int) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
Needs to be called, before getting individual conformers of the same molecule by getNextConformer().
initializeConformers(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
initializeConformers(StereoMolecule, int, int, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
initializeExistingSet(int) - Method in class com.actelion.research.chem.DiversitySelector
 
initialTransform(int) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
.
initRND(byte, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
 
initRND(byte, byte, int, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
initRND(double[][]) - Method in class com.actelion.research.util.DoubleVec
The array contains the maximum and the minimum values for the initialisation of each field in the double vector.
initRND(double, double) - Method in class com.actelion.research.util.DoubleVec
 
injectNewSeed() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
iNO_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
InputObjectFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
InputObjectFracDimCalc
InputObjectFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
 
InputObjectFracDimCalc(StereoMolecule, long, String) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
 
inRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns true if the atom is in any ring of a given size.
inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
Checks if an angle is in a ring of given size.
inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
Checks and returns the minimum ring size that a torsion is contained in.
inRings(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns the number of rings that an atom is a member of in a molecule.
inSameRing(MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns true if two atoms are in the same ring of a given size.
insertLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
insideBounds(Coordinates[]) - Method in class com.actelion.research.chem.Coordinates
 
INSTANCE - com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
 
instantiate(String) - Static method in class com.actelion.research.chem.AbstractDrawingObject
 
IntArray - Class in com.actelion.research.util.datamodel
 
IntArray() - Constructor for class com.actelion.research.util.datamodel.IntArray
 
IntArray(int) - Constructor for class com.actelion.research.util.datamodel.IntArray
 
IntArray(int[]) - Constructor for class com.actelion.research.util.datamodel.IntArray
Shallow constructor.
IntArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.IntArray
Deep constructor.
IntArrayComparator - Class in com.actelion.research.util
 
IntArrayComparator() - Constructor for class com.actelion.research.util.IntArrayComparator
 
intArrayToByteArray(int[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
IntegerDouble - Class in com.actelion.research.util.datamodel
IntegerDouble Oct 24, 2011 MvK: Start implementation
IntegerDouble() - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
 
IntegerDouble(int, double) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
 
IntegerDouble(IntegerDouble) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
 
INTERACTION_TYPE_NONE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
InteractionAtomTypeCalculator - Class in com.actelion.research.chem.interactionstatistics
 
InteractionAtomTypeCalculator() - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
InteractionAtomTypeCalculator.AtomFlagCount - Enum in com.actelion.research.chem.interactionstatistics
 
InteractionAtomTypeCalculator.AtomPropertyMask - Enum in com.actelion.research.chem.interactionstatistics
 
InteractionAtomTypeCalculator.AtomPropertyShift - Enum in com.actelion.research.chem.interactionstatistics
 
InteractionAtomTypeCalculator.FunctionalGroup - Enum in com.actelion.research.chem.interactionstatistics
 
InteractionDescriptor(SplineFunction) - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
InteractionDistanceStatistics - Class in com.actelion.research.chem.interactionstatistics
 
InteractionSimilarityTable - Class in com.actelion.research.chem.interactionstatistics
distance gives the distance of the point of highest potential.
InteractionSimilarityTable.InteractionDescriptor - Class in com.actelion.research.chem.interactionstatistics
 
InteractionTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
ProteinLigandTerm is used to represent the energy between 2 atoms.
InteractionTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
 
InteractionTypeMap(double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
 
intermediateColor(Color, Color, float) - Static method in class com.actelion.research.util.ColorHelper
Creates an intermediate color between color c1 and color c2 in the RGB color space.
interpolate(double[], double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
interrupt() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
interrupt() - Method in interface com.actelion.research.chem.forcefield.ForceField
 
intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
intersects(IRectangle2D) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
 
IntQueue - Class in com.actelion.research.chem.descriptor.flexophore.calculator
Implementation for a FIFO of int.
IntQueue - Class in com.actelion.research.util
Implementation for a FIFO of int.
IntQueue() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
Creeates a new Queue with an initial size of 100
IntQueue() - Constructor for class com.actelion.research.util.IntQueue
Creeates a new Queue with an initial size of 100
IntQueue(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
IntQueue(int) - Constructor for class com.actelion.research.util.IntQueue
 
intToByteArray(int) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
 
intValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
IntVec - Class in com.actelion.research.util.datamodel
 
IntVec() - Constructor for class com.actelion.research.util.datamodel.IntVec
 
IntVec(boolean[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
Puts an boolean array into an int array.
IntVec(int) - Constructor for class com.actelion.research.util.datamodel.IntVec
Don't forget to calculate the hash code after setting the bits!
IntVec(int[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
Deep copy, hash code is calculated.
IntVec(int[], boolean) - Constructor for class com.actelion.research.util.datamodel.IntVec
If true each int contains only a 0 or a 1.
IntVec(IntVec) - Constructor for class com.actelion.research.util.datamodel.IntVec
Deep copy, hash code is calculated.
IntVec(List<Integer>) - Constructor for class com.actelion.research.util.datamodel.IntVec
 
INumericalDataColumn - Interface in com.actelion.research.calc
 
invalidateCoordinates() - Method in class com.actelion.research.chem.Canonizer
 
invalidateHelperArrays(int) - Method in class com.actelion.research.chem.Molecule
Clears helperBits from mValidHelperArrays.
invalidateStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
invent(StereoMolecule) - Method in class com.actelion.research.chem.coords.CoordinateInventor
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
invent(StereoMolecule, long[]) - Method in class com.actelion.research.chem.coords.CoordinateInventor
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParser
 
inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
InventorAngle - Class in com.actelion.research.chem.coords
Created by thomas on 9/23/16.
InventorAngle(double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
 
InventorAngle(double, double, double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
 
InventorChain - Class in com.actelion.research.chem.coords
Created by thomas on 9/23/16.
InventorChain(int) - Constructor for class com.actelion.research.chem.coords.InventorChain
 
InventorCharge - Class in com.actelion.research.chem.coords
Created by thomas on 9/28/16.
InventorCharge(InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.InventorCharge
 
InventorDefaultTemplateList - Class in com.actelion.research.chem.coords
 
InventorDefaultTemplateList() - Constructor for class com.actelion.research.chem.coords.InventorDefaultTemplateList
 
InventorFragment - Class in com.actelion.research.chem.coords
 
InventorFragment(InventorFragment, int) - Constructor for class com.actelion.research.chem.coords.InventorFragment
 
InventorFragment(StereoMolecule, int, int) - Constructor for class com.actelion.research.chem.coords.InventorFragment
 
InventorTemplate - Class in com.actelion.research.chem.coords
 
InventorTemplate(StereoMolecule, long[]) - Constructor for class com.actelion.research.chem.coords.InventorTemplate
 
IO - Class in com.actelion.research.util
IO 2003 MvK: Start implementation
IO() - Constructor for class com.actelion.research.util.IO
 
IObjectiveCompleteGraph<T extends ICompleteGraph> - Interface in com.actelion.research.util.graph.complete
IObjectiveCompleteGraph
Iodine - Static variable in class com.actelion.research.chem.PeriodicTable
 
IonizableGroupDetector - Class in com.actelion.research.chem.phesa.pharmacophore
 
IonizableGroupDetector(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
 
IonizableGroupDetector2D - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
IonizableGroupDetector2D(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
 
IPharmacophorePoint - Interface in com.actelion.research.chem.phesa.pharmacophore
 
IPharmacophorePoint.Functionality - Enum in com.actelion.research.chem.phesa.pharmacophore
 
IPipeline<T> - Interface in com.actelion.research.util
IPipeline Interface to connect several Runable in a pipeline Mar 27, 2012 MvK: Start implementation Oct 9 2012 MvK: wereAllDataFetched() added.
IPolygon - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 4:45 PM
IPPNodeSimilarity - Interface in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
IPPNodeSimilarity
iPULLMAN - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IReactionArrow - Interface in com.actelion.research.share.gui.editor.chem
Project: User: rufenec Date: 11/24/2014 Time: 5:49 PM
IReactionMapper - Interface in com.actelion.research.chem.reaction
 
IRectangle2D - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 3:17 PM
IS_JAVA_10 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
IS_JAVA_11 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
IS_JAVA_8 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
IS_JAVA_8_OR_OLDER - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
IS_JAVA_9 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
IS_VENDOR_APPLE - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
 
is3D() - Method in class com.actelion.research.chem.Molecule
 
is3D(Molecule3D) - Static method in class com.actelion.research.chem.io.AbstractParser
 
is64BitJRE() - Static method in class com.actelion.research.util.Platform
 
isAcceptable(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
isAcceptor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isAcceptor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
isAcidicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isAcidicOxygenAtPhosphoricAcid(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isActive() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
isActive() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
isAlcoholicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isAliphatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isAliphaticAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isAlkaline(int) - Static method in class com.actelion.research.chem.PeriodicTable
 
isAlkylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isAllDataIn() - Method in interface com.actelion.research.util.IPipeline
 
isAllDataIn() - Method in class com.actelion.research.util.Pipeline
 
isAllLetter(String) - Static method in class com.actelion.research.util.StringFunctions
 
isAllLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
isAllUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
isAllylicAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
 
isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
 
isAmide(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isAmideTypeBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Evaluates, whether bond is an amide bond, thio-amide, or amidine bond.
isAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isAnimating() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
 
isAqua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
 
isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
isAromatic(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
isAromatic(int) - Method in class com.actelion.research.chem.RingCollection
Return whether the ring is considered aromatic.
isAromaticAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isAromaticBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isArylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isAtomColorSupported() - Method in class com.actelion.research.gui.JDrawArea
 
isAtomColorSupported() - Method in class com.actelion.research.share.gui.editor.Model
 
isAtomConfigurationUnknown(int) - Method in class com.actelion.research.chem.Molecule
 
isAtomFlag(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
isAtomicNoElectronegative(int) - Static method in class com.actelion.research.chem.Molecule
 
isAtomicNoElectropositive(int) - Static method in class com.actelion.research.chem.Molecule
 
isAtomMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
Checks whether this atom was marked to be deleted and not deleted yet.
isAtomMember(int, int) - Method in class com.actelion.research.chem.RingCollection
 
isAtomParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
Pseudo paries are parities that indicate a relative configuration.
isAtomStereoCenter(int) - Method in class com.actelion.research.chem.Molecule
Atoms with pseudo parities are not considered stereo centers.
isAutoMappedAtom(int) - Method in class com.actelion.research.chem.Molecule
 
isBackboneSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
A backbone search is a hash code comparison from encoding stereo and unsaturation depleted structures.
isBasicNitrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Checks whether bond is an axial chirality bond of the BINAP type.
isBinary - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
isBinaryFingerprint(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
isBitSet(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
isBitSet(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
isBitSet(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
isBitSet(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
isBitSet(int[], int) - Static method in class com.actelion.research.util.BitUtils
 
isBitSet(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
isBitSet(int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
isBondBackgroundHilited(int) - Method in class com.actelion.research.chem.Molecule
Used for depiction only.
isBondBridge(int) - Method in class com.actelion.research.chem.Molecule
 
isBondForegroundHilited(int) - Method in class com.actelion.research.chem.Molecule
Used for depiction only.
isBondMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
Checks whether this bond was marked to be deleted and not deleted yet.
isBondMember(int, int) - Method in class com.actelion.research.chem.RingCollection
 
isBondParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
 
isBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
isCancelled() - Method in class com.actelion.research.gui.JDrawDialog
 
isCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
If true not all index combinations were generated.
isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
If true not all index combinations where generated.
isCapitalizedWord(String) - Static method in class com.actelion.research.util.StringFunctions
 
isCarbonConnected2Hetero(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isCarbonExclusiveNode() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
isCarbonInteraction(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
isCarbonOnlyConnected2Hetero(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isCarbonTwoValencesMinimum(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isCarboxyC(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isCentralAlleneAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isChalcogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isChargeNeg(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isChargePos(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isCluster() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
 
isCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
isCommand() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
isCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
isConclusive() - Method in class com.actelion.research.util.DateAnalysis
Call this only once after calling analyse() once or multiple times.
isConnected2Hetero(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCS
 
isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCSFast
 
isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCS
 
isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCSFast
 
isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
 
isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
 
isCovered(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
Checks whether mask and data as elimination rule are covered by this rule.
isCyanoN(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isDarkLookAndFeel() - Static method in class com.actelion.research.gui.LookAndFeelHelper
 
isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
 
isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
 
isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
 
isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
isDeletable() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
isDelocalized(int) - Method in class com.actelion.research.chem.RingCollection
Return whether the ring is considered delocalized, which are 6-membered aromatic rings with no preference concerning where the double bonds are located.
isDelocalizedBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
A bond is considered delocalized, if it has different bond orders in different, but energetically equivalent mesomeric structures.
isDescriptorShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
isDonor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isDonor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
isDonor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isDonorHeavyAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
isDonorHydrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
 
isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
isEarthAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isEditable() - Method in class com.actelion.research.gui.JChemistryView
 
isEditable() - Method in class com.actelion.research.gui.JStructureView
 
isEditable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
isElectronegative(int) - Method in class com.actelion.research.chem.Molecule
 
isElectropositive(int) - Method in class com.actelion.research.chem.Molecule
 
isELUSIVE() - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
isEmpty() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
 
isEmpty() - Method in class com.actelion.research.chem.reaction.Reaction
 
isEmpty() - Method in class com.actelion.research.util.IntQueue
 
isEmpty() - Method in class com.actelion.research.util.Pipeline
 
isEmptyString(String) - Static method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
 
isEnabled() - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
isEnd() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
isEndOfRunReached() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
 
isEtherOxygenAtAromatic(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isExactSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
isExactSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
isExtensionListInDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFinalized() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
isFixedDistance() - Method in class org.openmolecules.chem.conf.so.DistanceRule
 
isFlatNitrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Checks whether this nitrogen atom is flat, because it has a double bond, is member of an aromatic ring or is part of amide, an enamine or in resonance with an aromatic ring.
isFlexible() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
isFragment() - Method in class com.actelion.research.chem.ExtendedDepictor
 
isFragment() - Method in class com.actelion.research.chem.Molecule
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
isFragment() - Method in class com.actelion.research.chem.reaction.Reaction
The naming of this method is in analogy to the corresponding method of the Molecule class.
isFragment() - Method in class com.actelion.research.share.gui.editor.Model
 
isFragmentIndexInMoleculeIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
Fastest check, whether the molecule contains the fragment.
isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
isFragmentInMolecule(int) - Method in class com.actelion.research.chem.SSSearcher
Fastest check, whether the molecule contains the fragment.
isFragmentInMoleculeWithoutIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
isGDIFontDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
isGDIPenDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
isGDIPenWidthDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
isGraphSimilarity - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
isGreaterThan(Angle) - Method in class com.actelion.research.util.Angle
Determines whether this angle is on the greater value side of angle a, i.e.
isHalogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isHetero(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
ISimilarityCalculator<T> - Interface in com.actelion.research.chem.descriptor
 
ISimilarityHandlerFactory - Interface in com.actelion.research.chem.descriptor
 
isInAromaticRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Returns true if the atom is in an aromatic ring of given size.
isInevitablePharmacophorePoint(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
 
isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isInMesoFragment(int) - Method in class com.actelion.research.chem.CanonizerMesoHelper
 
isInverted(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
 
isIsolatedCarbon(StereoMolecule, int, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isLargestFragmentOnly() - Method in class com.actelion.research.chem.StructureSearchSpecification
This setting is relevant for all search types except the substructure search.
isLayouted() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
isLinear - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
isLinkNode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
isLinux() - Static method in class com.actelion.research.util.Platform
 
isMacintosh() - Static method in class com.actelion.research.util.Platform
 
isMarked() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
isMarked(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isMarkedAtom(int) - Method in class com.actelion.research.chem.Molecule
Atom marking may be used for any external purpose
isMaxCapacityMatchListContainerReached() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
The sub structure search algortihm stops if the maximum capacity of the match list container is reached.
isMember(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
isMemberOfNitroGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isMeso() - Method in class com.actelion.research.chem.CanonizerMesoHelper
 
isMetalAtom(int) - Method in class com.actelion.research.chem.Molecule
 
isMissingParenthesis(String) - Static method in class com.actelion.research.util.StringFunctions
 
isModeQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
isMoleculeInOrder() - Method in class com.actelion.research.chem.Molecule3D
 
isMoleculeNext() - Method in class com.actelion.research.chem.io.RDFileParser
 
isMoreGeneral(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
Checks whether mask and data constitute a more general rule than this and therefore include this.
isMovable() - Method in class com.actelion.research.share.gui.Arrow
 
isMovable() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
isNaN() - Method in class com.actelion.research.chem.Coordinates
 
isNaturalAbundance(int) - Method in class com.actelion.research.chem.Molecule
 
isNewSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
This is Substance from version 5
isNewTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
isNitrogenFamily(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isNitroGroupN(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
 
isNonsingular() - Method in class com.actelion.research.calc.LUDecomposition
Is the matrix nonsingular?
isNoReactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
isNoStereoSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
A noStereo search is a hash code comparison from encoding stereo depleted structures.
isNoStereoSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
A noStereo search is a hash code comparison from encoding stereo depleted structures.
isNoStereoTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
A no-stereo-tautomer search is a hash code comparison from encoding stereo depleted generic tautomer structures.
isNoStructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
isOldSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
This is Substance version 3 or 4
IsomericSmilesCreator - Class in com.actelion.research.chem
 
IsomericSmilesCreator(StereoMolecule) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
Creates an IsomericSmilesCreator, which doesn't include atom mapping into generated smiles.
IsomericSmilesCreator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
Creates an IsomericSmilesCreator, which may include atom mapping numbers into generated smiles.
isOnlyCarbon(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
isOnlyOneConformer() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
isOnProductSide(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
isOnProductSide(double, double) - Method in class com.actelion.research.share.gui.editor.Model
 
isOnProductSide(float, float) - Method in class com.actelion.research.share.gui.Arrow
 
isOnProductSide(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
 
isOpen() - Method in class com.actelion.research.chem.io.CompoundFileParser
 
isOptimize3D() - Method in class com.actelion.research.chem.io.AbstractParser
 
isOrganicAtom(int) - Method in class com.actelion.research.chem.Molecule
 
IsotopeHelper - Class in com.actelion.research.chem
 
IsotopeHelper() - Constructor for class com.actelion.research.chem.IsotopeHelper
 
isOverlap(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
isOverlap(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
isOverlap(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
isOverlap(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
isOverlappingBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
isPerfectlyMapped() - Method in class com.actelion.research.chem.reaction.Reaction
Checks, whether all non-hydrogen atoms are mapped and whether every reactant atom has exactly one assigned product atom.
isPiConsidered(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
 
isPseudoRotatableBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
In a consecutive sequence of sp-hybridized atoms multiple single bonds cause redundant torsions.
isPurelyOrganic() - Method in class com.actelion.research.chem.Molecule
 
isQuaQua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
 
isQueryInReaction() - Method in class com.actelion.research.chem.reaction.SRSearcher
Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode
isQueryInReaction(int) - Method in class com.actelion.research.chem.reaction.SRSearcher
 
isReaction() - Method in class com.actelion.research.share.gui.editor.Model
 
isReactionLayoutRequired() - Method in class com.actelion.research.chem.reaction.Reaction
 
isReactionNext() - Method in class com.actelion.research.chem.io.RDFileParser
 
isRegexInString(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
isRetronSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
isRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isRingExclusively(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isRingInMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isRotatableBond(int) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
isSelected() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
isSelected() - Method in class com.actelion.research.share.gui.Arrow
 
isSelected() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
isSelected() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
isSelectedAtom(int) - Method in class com.actelion.research.chem.Molecule
 
isSelectedBond(int) - Method in class com.actelion.research.chem.Molecule
 
isSetRingMMFFAromaticity(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
Returns true if the given ring has had its MMFF aromaticity flag set.
isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
 
isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
 
isSimilaritySearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
isSimilaritySearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
isSimpleHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Uncharged hydrogen atoms with no isotop information nor with an attached custom label are considered simple and can usually be suppressed, effectively converting them from an explicit to an implicit hydrogen atom.
Note: This method returns true for uncharged, natural abundance hydrogens without custom labels even if they have a non-standard bonding situation (everything being different from having one single bonded non-simple-hydrogen neighbour, e.g.
isSingleConformationModeQuery() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
isSmallerThan(Angle) - Method in class com.actelion.research.util.Angle
Determines whether this angle is on the smaller value side of angle a, i.e.
isSmallRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isSmallRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isStabilizedAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
isStereoBond(int) - Method in class com.actelion.research.chem.Molecule
Checks whether bond is drawn as up/down single bond
isStereoBond(int, int) - Method in class com.actelion.research.chem.Molecule
Checks whether bond is drawn as up/down single bond and is connected to atom with its pointed tip
isSubreactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
isSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
 
isSubstructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
isSulfoxyGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isSupportedSearchType(ReactionSearchSpecification) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
isSupportedSearchType(StructureSearchSpecification) - Method in interface com.actelion.research.chem.StructureSearchDataSource
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
isSurroundedBy(Shape) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
isTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
A tautomer search is a hash code comparison from encoding generic tautomer structures.
isTerminal() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
 
isTerminalC() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
isThioEther(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isTransparent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
IStructureNameResolver - Interface in com.actelion.research.chem.name
Created by thomas on 7/13/17.
isUnix() - Static method in class com.actelion.research.util.Platform
 
isUpperAndLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
 
isUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
isUsed() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
isUserChange() - Method in class com.actelion.research.gui.DrawAreaEvent
 
isValid() - Method in class com.actelion.research.chem.conf.TorsionDetail
 
isValidBitIndex(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
isValidBitIndex(int[], int) - Static method in class com.actelion.research.util.BitUtils
 
isValidSolution(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
If a single histogram is not matching the solution is invalid.
isValidSolution(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
isValidSubstituentNameStart(String) - Static method in class com.actelion.research.chem.NamedSubstituents
 
isValidType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
isVector - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
isVoidTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
 
isWildcard(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
isWindows() - Static method in class com.actelion.research.util.Platform
 
isWorseThan(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.
itemStateChanged(ItemEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
 
iUSER_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
 
IValidationListener - Interface in com.actelion.research.share.gui.editor.listeners
Project: User: rufenec Date: 11/24/2014 Time: 3:27 PM

J

JAtomLabelDialog - Class in com.actelion.research.gui
 
JAtomLabelDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JAtomLabelDialog
 
JAtomQueryFeatureDialog - Class in com.actelion.research.gui
 
JAtomQueryFeatureDialog(Dialog, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
 
JAtomQueryFeatureDialog(Frame, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
 
JBondQueryFeatureDialog - Class in com.actelion.research.gui
 
JBondQueryFeatureDialog(Dialog, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
 
JBondQueryFeatureDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
 
JBrowseButtons - Class in com.actelion.research.gui.hidpi
 
JBrowseButtons(boolean, int, int, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
 
JBrowseButtons(boolean, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
 
JChemistryView - Class in com.actelion.research.gui
 
JChemistryView(int) - Constructor for class com.actelion.research.gui.JChemistryView
Creates a new JChemistryView for showing a reaction or molecules.
JChemistryView(int, int, int) - Constructor for class com.actelion.research.gui.JChemistryView
Creates a new JChemistryView for showing a reaction or molecules.
JDrawArea - Class in com.actelion.research.gui
 
JDrawArea(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawArea
 
JDrawDialog - Class in com.actelion.research.gui
 
JDrawDialog(Dialog, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Dialog, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, boolean) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, boolean, String) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, Reaction) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, Reaction, String) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, StereoMolecule[]) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, StereoMolecule[], String) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawDialog(Frame, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
 
JDrawPanel - Class in com.actelion.research.gui
 
JDrawPanel(StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawPanel
 
JDrawPanel(StereoMolecule, boolean) - Constructor for class com.actelion.research.gui.JDrawPanel
 
JDrawPanel(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawPanel
 
JDrawToolbar - Class in com.actelion.research.gui
 
JDrawToolbar(JDrawArea) - Constructor for class com.actelion.research.gui.JDrawToolbar
 
JDrawToolbar(JDrawArea, int) - Constructor for class com.actelion.research.gui.JDrawToolbar
 
JEditableChemistryView - Class in com.actelion.research.gui
 
JEditableChemistryView(int) - Constructor for class com.actelion.research.gui.JEditableChemistryView
Creates a new JEditableChemistryView for showing & editing a reaction or molecule(s).
JEditableStructureView - Class in com.actelion.research.gui
 
JEditableStructureView() - Constructor for class com.actelion.research.gui.JEditableStructureView
 
JEditableStructureView(int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
 
JEditableStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JEditableStructureView
 
JEditableStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
 
JFileChooserOverwrite - Class in com.actelion.research.gui
 
JFileChooserOverwrite() - Constructor for class com.actelion.research.gui.JFileChooserOverwrite
 
JFXCanvasDepictor - Class in com.actelion.research.jfx.gui.chem
Project: User: rufenec Date: 10/12/11 Time: 6:00 PM
JFXCanvasDepictor(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
JFXCanvasDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
JMessageBar - Class in com.actelion.research.gui
 
JStructureView - Class in com.actelion.research.gui
 
JStructureView() - Constructor for class com.actelion.research.gui.JStructureView
 
JStructureView(int, int) - Constructor for class com.actelion.research.gui.JStructureView
 
JStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
JStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
JStructureView(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
JStructureView(StereoMolecule, StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
JTextDrawingObjectDialog - Class in com.actelion.research.gui
 
JTextDrawingObjectDialog(Dialog, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
 
JTextDrawingObjectDialog(Frame, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
 

K

ka - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
ka(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
Returns 'ka' the force constant for a given index in the table.
ka(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
Returns 'ka' given a molecule and three connected atoms which form an angle.
KabschAlignment - Class in com.actelion.research.chem.alignment3d
described in: DOI 10.1002/jcc.20110 "Using Quaternions to Calculate RMSD"
KabschAlignment(Conformer, Conformer) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
first conformer is the reference, second conformer is rotated and translated to minimize the RMSD
KabschAlignment(Coordinates[], Coordinates[], int[][]) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
 
kb - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
 
kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
Returns 'kb' the force constant at a given index in the Bndk table.
kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
Returns the 'kb' value at the given index from the Bond table.
kb(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
kb(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
Returns the equivalent 'kb' value for a given set of three atoms.
Kb() - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
Kb(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
Kb(int) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
kba(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
Returns 'kba' for a given index in the table.
kba_ijk - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
kba_kji - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
kCDXObj_Bond - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
kCDXObj_Fragment - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
kCDXObj_Group - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
kCDXObj_Node - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
kCDXObj_Page - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
KEEP_INITIAL_COORDINATES - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
KEY_IS_ATOM_LABEL - Static variable in class com.actelion.research.share.gui.editor.Model
 
KEY_IS_INVALID - Static variable in class com.actelion.research.share.gui.editor.Model
 
KEY_IS_SUBSTITUENT - Static variable in class com.actelion.research.share.gui.editor.Model
 
KEY_IS_VALID_START - Static variable in class com.actelion.research.share.gui.editor.Model
 
keyPressed(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
 
keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
 
keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
 
keyReleased(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
 
keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
 
keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
 
KEYSTROKEFONTSIZE - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
 
keyTyped(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
 
keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
 
keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
 

L

lassoColor() - Static method in class com.actelion.research.gui.JDrawArea
 
lastHightlightPoint - Variable in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
lastIndexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
lastIndexOfNot(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
layoutChildren() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
layoutContainer(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
Description of the Method
LEFT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
Description of the Field
LEN_INTEGER_BYTES - Static variable in class com.actelion.research.util.datamodel.IntVec
 
length() - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
This function should return the total number of rows in a searchable table.
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
length() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns the length (or magnitude) of this vector.
length() - Method in class com.actelion.research.util.datamodel.IntArray
 
LIGAND - Static variable in class com.actelion.research.chem.Molecule3D
 
LIGAND_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
 
LigandPose - Class in com.actelion.research.chem.docking
 
LigandPose(Conformer, AbstractScoringEngine, double) - Constructor for class com.actelion.research.chem.docking.LigandPose
 
LIMIT_NEIGHBOURS_SINCE_LAST_ADDED - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
linear(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the linear bool of an atom given its MMFF type.
LinearRegression - Class in com.actelion.research.calc.regression.linear.simple
LinearRegression 2009 MvK: Start implementation
LinearRegression() - Constructor for class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
lineTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
lineTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
LINK_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
Linker - Class in com.actelion.research.chem.descriptor.flexophore.entity
Linker
Linker(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
LIPO_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
listeners - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
ListInteger<T> - Class in com.actelion.research.chem.io.pdb.parser
ListInteger
ListInteger(List<T>, int) - Constructor for class com.actelion.research.chem.io.pdb.parser.ListInteger
 
ListWithIntVec - Class in com.actelion.research.chem.mcs
 
ListWithIntVec() - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
 
ListWithIntVec(int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
 
ListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
 
ListWithIntVec(ListWithIntVec) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
 
ListWithIntVecIdCode - Class in com.actelion.research.chem.properties.complexity
 
ListWithIntVecIdCode(int) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
ListWithIntVecIdCode(ListWithIntVec) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
Flat constructor.
ListWithIntVecIdCode(ListWithIntVecIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
Deep constructor.
LittleEndianDataInputStream - Class in com.actelion.research.util
 
LittleEndianDataInputStream(InputStream) - Constructor for class com.actelion.research.util.LittleEndianDataInputStream
 
LittleEndianDataOutputStream - Class in com.actelion.research.util
 
LittleEndianDataOutputStream(OutputStream) - Constructor for class com.actelion.research.util.LittleEndianDataOutputStream
 
load(File) - Method in class com.actelion.research.chem.io.AbstractParser
 
load(String) - Method in class com.actelion.research.chem.io.AbstractParser
 
load(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
 
loadCache(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
Loads pre-calculated rigid fragment coordinates from a cache file, which is either a text file created by the createCacheFiles() method, or a zip archive of the text file.
loadDefaultCache() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
This loads the default cache file
loadGroup(String) - Method in class com.actelion.research.chem.io.AbstractParser
 
loadGroup(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
 
loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.AbstractParser
 
loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.Mol2FileParser
 
loadTable(String, Tables) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Loads and registers a tables object with the ForceField class so it can be used by new ForceField instances.
locateBonds() - Method in class com.actelion.research.chem.coords.InventorFragment
 
locateDelocalizedDoubleBonds(boolean[]) - Method in class com.actelion.research.chem.AromaticityResolver
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
locateDelocalizedDoubleBonds(boolean[], boolean, boolean) - Method in class com.actelion.research.chem.AromaticityResolver
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
log() - Method in class com.actelion.research.calc.Matrix
Log function from the class Math .
log2(int) - Static method in class com.actelion.research.calc.Logarithm
 
Logarithm - Class in com.actelion.research.calc
Logarithm Mar 14, 2013 MvK Start implementation
Logarithm() - Constructor for class com.actelion.research.calc.Logarithm
 
longValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
LookAndFeelHelper - Class in com.actelion.research.gui
 
LookAndFeelHelper() - Constructor for class com.actelion.research.gui.LookAndFeelHelper
 
lookupBondLength(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
Returns an estimate of the bond length based on atom and bond characteristics.
lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
 
lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
 
lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
 
lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
LUDecomposition - Class in com.actelion.research.calc
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class com.actelion.research.calc.LUDecomposition
LU Decomposition Structure to access L, U and piv.

M

main(String[]) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
 
main(String[]) - Static method in class com.actelion.research.calc.filter.SlidingWindow
 
main(String[]) - Static method in class com.actelion.research.calc.histogram.Histogram
 
main(String[]) - Static method in class com.actelion.research.chem.contrib.DiastereoIDTest
 
main(String[]) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
 
main(String[]) - Static method in class com.actelion.research.chem.contrib.testChiralDia
 
main(String[]) - Static method in class com.actelion.research.chem.contrib.testDiaID
 
main(String[]) - Static method in class com.actelion.research.chem.contrib.testHoses
 
main(String[]) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
 
main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
 
main(String[]) - Static method in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
 
main(String[]) - Static method in class com.actelion.research.chem.io.Mol2FileParser
 
main(String[]) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
 
main(String[]) - Static method in class com.actelion.research.chem.SmilesParser
 
main(String[]) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
 
main(String[]) - Static method in class com.actelion.research.util.BurtleHasher
 
main(String[]) - Static method in class com.actelion.research.util.CommandLineParser
 
main(String[]) - Static method in class com.actelion.research.util.convert.String2DoubleArray
 
main(String[]) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
 
main(String[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
 
main(String[]) - Static method in class com.actelion.research.util.ErrorHashMap
 
main(String[]) - Static method in class com.actelion.research.util.Formatter
 
main(String[]) - Static method in class com.actelion.research.util.SizeOf
 
main(String[]) - Static method in class com.actelion.research.util.StringFunctions
 
main(String[]) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
Test code...
makeColor(int, int, int) - Static method in class com.actelion.research.chem.SVGDepictor
 
makeProteinFlexible(Molecule3D, Coordinates, double, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
makeProteinRigid(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
makeSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
mAllAtoms - Variable in class com.actelion.research.chem.Molecule
 
mAllBonds - Variable in class com.actelion.research.chem.Molecule
 
mAllowedDragAction - Variable in class com.actelion.research.gui.JStructureView
 
mAllowedDropAction - Variable in class com.actelion.research.gui.JStructureView
 
manhattanBlockDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
manhattanBlockDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
mapReaction(int, Point2D, Point2D) - Method in class com.actelion.research.share.gui.editor.Model
 
mapReaction(Reaction, SSSearcher) - Method in interface com.actelion.research.chem.reaction.IReactionMapper
 
mapReaction(Reaction, SSSearcher) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
 
mapToolColor() - Static method in class com.actelion.research.gui.JDrawArea
 
mArea - Variable in class com.actelion.research.gui.JDrawPanel
 
markAtomForDeletion(int) - Method in class com.actelion.research.chem.Molecule
Marks this atom to be deleted in a later call to deleteMarkedAtomsAndBonds().
markBondForDeletion(int) - Method in class com.actelion.research.chem.Molecule
Marks this bond to be deleted in a later call to deleteMarkedAtomsAndBonds().
markDiastereotopicAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
In order to debug we could number the group of diastereotopic atoms
markLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Find the most likely ligand (in term of size, rings, polar atoms) and mark it
markLigand(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Marks a numbered ligand
markLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Find the most likely ligands (in term of size)
MarkushStructure - Class in com.actelion.research.chem
 
MarkushStructure() - Constructor for class com.actelion.research.chem.MarkushStructure
 
MarkushStructure(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.MarkushStructure
 
MASK_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_FIRST_SHORT - Static variable in class com.actelion.research.util.BitUtils
 
MASK_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_FOURTH_SHORT - Static variable in class com.actelion.research.util.BitUtils
 
MASK_INVERSE_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_INVERSE_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_INVERSE_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_INVERSE_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_SEC_SHORT - Static variable in class com.actelion.research.util.BitUtils
 
MASK_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
 
MASK_THIRD_SHORT - Static variable in class com.actelion.research.util.BitUtils
 
maskByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
match(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
match(T) - Method in interface com.actelion.research.jfx.gui.misc.Selector
 
MATCH_BALANCE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
MATCH_SIZE_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
matches(TorsionSetEliminationRule, double) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
matchFirst(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
matchReaction(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
 
matchSearch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
finds a set of balanced, high-scoring initial splits that are then used as an input for the extension match algorithm
MathHelper - Class in com.actelion.research.chem.phesaflex
 
mAtom - Variable in class com.actelion.research.chem.coords.InventorChain
 
mAtom - Variable in class org.openmolecules.chem.conf.so.ConformationRule
 
mAtomCharge - Variable in class com.actelion.research.chem.Molecule
 
mAtomCustomLabel - Variable in class com.actelion.research.chem.Molecule
 
mAtomFlags - Variable in class com.actelion.research.chem.Molecule
 
mAtomicNo - Variable in class com.actelion.research.chem.Molecule
 
mAtomList - Variable in class com.actelion.research.chem.Molecule
 
mAtomList - Variable in class com.actelion.research.chem.Mutation
 
mAtomMapNo - Variable in class com.actelion.research.chem.Molecule
 
mAtomMass - Variable in class com.actelion.research.chem.Molecule
 
mAtomQueryFeatures - Variable in class com.actelion.research.chem.Molecule
 
mAtomX - Variable in class com.actelion.research.chem.coords.InventorFragment
 
mAtomY - Variable in class com.actelion.research.chem.coords.InventorFragment
 
Matrix - Class in com.actelion.research.calc
 
Matrix() - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(boolean, double[]) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(boolean, int[]) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(boolean, List<Double>) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(byte[][]) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(double[][]) - Constructor for class com.actelion.research.calc.Matrix
Deep copy
Matrix(double[][], boolean) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(float[][]) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(int[][]) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(int, int) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(Matrix) - Constructor for class com.actelion.research.calc.Matrix
 
Matrix(List<DoubleVec>) - Constructor for class com.actelion.research.calc.Matrix
 
MatrixBasedHistogram - Class in com.actelion.research.calc.histogram
MatrixBasedHistogram
MatrixBasedHistogram() - Constructor for class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
max - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
max() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
max() - Method in class com.actelion.research.util.datamodel.IntArray
 
max(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
max(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
max(double[]) - Static method in class com.actelion.research.util.ArrayUtils
 
max(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
max(float[]) - Static method in class com.actelion.research.util.ArrayUtils
 
max(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
max(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
max(int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
max(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
max(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
 
max(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
MAX - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
MAX - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
MAX_ALLOWED_COLLISION_INTENSITY - Static variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
MAX_ATOM_BITS - Static variable in class com.actelion.research.chem.SimpleCanonizer
 
MAX_ATOMS - Static variable in class com.actelion.research.chem.Canonizer
 
MAX_BONDS - Static variable in class com.actelion.research.chem.Canonizer
 
MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
 
MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.Model
 
MAX_COUNT_VALUE - Static variable in class com.actelion.research.chem.descriptor.DescriptorEncoder
 
MAX_DEFAULT_CURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
MAX_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
 
MAX_NUM_BITS - Static variable in class com.actelion.research.chem.properties.complexity.BitArray128
 
MAX_NUM_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
MAX_NUM_HEAVY_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
MAX_NUM_NODES - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
MAX_NUM_NODES_FLEXOPHORE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
MAX_RING_SIZE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
 
MAX_SMALL_RING_SIZE - Static variable in class com.actelion.research.chem.RingCollection
 
MAX_UNDO_SIZE - Static variable in class com.actelion.research.share.gui.editor.Model
 
MAX_VAL_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
maxConfs - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
maxDouble(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
maxInt(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
MAXMOLS - Static variable in class com.actelion.research.util.Sketch
 
maxRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
 
MAXSTEP - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mBond - Variable in class com.actelion.research.chem.coords.InventorChain
 
mBondAtom - Variable in class com.actelion.research.chem.Molecule
 
mBondFlags - Variable in class com.actelion.research.chem.Molecule
 
mBondQueryFeatures - Variable in class com.actelion.research.chem.Molecule
 
mBondType - Variable in class com.actelion.research.chem.Molecule
 
mChirality - Variable in class com.actelion.research.chem.Molecule
 
mCoordinates - Variable in class com.actelion.research.chem.Molecule
 
MCS - Class in com.actelion.research.chem.mcs
 
MCS() - Constructor for class com.actelion.research.chem.mcs.MCS
 
MCS(int) - Constructor for class com.actelion.research.chem.mcs.MCS
 
MCS(int, SSSearcher) - Constructor for class com.actelion.research.chem.mcs.MCS
 
MCSFast - Class in com.actelion.research.chem.mcs
 
MCSFast() - Constructor for class com.actelion.research.chem.mcs.MCSFast
 
MCSFast(int) - Constructor for class com.actelion.research.chem.mcs.MCSFast
 
MCSFunctions - Class in com.actelion.research.chem.mcs
 
MCSFunctions() - Constructor for class com.actelion.research.chem.mcs.MCSFunctions
 
MCSReactionMapper - Class in com.actelion.research.chem.reaction
 
MCSReactionMapper() - Constructor for class com.actelion.research.chem.reaction.MCSReactionMapper
 
mDepictor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
MDHIndexTables - Class in com.actelion.research.chem.descriptor.flexophore
 
mDiagnosticCollisionAtoms - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
mDiagnosticCollisionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
mDiagnosticTorsionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
mDim - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mDisplayMode - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mDoLayoutMolecules - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mDotProduct - Variable in class com.actelion.research.chem.DiversitySelector.DiversitySelectorRecord
 
mDrawingObjectList - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mDropAdapter - Variable in class com.actelion.research.gui.JStructureView
 
MDYNE_A_TO_KCAL_MOL - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
 
mean(Angle, Angle) - Static method in class com.actelion.research.util.Angle
Determines the mean angle between a1 and a2 on that side of the circle where a1 and a2 have the shorter connection.
meanClust() - Static method in class com.actelion.research.util.datamodel.ByteVec
 
median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
median() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
medianRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
 
MedianStatisticFunctions - Class in com.actelion.research.calc.statistics.median
MedianStatisticFunctions Aug 5, 2011 MvK: Start implementation
MedianStatisticFunctions() - Constructor for class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
 
merge(MolDistHistViz, MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Deprecated. 
merge(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
merge(List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
Merges fragments containing a common atom index.
mergeOverlapping(List<SubGraphIndices>, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
Merges overlapping fragments.
MERGEPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ALDUS_APM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ANIMATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ARC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_BITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CHORD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEBITMAP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEBITMAPINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEBRUSHINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEFONTINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEPENINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_CREATEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_DELETEOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_DIBBITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_DIBCREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_DIBSTRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_DRAWTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ELLIPSE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ESCAPE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_EXCLUDECLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_EXTFLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_EXTTEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_FILLREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_FLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_FRAMEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_INTERSECTCLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_INVERTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_LINETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_MOVETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_ANSI_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_ANSI_VAR_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_BLACK_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_BLACK_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_DEFAULT_PALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_DEVICE_DEFAULT_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_DKGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_GRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_HOLLOW_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_LTGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_NULL_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_NULL_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_OEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_SYSTEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_SYSTEM_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_WHITE_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OBJ_WHITE_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OFFSETCLIPRGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OFFSETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_OFFSETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_PAINTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_PATBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_PIE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_POLYBEZIER16 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_POLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_POLYLINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_POLYPOLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_REALIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_RECTANGLE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_RESIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_RESTOREDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_ROUNDRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SAVEDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SCALEVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SCALEWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SELECTCLIPREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SELECTOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SELECTPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETBKCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETBKMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETDIBTODEV - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETMAPMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETMAPPERFLAGS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETPALENTRIES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETPIXEL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETPOLYFILLMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETRELABS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETROP2 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETSTRETCHBLTMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETTEXTALIGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETTEXTCHAREXTRA - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETTEXTCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETTEXTJUSTIFICATION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_SETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_STRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_STRETCHDIB - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
META_TEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MetaFile - Class in com.actelion.research.gui.wmf
 
MetaFile() - Constructor for class com.actelion.research.gui.wmf.MetaFile
 
METAL_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
MetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
 
MetropolisMonteCarloHelper - Class in com.actelion.research.chem.phesaflex
 
MetropolisMonteCarloHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
 
MFCOMMENT - Static variable in class com.actelion.research.gui.wmf.WMF
 
MFCOMMENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
mFixedAtoms - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mFragment - Variable in class com.actelion.research.chem.SSSearcher
 
mFragmentNoColor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mG - Variable in class com.actelion.research.chem.AbstractDepictor
 
mGlobalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
 
mGlobalBond - Variable in class com.actelion.research.chem.coords.InventorFragment
 
mGlobalToLocalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
 
mGrad - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
min - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
min() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
min(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
min(double[]) - Static method in class com.actelion.research.util.ArrayUtils
 
min(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
min(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
min(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
min(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
min(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
 
min(String, String) - Static method in class com.actelion.research.util.StringFunctions
 
MIN_BOND_LENGTH_SQUARE - Static variable in class com.actelion.research.share.gui.editor.Model
 
MIN_NUM_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
MIN_NUM_NODES_SIM - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
MINI_CUTOFF - Static variable in class com.actelion.research.chem.docking.DockingEngine
 
minimise() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
minimise() - Method in interface com.actelion.research.chem.forcefield.ForceField
 
minimise(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
Minimise the current molecule.
minimumLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
Description of the Method
MinimumSpanningTree - Class in com.actelion.research.calc.graph
MinimumSpanningTree Kruskal's algorithm
MinimumSpanningTree(Matrix) - Constructor for class com.actelion.research.calc.graph.MinimumSpanningTree
 
MINLEN_FRAG - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
minus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
minus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
minus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
mIsEnabled - Variable in class org.openmolecules.chem.conf.so.ConformationRule
 
mIsFragment - Variable in class com.actelion.research.chem.Molecule
 
mIsInterrupted - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mIsMarkushStructure - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mIsRacemate - Variable in class com.actelion.research.chem.Molecule
 
mIsSelected - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mix64(BurtleHasherABC) - Static method in class com.actelion.research.util.BurtleHasher
 
mkdirs(File) - Static method in class com.actelion.research.util.IO
 
mkdirs(String) - Static method in class com.actelion.research.util.IO
 
mltb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the MLTB type of an atom given its MMFF type.
MM_ANISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_ANISOTROPIC - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
 
MM_HIENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_HIMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_HITWIPS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_ISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_LOENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_LOMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
MM_TEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
mMaxAtoms - Variable in class com.actelion.research.chem.Molecule
 
mMaxBonds - Variable in class com.actelion.research.chem.Molecule
 
MMFF94 - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
MMFF94S - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
MMFF94SPLUS - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
MMFFMolecule - Class in com.actelion.research.chem.forcefield.mmff
MMFF molecule is a wrapper class for the ExtendedMolecule.
MMFFMolecule(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
 
mMol - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mMol - Variable in class com.actelion.research.gui.dnd.MoleculeTransferable
 
mMolecule - Variable in class com.actelion.research.chem.SSSearcher
 
mMolecule - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mMutationType - Variable in class com.actelion.research.chem.Mutation
 
mNewpos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
MODE_ADD_NA_AND_CL - Static variable in class com.actelion.research.chem.MoleculeStandardizer
 
MODE_ALLOW_CHARGE_CORRECTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
 
MODE_ANGLES - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
MODE_BINS - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
MODE_BUFFER_HEAD_AND_TAIL - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_CONSIDER_MARKED_ATOMS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
 
MODE_COORDINATES_PREFER_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_COORDINATES_PREFER_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_COORDINATES_REQUIRE_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_COORDINATES_REQUIRE_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JDrawArea
 
MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.share.gui.editor.Model
 
MODE_EXTRACT_DETAILS - Static variable in class com.actelion.research.chem.io.DWARFileParser
 
MODE_FULLY_MAP_REACTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
 
MODE_GET_PARENT - Static variable in class com.actelion.research.chem.MoleculeStandardizer
 
MODE_HARD_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
 
MODE_KEEP_HYDROGEN_MAP - Static variable in class com.actelion.research.chem.MolfileParser
 
MODE_KEEP_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
 
MODE_LARGEST_FRAGMENT_ONLY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.gui.JDrawArea
 
MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.share.gui.editor.Model
 
MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
 
MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.share.gui.editor.Model
 
MODE_PPNODE_SIMILARITY_COMPARISON - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
MODE_PREFER_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
 
MODE_REACTION - Static variable in class com.actelion.research.gui.JDrawArea
 
MODE_REACTION - Static variable in class com.actelion.research.share.gui.editor.Model
 
MODE_REMOVE_DUPLICATE_PRODUCTS - Static variable in class com.actelion.research.chem.reaction.Reactor
 
MODE_REMOVE_HYDROGEN - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
 
MODE_RETAIN_COORDINATES - Static variable in class com.actelion.research.chem.reaction.Reactor
 
MODE_SKIP_DEFAULT_TEMPLATES - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
 
MODE_SMALL_AND_LARGE_RINGS - Static variable in class com.actelion.research.chem.RingCollection
 
MODE_SMALL_AND_LARGE_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
 
MODE_SMALL_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
 
MODE_SMALL_RINGS_ONLY - Static variable in class com.actelion.research.chem.RingCollection
 
MODE_SOFT_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
 
model - Variable in class com.actelion.research.share.gui.editor.actions.CommandAction
 
model - Variable in class com.actelion.research.share.gui.editor.actions.DrawAction
 
Model - Class in com.actelion.research.share.gui.editor
Project: User: rufenec Date: 1/24/13 Time: 5:02 PM
Model(GeomFactory, int) - Constructor for class com.actelion.research.share.gui.editor.Model
 
Model.AtomHighlightCallback - Interface in com.actelion.research.share.gui.editor
 
Model.BondHighlightCallback - Interface in com.actelion.research.share.gui.editor
 
ModelExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
 
ModelExhaustiveStatistics(int, int, int, double) - Constructor for class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
ModelMedianDouble - Class in com.actelion.research.calc.statistics.median
 
ModelMedianDouble() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
ModelMedianDouble(double, double, double, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
ModelMedianDouble(ModelMedianDouble) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
ModelMedianFloat - Class in com.actelion.research.calc.statistics.median
 
ModelMedianFloat() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
ModelMedianFloat(float, float, float, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
ModelMedianFloat(ModelMedianFloat) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
ModelMedianInteger - Class in com.actelion.research.calc.statistics.median
ModelMedianInteger Feb 9, 2012 MvK: Start implementation
ModelMedianInteger() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
ModelMedianLong - Class in com.actelion.research.calc.statistics.median
ModelMedianInteger Feb 14, 2017 MvK: Start implementation
ModelMedianLong() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianLong
 
ModelParser - Class in com.actelion.research.chem.io.pdb.parser
ModelParser
ModelParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.ModelParser
 
ModelSampleFragments - Class in com.actelion.research.chem.mcs
 
ModelSampleFragments(int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
 
ModelSampleFragments(int, int, int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
 
mol - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
mol - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
mol - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
mol_ - Variable in class com.actelion.research.chem.AtomComparator
 
Mol2FileParser - Class in com.actelion.research.chem.io
 
Mol2FileParser() - Constructor for class com.actelion.research.chem.io.Mol2FileParser
 
MolDistHist - Class in com.actelion.research.chem.descriptor.flexophore
 
MolDistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
MolDistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
MolDistHist(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
MolDistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
 
MolDistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
 
MolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore
 
MolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
MolDistHistViz(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
MolDistHistViz(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
MolDistHistViz(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
MolDistHistViz(MolDistHistViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
MolDistHistVizEncoder - Class in com.actelion.research.chem.descriptor.flexophore
 
MolDistHistVizEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
 
MolDistHistVizFrag - Class in com.actelion.research.chem.descriptor.flexophore
 
MolDistHistVizFrag() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
MolDistHistVizFrag(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
MolDistHistVizFrag(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
MolDistHistVizFrag(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
MolDistHistVizFrag(MolDistHistVizFrag) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
MolecularComplexityCalculator - Class in com.actelion.research.chem.properties.complexity
 
MolecularComplexityCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
 
MolecularFormula - Class in com.actelion.research.chem
 
MolecularFormula(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolecularFormula
 
MolecularVolume - Class in com.actelion.research.chem.phesa
 
MolecularVolume(MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
 
MolecularVolume(MolecularVolume, Conformer) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
 
MolecularVolume(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
 
MolecularVolume(List<AtomicGaussian>, List<PPGaussian>, List<VolumeGaussian>, List<Coordinates>) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
 
Molecule - Class in com.actelion.research.chem
 
Molecule() - Constructor for class com.actelion.research.chem.Molecule
 
Molecule() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
 
Molecule(int, int) - Constructor for class com.actelion.research.chem.Molecule
 
MOLECULE_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
MOLECULE_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
MOLECULE_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
molecule3D - Variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
Molecule3D - Class in com.actelion.research.chem
 
Molecule3D() - Constructor for class com.actelion.research.chem.Molecule3D
 
Molecule3D(int, int) - Constructor for class com.actelion.research.chem.Molecule3D
 
Molecule3D(Molecule3D) - Constructor for class com.actelion.research.chem.Molecule3D
 
Molecule3D(StereoMolecule) - Constructor for class com.actelion.research.chem.Molecule3D
 
Molecule3DFunctions - Class in com.actelion.research.chem
 
Molecule3DFunctions() - Constructor for class com.actelion.research.chem.Molecule3DFunctions
 
MoleculeAutoMapper - Class in com.actelion.research.chem.reaction
 
MoleculeAutoMapper(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.MoleculeAutoMapper
 
moleculeChanged() - Method in class com.actelion.research.gui.JDrawArea
Use this to inform the JDrawArea after changing its molecule from outside.
moleculeChanged(boolean) - Method in class com.actelion.research.gui.JDrawArea
Ideally don't use this from outside JDrawArea.
MoleculeDataFormats - Class in com.actelion.research.jfx.dataformat
Deprecated.
MoleculeDataFormats() - Constructor for class com.actelion.research.jfx.dataformat.MoleculeDataFormats
Deprecated.
 
MoleculeDragAdapter - Class in com.actelion.research.gui.dnd
 
MoleculeDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
MoleculeDropAdapter - Class in com.actelion.research.gui.dnd
 
MoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
MoleculeFilter - Interface in com.actelion.research.chem
 
MoleculeGrid - Class in com.actelion.research.chem.io.pdb.converter
Class used to speed up the calculation of neighbours by creating a grid.
MoleculeGrid(StereoMolecule) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
MoleculeGrid(StereoMolecule, double, Coordinates) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
Creates the Grid: Complexity O(nAtoms)
MoleculeNeutralizer - Class in com.actelion.research.chem
 
MoleculeNeutralizer() - Constructor for class com.actelion.research.chem.MoleculeNeutralizer
 
moleculeQualifies(StereoMolecule) - Method in interface com.actelion.research.chem.MoleculeFilter
 
MoleculeStandardizer - Class in com.actelion.research.chem
MoleculeStandardizer
MoleculeStandardizer() - Constructor for class com.actelion.research.chem.MoleculeStandardizer
 
MoleculeTransferable - Class in com.actelion.research.gui.dnd
 
MoleculeTransferable(StereoMolecule) - Constructor for class com.actelion.research.gui.dnd.MoleculeTransferable
 
MoleculeView - Class in com.actelion.research.jfx.gui.chem
Project: User: rufenec Date: 10/12/11 Time: 4:03 PM
MoleculeView() - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
 
MoleculeView(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
 
MoleculeViewSkin - Class in com.actelion.research.jfx.gui.chem
Project: User: rufenec Date: 10/12/11 Time: 4:10 PM
MoleculeViewSkin(MoleculeView) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
MolfileCreator - Class in com.actelion.research.chem
 
MolfileCreator(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolfileCreator
This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileCreator
This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
This creates a new molfile version 2 from the given molecule.
MolfileParser - Class in com.actelion.research.chem
 
MolfileParser() - Constructor for class com.actelion.research.chem.MolfileParser
Constructor of a MolFileParser, which will mirror Y,Z coordinates
MolfileParser(int) - Constructor for class com.actelion.research.chem.MolfileParser
 
MolfileV3Creator - Class in com.actelion.research.chem
This class generates an MDL molfile version 3.0 from a StereoMolecule as described by MDL in 'CTFile Formats June 2005'.
MolfileV3Creator(StereoMolecule) - Constructor for class com.actelion.research.chem.MolfileV3Creator
This creates a new molfile version 3 from the given molecule.
MolfileV3Creator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileV3Creator
This creates a new molfile version 3 from the given molecule.
MolfileV3Creator(StereoMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
This creates a new molfile version 3 from the given molecule.
MolfileV3Creator(StereoMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
This creates a new molfile version 3 from the given molecule.
moreRecordsAvailable() - Method in class com.actelion.research.chem.io.ODEFileParser
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableChemistryView
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableStructureView
 
mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mouseExited(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mousePressed(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
 
mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
 
mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
 
mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
 
move(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
move(double, double) - Method in class com.actelion.research.chem.DepictorTransformation
 
move(float, float) - Method in class com.actelion.research.share.gui.Arrow
 
move(float, float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
move(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
moveAtomWithUnboundedNeighbors(Conformer, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
moveFieldToStart(String) - Method in class com.actelion.research.chem.SDFileMolecule
 
moveGroup(Conformer, int, int[], double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
moveSubstituent(Conformer, int, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
moveTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
moveTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
MOVETOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mPoint - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mPos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mPriority - Variable in class com.actelion.research.chem.coords.InventorFragment
 
mProbability - Variable in class com.actelion.research.chem.Mutation
 
mProtectedFromDeletion - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mProtectHydrogen - Variable in class com.actelion.research.chem.Molecule
 
mReactantOrCoreCount - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mReaction - Variable in class com.actelion.research.gui.dnd.ReactionTransferable
 
mReader - Variable in class com.actelion.research.chem.io.CompoundFileParser
 
mRigidFragment - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
mRotatableBond - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
MSDIFF_OFFSET - Static variable in class com.actelion.research.util.Sketch
 
mSmiles - Variable in class com.actelion.research.chem.SmilesCreator
 
mSpecifier1 - Variable in class com.actelion.research.chem.Mutation
 
mSpecifier2 - Variable in class com.actelion.research.chem.Mutation
 
mTables - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
mTimeInterval - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mToolBar - Variable in class com.actelion.research.gui.JDrawPanel
 
mTotalEnergy - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
mTransformation - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mTransformationReferenceX - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mTransformationReferenceY - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mTransformationValue1 - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mTransformationValue2 - Variable in class com.actelion.research.chem.AbstractDrawingObject
 
mult(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
mult(double) - Method in class com.actelion.research.util.datamodel.ByteVec
 
mult(double) - Method in class com.actelion.research.util.datamodel.IntVec
 
mult(double) - Method in class com.actelion.research.util.DoubleVec
 
mult(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
mult(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
mult(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
MULT_FREQ - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
multByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
 
multByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
multCols(Matrix) - Method in class com.actelion.research.calc.Matrix
 
MultCoordFragIndex - Class in com.actelion.research.chem.descriptor.flexophore.generator
 
MultCoordFragIndex(int[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
 
multEl(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
Elementwise multiplication
multEl(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Elementwise multiplication
multEl(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
Elementwise multiplication
MultipleNonOverlapSolution - Class in com.actelion.research.chem.properties.complexity
 
MultipleNonOverlapSolution(int, FragmentDefinedByBondsIdCode, int) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
MultipleNonOverlapSolution(MultipleNonOverlapSolution) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
multiply(boolean, boolean, Matrix) - Method in class com.actelion.research.calc.Matrix
Multiplication of two matrices.
multiply(double) - Method in class com.actelion.research.calc.Matrix
 
multiply(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
 
multiply(Matrix) - Method in class com.actelion.research.calc.Matrix
 
multiply(Quaternion) - Method in class com.actelion.research.chem.phesa.Quaternion
convert Quaternion to a rotation matrix
multiplyInverseMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
multiplyMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
multiplyValByVal(Matrix) - Method in class com.actelion.research.calc.Matrix
Value by value multiplication Matrices must have the same dimensions.
mUseGraphics2D - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
mutate(StereoMolecule) - Method in class com.actelion.research.chem.Mutator
Does an in-place mutation of the molecule allowing any kind of mutation at any of the molecules non-selected atoms aiming for 4-24 non-H atoms with an optimum of 9 atoms.
mutate(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
Does an in-place mutation of the molecule allowing the defined mutation kinds at any of the molecules unselected atoms.
mutate(StereoMolecule, ArrayList<Mutation>) - Method in class com.actelion.research.chem.Mutator
Selects a likely mutation from the list, performs the mutation and removes it from the list.
Mutation - Class in com.actelion.research.chem
 
Mutation() - Constructor for class com.actelion.research.chem.Mutation
 
Mutation(int, int, int, int, int[], double) - Constructor for class com.actelion.research.chem.Mutation
 
Mutation(int, int, int, int, int, double) - Constructor for class com.actelion.research.chem.Mutation
 
MUTATION_ADD_ATOM - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_ANY - Static variable in class com.actelion.research.chem.Mutator
 
MUTATION_CHANGE_ATOM - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CHANGE_BOND - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CHANGE_RING - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CLOSE_RING - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CLOSE_RING_AND_AROMATIZE - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CUTOUT_ATOM - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_CUTOUT_SFRAGMENT - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_DELETE_ATOM - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_DELETE_BOND - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_DELETE_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_GROW - Static variable in class com.actelion.research.chem.Mutator
 
MUTATION_INSERT_ATOM - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_KEEP_SIZE - Static variable in class com.actelion.research.chem.Mutator
 
MUTATION_MIGRATE - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_SHRINK - Static variable in class com.actelion.research.chem.Mutator
 
MUTATION_SWAP_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
 
MUTATION_TOGGLE_AMID_SULFONAMID - Static variable in class com.actelion.research.chem.Mutation
 
MutationBiasProvider - Interface in com.actelion.research.chem
 
Mutator - Class in com.actelion.research.chem
 
Mutator(AtomTypeList) - Constructor for class com.actelion.research.chem.Mutator
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type list.
Mutator(String) - Constructor for class com.actelion.research.chem.Mutator
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type file.
mValidHelperArrays - Variable in class com.actelion.research.chem.Molecule
 
mValue - Variable in class com.actelion.research.chem.CanonizerBaseValue
 
mWhere1 - Variable in class com.actelion.research.chem.Mutation
 
mWhere2 - Variable in class com.actelion.research.chem.Mutation
 

N

N - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
n_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'N-i' from the table.
N_SP2_TAUT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
name - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
 
name - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
name(int) - Static method in class com.actelion.research.chem.PeriodicTable
 
NAME_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
 
NamedSubstituents - Class in com.actelion.research.chem
 
NamedSubstituents() - Constructor for class com.actelion.research.chem.NamedSubstituents
 
nameToShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
Native() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
 
NativeClipboardAccessor - Class in com.actelion.research.gui.clipboard
 
NativeClipboardAccessor() - Constructor for class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_ALDUSMETAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_BITMAP - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_CHEMDRAWINTERCHANGE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_CTAB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_DIB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_EMBEDDEDSKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_IDCODE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_METAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_MOLFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_SERIALIZEMOLECULE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_SERIALIZEREACTION - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
NC_SKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
needsCoordinates - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
needsLayout() - Method in class com.actelion.research.share.gui.editor.Model
 
needsLayout(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
NEG_CHARGE - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
negate() - Method in class com.actelion.research.chem.Coordinates
 
negate() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns this vector negated (signs swapped).
neglectSpaceDelimitedCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
IDCodeParsers allow passing idcode and coordinates as one String with a space as separator in between.
NEIGHBOURS_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
 
neutralizeChargedMolecule(StereoMolecule) - Method in class com.actelion.research.chem.MoleculeNeutralizer
Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
NewBondAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 1:28 PM
NewBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewBondAction
 
NewChainAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 3/26/13 Time: 3:42 PM
NewChainAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewChainAction
 
NEWLINE - Static variable in class com.actelion.research.chem.io.AbstractParser
 
NEWLINE_REGEX - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
NEWLINE_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
newMMFF94(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Tables
Returns a new MMFF94 table.
next() - Method in class com.actelion.research.chem.io.CompoundFileParser
Advances the row counter to the next row
next(String) - Static method in class com.actelion.research.util.IO
 
next(String, DecimalFormat) - Static method in class com.actelion.research.util.IO
 
nextClosing(String, int, char, char) - Static method in class com.actelion.research.util.StringFunctions
finds the next corresponding closing bracket char to the first open char
nextClosingBracket(String, int) - Static method in class com.actelion.research.util.StringFunctions
finds the next balanced closing bracket "]" to the first open bracket "[" in the string.
NITRO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
Nitrogen - Static variable in class com.actelion.research.chem.PeriodicTable
 
NONHNEIGHBOURS - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
NONPOLAR_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
 
nonZero() - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
Checks that at least one of the constants is non-zero.
norm2() - Method in class com.actelion.research.calc.SingularValueDecomposition
Two norm
norm2One() - Method in class com.actelion.research.util.datamodel.ByteVec
 
norm2One() - Method in class com.actelion.research.util.datamodel.IntVec
 
norm2One() - Method in class com.actelion.research.util.DoubleVec
 
NORMAL - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
 
normalise() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Normalises a vector.
normalize() - Method in class com.actelion.research.chem.phesa.Quaternion
 
normalize() - Method in class com.actelion.research.util.Angle
 
normalizeAmbiguousBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
Normalizes different forms of functional groups (e.g.
normalizeCoordinates() - Method in class com.actelion.research.chem.coords.InventorTemplate
 
normalizeEnantiomer() - Method in class com.actelion.research.chem.Canonizer
This normalizes all absolute tetrahedral-, allene- and atrop-parities within the molecule.
normalizeESRGroups() - Method in class com.actelion.research.chem.CanonizerMesoHelper
If a meso fragment contains stereo atoms belonging to ESR groups then there may be an alternative way of specifying the same meso fragment because of the symmetry of the fragment.
normalizeESRGroupSwappingAndRemoval(int[]) - Method in class com.actelion.research.chem.CanonizerMesoHelper
 
normalizeID(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
 
normalizeValue(double) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
normalizeValue(double) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
 
normSquared() - Method in class com.actelion.research.chem.phesa.Quaternion
 
NOSTEREO - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
 
NOSTEREO_TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
 
NOT_SET - com.actelion.research.chem.forcefield.mmff.RingBoolean
 
NOTSRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
NOTSRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
NULL_MATCH_SCALING - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
NUM_BONDS_START_REGRESSION_SMALL_MOLECULE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
NUM_BYTES_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
NUM_CONFORMATIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
number(String) - Static method in class com.actelion.research.chem.PeriodicTable
 
NUMBER_ELEMENTS - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
 

O

OBJECT_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
OBJECT_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
ObjectiveExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
 
ObjectiveExhaustiveStatistics() - Constructor for class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
ObjectiveFlexophoreHardMatchUncovered - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
ObjectiveFlexophoreHardMatchUncovered The weighting of the coverage is hard.
ObjectiveFlexophoreHardMatchUncovered() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
ObjectiveFlexophoreHardMatchUncovered(int, int, double, double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
 
OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
ODE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
 
ODEFileParser - Class in com.actelion.research.chem.io
 
ODEFileParser(File) - Constructor for class com.actelion.research.chem.io.ODEFileParser
 
ODEFileParser(Reader) - Constructor for class com.actelion.research.chem.io.ODEFileParser
 
ODEFileParser(String) - Constructor for class com.actelion.research.chem.io.ODEFileParser
 
OEM_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
onActionEnter() - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
onActionLeave() - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onAddBond(int, int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
onChange() - Method in interface com.actelion.research.share.gui.editor.listeners.IChangeListener
 
onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
 
onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
 
onCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CleanAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.ClearAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CutAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
 
onCommand() - Method in class com.actelion.research.share.gui.editor.actions.UndoAction
 
onDoubleClick(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
 
onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
 
onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
onDragEnter() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
onDragEnter() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
onDragEnter() - Method in class com.actelion.research.gui.JChemistryView
 
onDragEnter() - Method in class com.actelion.research.gui.JStructureView
 
onDragExit() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
onDragExit() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
onDragExit() - Method in class com.actelion.research.gui.JChemistryView
 
onDragExit() - Method in class com.actelion.research.gui.JStructureView
 
onDragOver() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
 
onDragOver() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
 
onDragOver() - Method in class com.actelion.research.gui.JChemistryView
 
onDragOver() - Method in class com.actelion.research.gui.JStructureView
 
onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
 
onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
 
onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
 
onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
 
onDrop() - Method in class com.actelion.research.gui.JChemistryView
 
onDrop() - Method in class com.actelion.research.gui.JStructureView
 
onDropMolecule(StereoMolecule, Point) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
onDropReaction(Reaction, Point) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
ONE_FOUR - com.actelion.research.chem.forcefield.mmff.Separation.Relation
 
ONE_ONE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
 
ONE_THREE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
 
ONE_TWO - com.actelion.research.chem.forcefield.mmff.Separation.Relation
 
ONE_X - com.actelion.research.chem.forcefield.mmff.Separation.Relation
 
onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.AtomHighlightCallback
 
onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.BondHighlightCallback
 
onKeyPressed(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onKeyReleased(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onMouseDown(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
Handles Mouse down events
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
onMouseMove(IMouseEvent, boolean) - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
onMouseUp(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
Handles the MouseUp event
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.UnknownParityAction
 
onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
oop - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
openDocument(String) - Static method in class com.actelion.research.util.Platform
Given a filename, open this file with the default application
openReader(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
 
optimalDist - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
optimalStrength - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
optimize(Evaluable) - Method in class com.actelion.research.chem.optimization.OptimizerLBFGS
Optimization routine using the limited Broyden-Fletcher-Goldfarb-Shanno algorithm
optimize(SelfOrganizedConformer, int, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
OPTIMIZE_RIGID_FRAGS - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
 
optimize3D - Variable in class com.actelion.research.chem.io.AbstractParser
 
optimizeAtomCoordinates(int) - Method in class com.actelion.research.chem.coords.InventorFragment
 
OptimizerLBFGS - Class in com.actelion.research.chem.optimization
taken from DD_chem3d, small changes necessary because a different output structure is needed it returns not only a value (the objective function), but the transformation array for achieving the best alignment
OptimizerLBFGS(int, double) - Constructor for class com.actelion.research.chem.optimization.OptimizerLBFGS
 
OR(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
Makes an logical OR and calculates the hash code.
OR(List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
Makes an logical OR and calculates the hash code.
org.openmolecules.chem.conf.gen - package org.openmolecules.chem.conf.gen
 
org.openmolecules.chem.conf.so - package org.openmolecules.chem.conf.so
 
originalToExtendedAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
 
OUT_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_DEVICE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_RASTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_SEPARATOR_COL - Static variable in class com.actelion.research.calc.Matrix
 
OUT_SEPARATOR_ROW - Static variable in class com.actelion.research.calc.Matrix
 
OUT_STRING_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OUT_TT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff
Out of plane energy term class.
OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff.table
 
OutOfPlane(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.OutOfPlane
Construct a new out of plane energy term.
OutOfPlane(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
 
overlapDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
Oxygen - Static variable in class com.actelion.research.chem.PeriodicTable
 

P

p - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
 
PACKAGE_DATAWARRIOR_IDORSIA - Static variable in class com.actelion.research.util.ConstantsDWAR
 
paint(IDrawContext) - Method in interface com.actelion.research.share.gui.editor.actions.Action
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
 
paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
paint(IDrawContext<T>) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
 
paint(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
 
paint(Object) - Method in class com.actelion.research.chem.AbstractDepictor
 
paint(Object) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
paint(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JChemistryView
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawArea
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableChemistryView
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableStructureView
 
paintComponent(Graphics) - Method in class com.actelion.research.gui.JStructureView
 
paintDrawingObjects(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
 
paintDrawingObjects(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
paintFragmentNumbers(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
 
paintFragmentNumbers(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
paintIcon(Component, Graphics, int, int) - Method in class com.actelion.research.gui.hidpi.HiDPIIcon
 
paintStructures(Object) - Method in class com.actelion.research.chem.ExtendedDepictor
 
paintStructures(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
 
PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
 
PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
 
PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
 
PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
 
PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
 
PARA_TAG_HISTOGRAM_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
PARA_TAG_MODE_MATCH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
PARA_TAG_PPNODE_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
ParameterizedStringList - Class in com.actelion.research.chem.prediction
 
ParameterizedStringList() - Constructor for class com.actelion.research.chem.prediction.ParameterizedStringList
 
parent - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
parse(Reaction, BufferedReader) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(Reaction, BufferedReader, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(Reaction, File) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(Reaction, File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(Reaction, String) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(Reaction, String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
 
parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.SmilesParser
 
parse(StereoMolecule, byte[], boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
 
parse(StereoMolecule, byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(StereoMolecule, byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(StereoMolecule, byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(StereoMolecule, byte[], int, int) - Method in class com.actelion.research.chem.SmilesParser
 
parse(StereoMolecule, byte[], int, int, boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
 
parse(StereoMolecule, BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
 
parse(StereoMolecule, File) - Method in class com.actelion.research.chem.MolfileParser
 
parse(StereoMolecule, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(StereoMolecule, String) - Method in class com.actelion.research.chem.MolfileParser
 
parse(StereoMolecule, String) - Method in class com.actelion.research.chem.SmilesParser
Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
parse(StereoMolecule, StringBuffer) - Method in class com.actelion.research.chem.MolfileParser
 
parse(StereoMolecule, String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
Parses the idcode and populates the given molecule to represent the passed idcode.
parse(BufferedInputStream) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
parse(BufferedReader) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
parse(File) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
parse(String[]) - Method in class com.actelion.research.util.CommandLineParser
 
parse(List<String>, int, List<AtomRecord>, List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
 
parseCoordinates(byte[], int, StereoMolecule, Coordinates[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
This method parses an id-coordinate string (new format only) and writes the coordinates into a Coordinates array.
parseDate(String) - Static method in class com.actelion.research.util.Formatter
 
parseDateTime(String) - Static method in class com.actelion.research.util.Formatter
 
parseInteger(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
 
parseInteger(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
parseLong(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
 
parseMapping(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
parseMapping(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
parseReaction(byte[]) - Method in class com.actelion.research.chem.SmilesParser
 
parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
paste() - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
PASTE_AND_DROP_OPTION_ALLOW_FRAGMENT_STATE_CHANGE - Static variable in class com.actelion.research.gui.JChemistryView
 
PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS - Static variable in class com.actelion.research.gui.JChemistryView
 
PASTE_AND_DROP_OPTION_KEEP_BOND_HIGHLIGHTING - Static variable in class com.actelion.research.gui.JChemistryView
 
PASTE_AND_DROP_OPTION_LAYOUT_REACTION - Static variable in class com.actelion.research.gui.JChemistryView
 
PASTE_AND_DROP_OPTION_REMOVE_CATALYSTS - Static variable in class com.actelion.research.gui.JChemistryView
 
PASTE_AND_DROP_OPTION_REMOVE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JChemistryView
 
PasteAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 5/16/13 Time: 3:39 PM
PasteAction(Model, Dimension) - Constructor for class com.actelion.research.share.gui.editor.actions.PasteAction
 
pasteImage() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
 
pasteImage() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
pasteImage() - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
 
pasteMolecule() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Get one Molecule from the Clipboard.
pasteMolecule() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
pasteMolecule() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
 
pasteMolecule(boolean) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
 
pasteMolecule(double, double) - Method in class com.actelion.research.share.gui.editor.Model
 
pasteMolecules() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Get one or more Molecule(s) from the Clipboard.
pasteMolecules() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
pasteReaction() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
Get a Reaction from the Clipboard
pasteReaction() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
 
pasteReaction() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
 
pasteReaction(double, double) - Method in class com.actelion.research.share.gui.editor.Model
 
pasteReactionWindowsNative() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
 
pasteText() - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
 
PAT_NOT_ALPHANUMERIC - Static variable in class com.actelion.research.util.StringFunctions
 
PAT_WHITESPACE - Static variable in class com.actelion.research.util.StringFunctions
 
PATCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PATINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PATPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PATTERN_NF_DWAR - Static variable in class com.actelion.research.util.ConstantsDWAR
 
PATTERN_NF_DWAR4 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
PDBCoordEntryFile - Class in com.actelion.research.chem.io.pdb.parser
PDBCoordEntryFile
PDBCoordEntryFile() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
PDBFileParser - Class in com.actelion.research.chem.io.pdb.parser
PDBFileParser
PDBFileParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
peek() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
Peek the first element of the Queue (do not increment the queue index)
peek() - Method in class com.actelion.research.util.IntQueue
Peek the first element of the Queue (do not increment the queue index)
perceivedBrightness(Color) - Static method in class com.actelion.research.util.ColorHelper
This is a color's perceived brightness by the human eye
performMutation(StereoMolecule, Mutation) - Method in class com.actelion.research.chem.Mutator
Performs the given mutation on the molecule, updates atom coordinates, and updates stereo bonds to reflect lost or new stereo centers.
PeriodicTable - Class in com.actelion.research.chem.forcefield.mmff
 
PeriodicTable - Class in com.actelion.research.chem
 
PERIPHERY_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
PharmacophoreCalculator - Class in com.actelion.research.chem.phesa.pharmacophore
 
PharmacophoreNode - Class in com.actelion.research.chem.descriptor.pharmacophoretree
A PharmacophoreNode represents a node in a PharmacophoreTree.
PharmacophoreNode(List<Integer>, int[][], double[]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
PharmacophoreNode(List<Integer>, int[][], double[], int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
PharmacophoreNode(List<Integer>, int[], List<Double>, List<Double>, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
PharmacophorePointFactory - Class in com.actelion.research.chem.phesa.pharmacophore
 
PharmacophorePointFactory() - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PharmacophorePointFactory
 
PharmacophoreTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon (DOI:10.1023/a:1008068904628).
PharmacophoreTree(List<PharmacophoreNode>, List<int[]>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
PharmacophoreTree.BiGramInt - Class in com.actelion.research.chem.descriptor.pharmacophoretree
container of an undirected edge
PharmacophoreTreeGenerator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
Generates a PharmacophoreTree from a StereoMolecule.
PHESA - com.actelion.research.chem.docking.DockingEngine.StartPosition
 
PheSAAlignment - Class in com.actelion.research.chem.phesa
 
PheSAAlignment(MolecularVolume, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
 
PheSAAlignment(MolecularVolume, MolecularVolume, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
 
PheSAAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
 
PheSAAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
 
PheSAAlignment.axis - Enum in com.actelion.research.chem.phesa
 
PheSAAlignment.PheSAResult - Class in com.actelion.research.chem.phesa
 
PheSAAlignmentOptimizer - Class in com.actelion.research.chem.alignment3d
 
PheSABindingHypothesis - Class in com.actelion.research.chem.phesa
 
PheSABindingHypothesis(List<StereoMolecule>) - Constructor for class com.actelion.research.chem.phesa.PheSABindingHypothesis
 
PheSABindingHypothesis(List<StereoMolecule>, int) - Constructor for class com.actelion.research.chem.phesa.PheSABindingHypothesis
 
PheSAMolecule - Class in com.actelion.research.chem.phesa
 
PheSAMolecule() - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
 
PheSAMolecule(StereoMolecule, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
 
PheSAMolecule(StereoMolecule, ArrayList<MolecularVolume>) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
 
PheSAResult(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
 
PHOSPHONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
Phosphorus - Static variable in class com.actelion.research.chem.PeriodicTable
 
PI - Static variable in class com.actelion.research.util.Sketch
 
pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
pilp(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the PILP type of an atom given its MMFF type.
Pipeline<T> - Class in com.actelion.research.util
Pipeline Enables concurrent access to a queue.
Pipeline() - Constructor for class com.actelion.research.util.Pipeline
 
Pipeline(List<T>) - Constructor for class com.actelion.research.util.Pipeline
The 'all data in' flag is set true.
PlaneRule - Class in org.openmolecules.chem.conf.so
 
PlaneRule(int[], StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.PlaneRule
 
Platform - Class in com.actelion.research.util
Requires JRE 1.6
Platform() - Constructor for class com.actelion.research.util.Platform
 
PLATFORM_NAME_DATAWARRIOR - Static variable in class com.actelion.research.util.ConstantsDWAR
 
PLPTerm - Class in com.actelion.research.chem.docking.scoring.plp
piecewise linear potential (PLP) as described in doi:10.1021/ci800298z parameters from model 3 (M3)
plus(Matrix) - Method in class com.actelion.research.calc.Matrix
 
plus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
plus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
plus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
 
PointDouble - Class in com.actelion.research.util.datamodel
 
PointDouble() - Constructor for class com.actelion.research.util.datamodel.PointDouble
 
PointDouble(double, double) - Constructor for class com.actelion.research.util.datamodel.PointDouble
 
PointDouble(Point) - Constructor for class com.actelion.research.util.datamodel.PointDouble
 
PointUtils - Class in com.actelion.research.util
 
PointUtils() - Constructor for class com.actelion.research.util.PointUtils
 
PolarSurfaceAreaPredictor - Class in com.actelion.research.chem.prediction
This class predicts the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
PolarSurfaceAreaPredictor() - Constructor for class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
 
pollAll() - Method in class com.actelion.research.util.Pipeline
 
pollAllWithWait() - Method in class com.actelion.research.util.Pipeline
all data in flag has to be set.
pollData() - Method in class com.actelion.research.util.Pipeline
 
polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
 
Polygon - Class in com.actelion.research.share.gui
 
Polygon() - Constructor for class com.actelion.research.share.gui.Polygon
 
polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
 
Polynome(double[]) - Constructor for class com.actelion.research.util.FastSpline.Polynome
 
polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.MetaFile
 
polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMF
 
pop() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
Pop the first element of the Queue
pop() - Method in class com.actelion.research.util.IntQueue
Pop the first element of the Queue
popUndo() - Method in class com.actelion.research.share.gui.editor.Model
 
POS_CHARGE - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
 
PositionConstraint - Class in com.actelion.research.chem.forcefield.mmff
 
PositionConstraint(StereoMolecule, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.PositionConstraint
 
PotentialEnergyTerm - Interface in com.actelion.research.chem.potentialenergy
 
pow(double) - Method in class com.actelion.research.calc.Matrix
 
power - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
PPGaussian - Class in com.actelion.research.chem.phesa.pharmacophore
 
PPGaussian(int, IPharmacophorePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
PPGaussian(PPGaussian) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
PPNode - Class in com.actelion.research.chem.descriptor.flexophore
 
PPNode() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
 
PPNode(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
 
PPNodeRGroup - Class in com.actelion.research.chem.descriptor.flexophore.entity
PPNodeStructure
PPNodeRGroup() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
PPNodeRGroup(PPNode, String) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
PPNodeSimilarity - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
PPNodeSimilarity
PPNodeSimilarity(int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
This constructor is used for parallel mode.
PPNodeViz - Class in com.actelion.research.chem.descriptor.flexophore
 
PPNodeViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
PPNodeViz(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
PPNodeViz(PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
PPNodeVizTriangle - Class in com.actelion.research.chem.descriptor.flexophore
 
PPNodeVizTriangle(PPNodeViz, PPNodeViz, PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
PPTriangle - Class in com.actelion.research.chem.phesa.pharmacophore
 
PPTriangle(IPharmacophorePoint, IPharmacophorePoint, IPharmacophorePoint, double, double, double, Coordinates) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
 
PPTriangleCreator - Class in com.actelion.research.chem.phesa.pharmacophore
 
PPTriangleMatcher - Class in com.actelion.research.chem.phesa.pharmacophore
 
PPTriangleMatcher.AlignmentResult - Class in com.actelion.research.chem.phesa.pharmacophore
 
ppWeight - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
predictAtomSequence(StereoMolecule, int, int[], int[]) - Static method in class com.actelion.research.chem.conf.BondRotationHelper
 
preferredLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
Description of the Method
PREFIX_OUTPUT - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
 
PREOPTIMIZED - Static variable in class com.actelion.research.chem.Molecule3D
 
preProcess(Conformer, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system
PRINT_DEBUG_INDEXES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
PRINT_ELIMINATION_RULES_WITH_STRUCTURES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
PRINT_EXIT_REASON - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
PRINT_TORSION_AND_FRAGMENT_LIKELYHOODS - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
printAtomType(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
printAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
printContent(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
 
printMutationList(ArrayList<Mutation>, boolean) - Method in class com.actelion.research.chem.Mutator
 
printTime(double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
process(InputObjectFracDimCalc) - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
 
process(Pipeline<StereoMolecule>, int, boolean, boolean) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
 
process(List<StereoMolecule>, File) - Method in class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
 
processMolecule(StereoMolecule, TreeSet<String>) - Method in class com.actelion.research.chem.AtomTypeList
 
PRODUCT_IDENTIFIER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
ProgressController - Interface in com.actelion.research.calc
 
ProgressListener - Interface in com.actelion.research.calc
 
PROOF_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PropertyCalculator - Class in com.actelion.research.chem
 
PropertyCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.PropertyCalculator
 
PROTEIN_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
 
ProteinSynthesizer - Class in com.actelion.research.chem.io.pdb.parser
 
ProteinSynthesizer() - Constructor for class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
 
PS_DASH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_DASHDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_DASHDOTDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_DOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_INSIDEFRAME - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
PURITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
 
push(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
Push an element on top of the queue
push(int) - Method in class com.actelion.research.util.IntQueue
Push an element on top of the queue
pushUndo() - Method in class com.actelion.research.share.gui.editor.Model
 
putContent(Clipboard) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
putImage(Image) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
Deprecated.
You may use ImageClipboardHandler.copyImage for consistency reasons

Q

qualifiesAsAmideTypeBond(int) - Method in class com.actelion.research.chem.RingCollection
Checks, whether this bond may contribute pi-electrons from an amide-resonance to an aromatic ring.
Quaternion - Class in com.actelion.research.chem.phesa
 
Quaternion(double, double, double, double) - Constructor for class com.actelion.research.chem.phesa.Quaternion
 
Quaternion(Coordinates, double) - Constructor for class com.actelion.research.chem.phesa.Quaternion
 
quickExp(double) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
 
QuickMathCalculator - Class in com.actelion.research.chem.phesa
 

R

r_star(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
Returns 'R*' which is derived from the table.
r0 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
 
r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
Returns 'r0' the ideal bond length at a given index in the Bndk table.
r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
Returns the 'r0' value at the given index from the Bond table.
r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
Returns the 'r0' (or covRad) parameter from the table given an index.
r0(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
r0i - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
r0k - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
R2_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_COPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MASKNOTPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MASKPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MERGENOTPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_MERGEPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOTCOPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOTMASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOTMERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_NOTXORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_WHITE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
R2_XORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
RAD2DEG - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
 
random() - Static method in class com.actelion.research.chem.Coordinates
 
RANDOM - com.actelion.research.chem.docking.DockingEngine.StartPosition
 
RANDOM - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
randomPerturbation(Random) - Method in class com.actelion.research.chem.docking.LigandPose
 
randomVectorInSphere(Random) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
RANGE_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
Range histogram in Angstrom.
RangeStatistics() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
 
rank() - Method in class com.actelion.research.calc.SingularValueDecomposition
Effective numerical matrix rank
RDFileParser - Class in com.actelion.research.chem.io
Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
RDFileParser(File) - Constructor for class com.actelion.research.chem.io.RDFileParser
 
RDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.RDFileParser
 
RDFileParser(String) - Constructor for class com.actelion.research.chem.io.RDFileParser
 
Reaction - Class in com.actelion.research.chem.reaction
 
Reaction() - Constructor for class com.actelion.research.chem.reaction.Reaction
 
Reaction(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reaction
 
Reaction(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.reaction.Reaction
 
Reaction(String) - Constructor for class com.actelion.research.chem.reaction.Reaction
 
REACTION_CENTER_LONG_COUNT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
REACTION_CENTER_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
 
REACTION_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
 
REACTION_TYPE_NOMOLS - Static variable in class com.actelion.research.chem.ChemistryHelper
 
REACTION_TYPE_NOPRODUCTS - Static variable in class com.actelion.research.chem.ChemistryHelper
 
REACTION_TYPE_NORMAL - Static variable in class com.actelion.research.chem.ChemistryHelper
 
REACTION_TYPE_REACTANTS - Static variable in class com.actelion.research.chem.ChemistryHelper
 
ReactionArrow - Class in com.actelion.research.chem.reaction
 
ReactionArrow() - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
 
ReactionArrow(String) - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
 
ReactionDragAdapter - Class in com.actelion.research.gui.dnd
 
ReactionDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.ReactionDragAdapter
 
ReactionDropAdapter - Class in com.actelion.research.gui.dnd
 
ReactionDropAdapter() - Constructor for class com.actelion.research.gui.dnd.ReactionDropAdapter
 
ReactionEncoder - Class in com.actelion.research.chem.reaction
 
ReactionSearch - Class in com.actelion.research.chem.reaction
 
ReactionSearch(ReactionSearchSpecification, ReactionSearchDataSource, StructureSearchController, ProgressController) - Constructor for class com.actelion.research.chem.reaction.ReactionSearch
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
ReactionSearchDataSource - Interface in com.actelion.research.chem.reaction
 
ReactionSearchSpecification - Class in com.actelion.research.chem.reaction
 
ReactionSearchSpecification(int, String[], long[][], long[][], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
Creates a complete specification for a reaction substructure search with one or more query generic reactions.
ReactionSearchSpecification(int, String[], long[][], long[][], long[][], float, float) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
Creates a complete specification for a reaction similarity search with one or more query reactions.
ReactionSearchSpecification(String[], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
Creates a complete specification for a retron search with one or more query retron substructures.
ReactionTransferable - Class in com.actelion.research.gui.dnd
 
ReactionTransferable(Reaction) - Constructor for class com.actelion.research.gui.dnd.ReactionTransferable
 
Reactor - Class in com.actelion.research.chem.reaction
 
Reactor(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reactor
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
Reactor(Reaction, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
Reactor(Reaction, boolean, boolean, int, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
Deprecated.
Reactor(Reaction, int, int) - Constructor for class com.actelion.research.chem.reaction.Reactor
Constructs a Reactor that is able to build products from a generic reaction (transformation) and a list of real world reactants.
read() - Method in class com.actelion.research.util.BinaryDecoder
 
read(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
read(File) - Static method in class com.actelion.research.util.datamodel.IntVec
 
read(File) - Static method in class com.actelion.research.util.datamodel.ScorePoint
 
read(File) - Static method in class com.actelion.research.util.IO
 
read(InputStream) - Static method in class com.actelion.research.chem.mcs.ListWithIntVec
 
read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
 
read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
 
read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntVec
 
read(InputStream) - Static method in class com.actelion.research.util.IO
 
read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
read(String) - Static method in class com.actelion.research.util.datamodel.IntArray
 
read(String) - Method in class com.actelion.research.util.datamodel.IntVec
 
readBetweenTags(String, String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
 
readBitStringDense(File) - Static method in class com.actelion.research.util.datamodel.IntVec
 
readBitStringDense(String) - Static method in class com.actelion.research.util.datamodel.IntVec
 
readBoolean() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readChar() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readContent(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
readDouble() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readDoubleArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
readDoubleArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
readEncoded(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
 
readFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
Read a file at location 'path' and parse it as a CSV file.
readFloat() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readFromFile() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
readFromTag(String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
Reads all lines after a given tag and stores the lines as Strings in a vector object.
readFully(byte[]) - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readFully(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readIDCodesFromFile() - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
readIDCodesFromFile(File) - Method in class com.actelion.research.chem.io.CompoundFileHelper
Reads all compounds as idcode list from the given file.
readIDCodesWithNamesFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
Reads all compounds as idcode list with identifiers from the given file.
readInput(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
readInt() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readIntArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
Separator is ','.
readIntArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
readIntsFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
A helper function that casts and returns a CSV file consisting entirely of ints on all rows and columns.
readLine() - Method in class com.actelion.research.io.StringReadChannel
 
readLine() - Method in class com.actelion.research.util.LittleEndianDataInputStream
Deprecated.
readLine(InputStream) - Static method in class com.actelion.research.util.IO
 
readLine(Reader) - Static method in class com.actelion.research.util.IO
 
readLine(FileChannel) - Static method in class com.actelion.research.util.IO
 
readLines2DoubleArray(File) - Static method in class com.actelion.research.util.IO
 
readLines2IntArray(File) - Static method in class com.actelion.research.util.IO
Reads a file that contains one int per line.
readLines2List(File) - Static method in class com.actelion.research.util.IO
 
readLines2List(InputStream) - Static method in class com.actelion.research.util.IO
The stream is not closed.
readLines2List(List<File>) - Static method in class com.actelion.research.util.IO
 
readListIntger(File) - Static method in class com.actelion.research.util.IO
 
readLong() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
reads a MolDistHist from the toString() method.
readSerialized(File) - Static method in class com.actelion.research.calc.Matrix
 
readShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readStructuresFromFile(boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
readStructuresFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
readUnsignedByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readUnsignedShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readUTF() - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
readUTF(DataInput) - Static method in class com.actelion.research.util.LittleEndianDataInputStream
 
readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
Resizes the node array to the needed length.
realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
realize() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
May be called after finishing adding new interaction types.
recalculateCoordPPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Recalculates the coordinates off the pharmacophore nodes.
recentException - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
receptorConf - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
receycle(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
rect - Variable in class com.actelion.research.share.gui.Arrow
 
rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
RED - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
reduce(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntVec
Removes all values with no corresponding index in the list.
reduce(Vector<Integer>) - Method in class com.actelion.research.util.datamodel.ByteVec
 
reduce(Vector<Integer>) - Method in class com.actelion.research.util.DoubleVec
 
REGEX_FILE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
 
REGEX_META_CHARACTERS - Static variable in class com.actelion.research.util.StringFunctions
 
registerAtomHighlightCallback(Model.AtomHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
 
registerBondHighlightCallback(Model.BondHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
 
registerDragEvent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
regress() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
rel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
 
RemarkParser - Class in com.actelion.research.chem.io.pdb.parser
RemarkParser
RemarkParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.RemarkParser
 
remove(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
remove(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
remove(int) - Method in class com.actelion.research.util.hash.HashSetInt
 
remove(int) - Method in class com.actelion.research.util.SortedList
 
remove(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
 
remove(Point2D) - Method in class com.actelion.research.share.gui.Polygon
 
removeAll() - Method in class com.actelion.research.util.SortedList
 
removeAllAtomsWithoutNeighbours(Molecule3D) - Static method in class com.actelion.research.chem.Molecule3DFunctions
 
removeAllStrings() - Method in class com.actelion.research.chem.SortedStringList
 
removeAtomColors() - Method in class com.actelion.research.chem.Molecule
 
removeAtomCustomLabels() - Method in class com.actelion.research.chem.Molecule
This removes all custom labels from the atoms.
removeAtomMarkers() - Method in class com.actelion.research.chem.Molecule
 
removeAtomSelection() - Method in class com.actelion.research.chem.Molecule
 
removeBondHiliting() - Method in class com.actelion.research.chem.Molecule
 
removeCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
 
removeChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
 
removeCharacter(StringBuilder, char) - Static method in class com.actelion.research.util.StringFunctions
 
removeCharacter(String, char) - Static method in class com.actelion.research.util.StringFunctions
 
removeCol(int) - Method in class com.actelion.research.calc.Matrix
 
removeCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
removeCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
removeDescriptors() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
removeDescriptors() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
removeDoubletsInt(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
removeDoubletsIntOrderIndepend(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
Removes arrays which contains identical integer.
removeDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
 
removeExplicitHydrogens() - Method in class com.actelion.research.chem.ExtendedMolecule
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
removeExplicitHydrogens(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
removeExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
Provided that filePath has a recognized extension, then the extension is removed.
removeInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
removeLast() - Method in class com.actelion.research.util.datamodel.IntArray
 
removeLayoutComponent(Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
Description of the Method
removeLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
removeLonePairs(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
removeMapping(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
 
removeMappingNo(int) - Method in class com.actelion.research.chem.Molecule
 
removeNode(PharmacophoreNode) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
 
removePathAndExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
Provided that fileName has a leading file path, then path and separator are removed.
removeProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
 
removeQueryFeatures() - Method in class com.actelion.research.chem.Molecule
Removes any query features from the molecule
removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
 
removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
 
removeSubstructureFromMolecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
removeSubStructures(List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Removes all molecules that are a substructure of one of the molecules in the input list.
removeSubstructuresFromMolecule(StereoMolecule, List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
Deletes the substructures, if found, in the molecule.
removeValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
 
removeValue(int) - Method in class com.actelion.research.util.datamodel.IntArray
Computational expensive operation!
removeWater(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
removeWater(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
removeWaterSalts(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
removeWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
renumberESRGroups(int) - Method in class com.actelion.research.chem.Molecule
For the given ESR type (AND or OR) renumbers all group indexes starting from 0.
reorderAtoms() - Method in class com.actelion.research.chem.Molecule3D
Reorganizes atom indexes, so that moveable atoms are first
repairLig(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
 
replaceAtoms(ExtendedMolecule[], int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
replaceAtoms(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
replaceLigand(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
replaceLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Replaces the preoptimized ligand in mol
REPTerm - Class in com.actelion.research.chem.docking.scoring.plp
repulsive term, see PLPTerm for reference
reset() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
 
reset() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
reset() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
reset() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
reset() - Method in class com.actelion.research.util.datamodel.IntArray
 
reset() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
 
reset() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
 
reset() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
reset() - Method in class com.actelion.research.util.Pipeline
Sets all to 0 and allDataIn to false..
reset(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
Clears the hash map with the records that contain the given number of bits set.
resetAllCounters() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
 
resetFragments(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
 
resetInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
Residue - Class in com.actelion.research.chem.io.pdb.parser
ModelGroupAtoms handles a group of atoms, e.g.
Residue(List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.Residue
 
resize(boolean[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(boolean[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(boolean[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(double[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
resize(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
resize(int[], int) - Static method in class com.actelion.research.util.datamodel.IntArray
 
resize(int, int) - Method in class com.actelion.research.calc.Matrix
Resizes the matrix, the old data are written to the new matrix, if possible.
resize(Object, int) - Static method in class com.actelion.research.util.ArrayUtils
Resize an array
resize(String[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
Resize an array of Object
resolve(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
 
resolveLocal(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
Local and typically quick name resolution
resolveLocal(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
resolveRemote(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
Typically remote server based name resolution that requires a network round trip
resolveRemote(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
resolveRemote(String[]) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
Remote server based name resolution of multiple names packed into one network round trip
resolveRemote(String[]) - Static method in class com.actelion.research.chem.name.StructureNameResolver
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name list, i.e.
RESOURCE_AAS_LABELED - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
 
restore() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
restore() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
restoreState() - Method in class com.actelion.research.gui.JDrawArea
 
restrainedRelaxation(StereoMolecule, double) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
 
ResultFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
ResultFracDimCalc
ResultFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
ResultFragmentsStatistic - Class in com.actelion.research.chem.properties.complexity
 
ResultFragmentsStatistic(StereoMolecule, List<ModelExhaustiveStatistics>) - Constructor for class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
ResultObjective - Class in com.actelion.research.chem.properties.complexity
 
ResultObjective() - Constructor for class com.actelion.research.chem.properties.complexity.ResultObjective
 
RETAIN_REACTANT_AND_PRODUCT_ORDER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
 
retrieveHighestValuesFrom2DArray(double[][], double[], int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
 
retrieveProtein() - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
 
reverse(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
reverse(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
reverse(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
RGROUPS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
 
RIGHT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
Description of the Field
RIGID - Static variable in class com.actelion.research.chem.Molecule3D
 
RigidFragment - Class in org.openmolecules.chem.conf.gen
 
RigidFragment(int, int[], int[], int[], int[], Conformer[], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragment
 
RigidFragmentCache - Class in org.openmolecules.chem.conf.gen
This class implements a thread-save, concurrent cache of rigid fragments' 3D-atom-coordinates.
RigidFragmentCache.CacheEntry - Class in org.openmolecules.chem.conf.gen
 
RigidFragmentProvider - Class in org.openmolecules.chem.conf.gen
An instance of this class is used by any ConformerGenerator to hand out one or multiple 3D-coordinate sets for rigid fragments within a molecules.
RigidFragmentProvider(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentProvider
 
rik2 - Variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
 
RingBoolean - Enum in com.actelion.research.chem.forcefield.mmff
 
RingCollection - Class in com.actelion.research.chem
 
RingCollection(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.RingCollection
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic.
RingCollection(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.RingCollection
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic.
ringIsMMFFAromatic(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
Determine if a ring is aromatic according to MMFF criteria.
ringIsMMFFAromatic(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
Determine if a ring is aromatic according to MMFF criteria.
RISK_NAME - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
 
rot(long, long) - Static method in class com.actelion.research.util.BurtleHasher
 
RotatableBond - Class in org.openmolecules.chem.conf.gen
A RotatableBond knows the two rigid fragments within a molecule that are connected by this bond.
RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
 
RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
 
rotate(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
rotate(double[][]) - Method in class com.actelion.research.chem.Coordinates
 
rotate(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
 
rotate(double, double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
rotate(Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
 
rotateAroundBond(int, double, Conformer, boolean) - Method in class com.actelion.research.chem.conf.BondRotationHelper
rotate torsion angle of a conformer
rotateAtom(Conformer, int, int, Coordinates, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
rotateBond(Molecule3D, int, int, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
Make sure the parity of mol match the one from ref, otherwise fix it.
rotateC(double[][]) - Method in class com.actelion.research.chem.Coordinates
 
rotateLigand(Molecule3D, double, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
rotateMol(Conformer, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(Conformer, Matrix) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(Conformer, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(StereoMolecule, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(StereoMolecule, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(StereoMolecule, Matrix) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateMol(StereoMolecule, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
rotateShift(Matrix) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
rotateSmallerSide(int, double) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
rotateTo(Conformer, short) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
Rotate the smaller side of the molecule around this bond to reach the defined torsion angle.
rotateToIndex(Conformer, int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
Rotate the smaller side of the molecule around this bond to reach the torsion angle defined by torsionIndex.
roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
row(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
Returns which row in the periodic table an atom with given atomic number is in.
row2Matrix(int, int) - Method in class com.actelion.research.calc.Matrix
 
rowFromESRType(int) - Static method in class com.actelion.research.share.gui.editor.Model
 
rowQualifies(int) - Method in interface com.actelion.research.chem.StructureSearchController
If the structure search specification is part of a broader criteria list, then this method determines, whether all other, i.e.
rows() - Method in class com.actelion.research.calc.Matrix
 
rowtm(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
Returns which row in the periodic table an atom is in with transition metals having their row number multiplied by 10.
rstar_ij - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
RULE_NAME - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_BINAP - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_DISTANCE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_LINE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_PLANE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_STEREO - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
RULE_TYPE_TORSION - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
 
run() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
 
run_minimiser(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
RunBondVector2IdCode - Class in com.actelion.research.chem.mcs
 
RunBondVector2IdCode(int, Pipeline<IBitArray>, Pipeline<FragmentDefinedByBondsIdCode>) - Constructor for class com.actelion.research.chem.mcs.RunBondVector2IdCode
 
RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileCreator
 
RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileV3Creator
 
RXNFileCreator - Class in com.actelion.research.chem.io
 
RXNFileCreator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
 
RXNFileCreator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
 
RXNFileParser - Class in com.actelion.research.chem.io
 
RXNFileParser() - Constructor for class com.actelion.research.chem.io.RXNFileParser
 
RXNFileV3Creator - Class in com.actelion.research.chem.io
 
RXNFileV3Creator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
 
RXNFileV3Creator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
 

S

s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
Function used in swapping variables in one line.
s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
 
save() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
save() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
 
save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
 
save(Molecule3D, String) - Method in class com.actelion.research.chem.io.AbstractParser
 
save(List<Molecule3D>, int, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
Writes also the partial charges
save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
If not subclassed, save the files separately
save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
 
save(List<Molecule3D>, String) - Method in class com.actelion.research.chem.io.AbstractParser
 
saveRXNFile(Reaction) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
sbmb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the SBMB type of an atom given its MMFF type.
ScaffoldHelper - Class in com.actelion.research.chem
 
ScaffoldHelper() - Constructor for class com.actelion.research.chem.ScaffoldHelper
 
scale(double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
scale(double) - Method in class com.actelion.research.chem.Coordinates
 
scale(double) - Method in class com.actelion.research.chem.TextDrawingObject
 
scale(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
scale(float) - Method in class com.actelion.research.share.gui.Arrow
 
scale(float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
scale(float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
scale(float, float) - Method in class com.actelion.research.share.gui.editor.Model
 
scale(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
This is a convenience method that scales the passed int value with getUIScaleFactor() and returns the rounded result.
scale(BufferedImage) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
 
SCALE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
scaleC(double) - Method in class com.actelion.research.chem.Coordinates
 
scaleCoords(double) - Method in class com.actelion.research.chem.Molecule
 
ScaledEditorKit - Class in com.actelion.research.gui.hidpi
 
ScaledEditorKit() - Constructor for class com.actelion.research.gui.hidpi.ScaledEditorKit
 
ScaledHTML - Class in com.actelion.research.gui.hidpi
 
ScaledHTML() - Constructor for class com.actelion.research.gui.hidpi.ScaledHTML
 
ScaledStyleSheet - Class in com.actelion.research.gui.hidpi
 
ScaledStyleSheet() - Constructor for class com.actelion.research.gui.hidpi.ScaledStyleSheet
 
scaleInto(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
scaleIntoF(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
scaleIntoOld(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
scaleRetinaAndUI(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
This is a convenience method that scales the passed int value with getUIScaleFactor() and with getRetinaScaleFactor() and returns the rounded result.
ScorePoint - Class in com.actelion.research.util.datamodel
 
ScorePoint() - Constructor for class com.actelion.research.util.datamodel.ScorePoint
 
ScorePoint(int, int) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
 
ScorePoint(int, int, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
 
ScorePoint(Point) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
 
ScorePoint(Point, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
 
ScrollPaneAutoScrollerWhenDragging - Class in com.actelion.research.gui
 
ScrollPaneAutoScrollerWhenDragging(JScrollPane, boolean) - Constructor for class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
 
Sdf - Class in com.actelion.research.chem.forcefield.mmff
The Sdf class provides helper functions for dealing with the SDF file format.
Sdf() - Constructor for class com.actelion.research.chem.forcefield.mmff.Sdf
 
SDF_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
 
Sdf.OnMolecule - Interface in com.actelion.research.chem.forcefield.mmff
 
SDFileMolecule - Class in com.actelion.research.chem
 
SDFileMolecule() - Constructor for class com.actelion.research.chem.SDFileMolecule
 
SDFileMolecule(Molecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
 
SDFileMolecule(SDFileMolecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
 
SDFileMoleculeDropAdapter - Class in com.actelion.research.gui.dnd
 
SDFileMoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
 
SDFileMoleculeTransferable - Class in com.actelion.research.gui.dnd
 
SDFileMoleculeTransferable(StereoMolecule, StructureInfo) - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
SDFileParser - Class in com.actelion.research.chem.io
 
SDFileParser(File) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SDFileParser(File, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SDFileParser(Reader, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SDFileParser(String) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SDFileParser(String, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
 
SE_RESIZE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
Search - Class in com.actelion.research.chem.forcefield.mmff
The search class provides binary searching on arrays.
Search() - Constructor for class com.actelion.research.chem.forcefield.mmff.Search
 
SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
 
SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.StructureSearchDataSource
 
Searchable - Interface in com.actelion.research.chem.forcefield.mmff
Interface that must be implemented for array objects that can be searched by the binary search function.
SEED - Static variable in class com.actelion.research.chem.docking.LigandPose
 
select(long[][], int) - Method in class com.actelion.research.chem.DiversitySelector
 
selectFileToOpen(String, int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
selectFileToOpen(String, int) - Method in class com.actelion.research.gui.FileHelper
 
selectFileToOpen(String, int, String) - Method in class com.actelion.research.gui.FileHelper
Shows a file-open-dialog, lets the user choose and returns the selected file.
selectFileToSave(String, int, String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
selectFileToSave(String, int, String) - Method in class com.actelion.research.gui.FileHelper
Shows a file-save-dialog, lets the user choose and return the file's path and name.
selectFragmentByAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
 
SELECTION_COLOR - Static variable in class com.actelion.research.chem.AbstractDrawingObject
 
SelectionAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/24/13 Time: 5:57 PM
SelectionAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.SelectionAction
 
selectionColor() - Static method in class com.actelion.research.gui.JDrawArea
 
selectObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
selectObject(int) - Method in class com.actelion.research.gui.wmf.WMF
 
selectOption(String, String, String[]) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
selectOption(String, String, String[]) - Method in class com.actelion.research.gui.FileHelper
 
Selector<T> - Interface in com.actelion.research.jfx.gui.misc
Created with IntelliJ IDEA.
SelfOrganizedConformer - Class in org.openmolecules.chem.conf.so
 
SelfOrganizedConformer(StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
SEP - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
 
SEP - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
SEP - Static variable in class com.actelion.research.util.IO
 
SEP - Static variable in class com.actelion.research.util.StringFunctions
 
SEP_LINE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
SEP_PARAMETER - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
SEP_VALUE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
Separation - Class in com.actelion.research.chem.forcefield.mmff
The Separation class is an efficient storage of an adjacency matrix representing how many degrees of separation there are between any two atoms.
Separation(MMFFMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.Separation
Constructs a new separation table for a molecule.
Separation.Relation - Enum in com.actelion.research.chem.forcefield.mmff
Relation class shows the relationship between two atoms A1 and A2.
SEPARATOR_ATOMS - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
serializeCache(String, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
Writes for every distinct fragment: one idcode, multiple encoded coordinate sets, multiple conformer likelihoods
serialVersionUID - Static variable in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
 
serialVersionUID - Static variable in class com.actelion.research.gui.JAtomLabelDialog
 
set(boolean[], boolean) - Static method in class com.actelion.research.util.ArrayUtils
 
set(byte) - Method in class com.actelion.research.util.datamodel.ByteVec
 
set(byte[], byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
Flat copy from node into this.
set(double) - Method in class com.actelion.research.calc.Matrix
 
set(double) - Method in class com.actelion.research.util.DoubleVec
 
set(double[]) - Method in class com.actelion.research.util.DoubleVec
 
set(double[][]) - Method in class com.actelion.research.calc.Matrix
 
set(double[][], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(double, double) - Method in class com.actelion.research.util.datamodel.PointDouble
 
set(double, double, double) - Method in class com.actelion.research.chem.Coordinates
 
set(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
set(float[][], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(float[], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(int) - Method in class com.actelion.research.util.datamodel.IntVec
Don't forget to set the hash code!
set(int[]) - Method in class com.actelion.research.util.DoubleVec
 
set(int[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(int, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
Hash value has to be recalculated!
set(int, double) - Method in class com.actelion.research.util.DoubleVec
 
set(int, int) - Method in class com.actelion.research.util.datamodel.IntArray
 
set(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
Don't forget to set the hash code!
set(int, int, double) - Method in class com.actelion.research.calc.Matrix
 
set(int, int, double) - Method in class com.actelion.research.util.DoubleVec
 
set(int, int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
set(short[][], short) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
set(Matrix) - Method in class com.actelion.research.calc.Matrix
 
set(Matrix, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
set(Coordinates) - Method in class com.actelion.research.chem.Coordinates
Copies x,y,z from c to this
set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
 
set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
 
set(Molecule3D) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCS
mol should contain equal or more bonds than frag.
set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFast
 
set(StereoMolecule, StereoMolecule, boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
mol should contain equal or more bonds than frag.
set(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
Don't forget to set the hash code!
set(PointDouble) - Method in class com.actelion.research.util.datamodel.PointDouble
 
set(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
set(String, String, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
set(List<PPNodeViz>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
set(T, T) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
setAccessory(Component) - Method in class com.actelion.research.gui.JDrawDialog
 
setActive(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
 
setActive(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
 
setAlignment(int, int) - Method in class com.actelion.research.gui.VerticalFlowLayout
Sets the Alignment attribute of the VerticalFlowLayout object
setAllAtomFlag(int, boolean) - Method in class com.actelion.research.chem.Molecule3D
 
setAllAtoms(int) - Method in class com.actelion.research.chem.Molecule
Low level method for constructing/modifying a molecule from scratch.
setAllBonds(int) - Method in class com.actelion.research.chem.Molecule
Low level method for constructing/modifying a molecule from scratch.
setAllDataIn() - Method in class com.actelion.research.util.Pipeline
 
setAllDataIn(boolean) - Method in interface com.actelion.research.util.IPipeline
 
setAllDataIn(boolean) - Method in class com.actelion.research.util.Pipeline
has to be set true or wereAllDataFetched() will never become true.
setAllowDropOrPasteWhenDisabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
 
setAllowFragmentStatusChangeOnPasteOrDrop(boolean) - Method in class com.actelion.research.gui.JStructureView
When fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JDrawArea
If set to false then any query features will be removed from the molecule and any functionality that allows to define atom- or bond-query features won't be available.
setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JEditableStructureView
 
setAnisou(String) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
setArea(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
setArrIndexParentNodes(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
 
setArrNode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
setAssignParitiesToNitrogen(boolean) - Method in class com.actelion.research.chem.StereoMolecule
This is a policy setting for this StereoMolecule as molecule container.
setAtomAbnormalValence(int, int) - Method in class com.actelion.research.chem.Molecule
Set an atom's maximum valance to be different from the default one.
setAtomAmino(int, String) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomBfactor(int, double) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomChainId(int, String) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomCharge(int, int) - Method in class com.actelion.research.chem.Molecule
 
setAtomCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
setAtomColor(int, int) - Method in class com.actelion.research.chem.Molecule
 
setAtomColorSupported(boolean) - Method in class com.actelion.research.gui.JDrawArea
 
setAtomColorSupported(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
setAtomConfigurationUnknown(int, boolean) - Method in class com.actelion.research.chem.Molecule
This is a user applied information, rather than a calculated value.
setAtomCustomLabel(int, byte[]) - Method in class com.actelion.research.chem.Molecule
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
setAtomCustomLabel(int, String) - Method in class com.actelion.research.chem.Molecule
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
setAtomDescription(int, String) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
This is MDL's enhanced stereo representation (ESR).
setAtomFlag(int, int, boolean) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomFlags(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomicNo(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
setAtomicNo(int, int) - Method in class com.actelion.research.chem.Molecule
Set an atom's atomic number and defines the isotop to be natural abundance.
setAtomId(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
setAtomIndexConnectionFlexophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
setAtomIndexFirstLinkerAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
setAtomList(int, int[]) - Method in class com.actelion.research.chem.Molecule
Defines a list of allowed/excluded atomic numbers for sub-structure matching.
setAtomList(int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
Defines an atom list as query feature for substructure search
setAtomMapNo(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
Defines an atom mapping number within the context of a reaction.
setAtomMarker(int, boolean) - Method in class com.actelion.research.chem.Molecule
Atom marking may be used for any external purpose
setAtomMass(int, int) - Method in class com.actelion.research.chem.Molecule
Set atom to specific isotop or to have a natural isotop distribution
setAtomName(int, String) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
The atom parity is a calculated property available above/equal helper level cHelperParities.
setAtomQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
Introduce or remove an atom query feature and make sure, the molecule is flagged to be a sub-structure fragment (see setFragment()).
setAtomRadical(int, int) - Method in class com.actelion.research.chem.Molecule
Sets an atom's radical state as singulet,dublet,triplet or none
setAtoms(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
setAtomSelection(int, boolean) - Method in class com.actelion.research.chem.Molecule
 
setAtomSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
setAtomStereoCenter(int, boolean) - Method in class com.actelion.research.chem.Molecule
An atom is considered a stereo center, if it is a stereo center in at least in one of the molecule configurations represented by the ESR definitions.
setAtomText(String[]) - Method in class com.actelion.research.chem.AbstractDepictor
Defines additional atom text to be displayed in top right position of some/all atom label.
setAtomText(String[]) - Method in class com.actelion.research.gui.JDrawArea
Defines additional atom text to be displayed in top right position of some/all atom label.
setAtomText(String[]) - Method in class com.actelion.research.gui.JStructureView
Defines additional atom text to be displayed in top right position of some/all atom labels.
setAtomX(int, double) - Method in class com.actelion.research.chem.Molecule
 
setAtomY(int, double) - Method in class com.actelion.research.chem.Molecule
 
setAtomZ(int, double) - Method in class com.actelion.research.chem.Molecule
 
setAttachedHydrogenCount(int, int) - Method in class com.actelion.research.chem.Molecule3D
Defines a number of attached hydrogens without known 3D-coordinates
setAuthor(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setAuxiliaryInfo(String, Object) - Method in class com.actelion.research.chem.Molecule3D
 
setAverageBondLength(Reaction, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setBackgroundColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
 
setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
setBase(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
setBase(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
setBiasProvider(MutationBiasProvider) - Method in class com.actelion.research.chem.Mutator
 
setBiasReference(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
 
setBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
setBit(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
setBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
Counts from the left to the right Don't forget to set the hash code!
setBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
 
setBit(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
setBits(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
 
setBKColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setBKColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
 
setBKMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setBKMode(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setBondAtom(int, int, int) - Method in class com.actelion.research.chem.Molecule
 
setBondBackgroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
Used for depiction only.
setBondCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
setBondESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
MDL's enhanced stereo representation for BINAP type of stereo bonds.
setBondForegroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
Used for depiction only.
setBondIndex(IntVec) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
 
setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule
Sets the bond type based on bond order without stereo orientation.
setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
setBondParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
The bond parity is a calculated property available above/equal helper level cHelperParities.
setBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
setBondQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
 
setBondsMolecule(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
setBondTorsion(int, short) - Method in class com.actelion.research.chem.conf.Conformer
Sets the current bond torsion to be retrieved later.
setBondType(int, int) - Method in class com.actelion.research.chem.Molecule
Defines a bond type combining bod order and stereo orientation.
setBorderColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
setBrushFillStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setBrushHatch(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setBrushPattern(Image) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setBusyColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
 
setByte(int[], int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
setByte(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
Counts from the left to the right Don't forget to set the hash code!
setBytes(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
setBytes(int, int, int) - Method in class com.actelion.research.util.datamodel.IntVec
 
setCache(RigidFragmentCache) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
 
setCaveat(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
setChargeAtom(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
setChiralDrawPosition(int) - Method in class com.actelion.research.gui.JStructureView
 
setChirality(int) - Method in class com.actelion.research.chem.Molecule
Sets the overall chirality of the molecule taking into account: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
setCIPParities() - Method in class com.actelion.research.chem.Canonizer
 
setCisPep(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setClassification(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
 
setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
 
setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.CompoundCollectionPane
call this in order to get clipboard support
setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JDrawArea
Call this after initialization to get clipboard support
setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JStructureView
Call this in order to get clipboard support: setClipboardHandler(new ClipboardHandler());
setClipRgn() - Method in class com.actelion.research.gui.wmf.MetaFile
 
setClipRgn() - Method in class com.actelion.research.gui.wmf.WMF
 
setCol(int, double) - Method in class com.actelion.research.calc.Matrix
 
setCol(int, double[]) - Method in class com.actelion.research.calc.Matrix
 
setCollectFragmentIdCodes(boolean) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
setCollisionIntensity(double, double[][]) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
setColName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
setColor(int) - Method in class com.actelion.research.chem.AbstractDepictor
 
setColor(Color) - Method in class com.actelion.research.chem.AbstractDepictor
 
setColor(Color) - Method in class com.actelion.research.chem.Depictor
 
setColor(Color) - Method in class com.actelion.research.chem.Depictor2D
 
setColor(Color) - Method in class com.actelion.research.chem.SVGDepictor
 
setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setColor(Color) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
setColorMCS2Molecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
setColorMolecule(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
setColorMoleculeFromBondIndex(StereoMolecule, int[], int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
setColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
Colors to be passed to Depictor.
setComposite(Composite) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
setCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
setCompound(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setCompoundFilter(MoleculeFilter) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
setCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
setCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
setConformationMode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
setContent(Reaction) - Method in class com.actelion.research.gui.JChemistryView
 
setContent(Reaction) - Method in class com.actelion.research.gui.JEditableChemistryView
 
setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
 
setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
 
setContent(StereoMolecule) - Method in class com.actelion.research.gui.JChemistryView
 
setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JChemistryView
 
setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JEditableChemistryView
 
setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
 
setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
 
setContent(StereoMolecule, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
 
setCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
setCoordinates(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
 
setCoordinates(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setCoordinates(double, double, double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
setCoordinates(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
 
setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
Copies x,y,z from coords into this atom's coordinates
setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.Molecule3D
 
setCoordinates(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setCoordinates(String) - Method in class com.actelion.research.chem.shredder.Fragment3D
 
setCoordinatesNull() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setCoordinatesNull(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
 
setCoordinatesReplace(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
Replaces the atom's Coordinates object by the given one
setCreateFragments(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines whether new created structures are fragments of molecules.
setCryst1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setCurrentDirectory(File) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
 
setCurrentTool(int) - Method in class com.actelion.research.gui.JDrawToolbar
 
setCustomTemplateList(List<InventorTemplate>) - Method in class com.actelion.research.chem.coords.CoordinateInventor
By providing a custom template list containing substructures with predefined atom coordinates, any occurence of any of these substructures will receive the relative atom coordinates of the provided template, unless the substructure shares more than one atom with a previously found substructure or the substructure shares more than one atom with the non marked atoms and mode is MODE_????_MARKED_ATOM_COORDS.
setData(String, Object) - Method in class com.actelion.research.chem.StructureInfo
 
setData(T) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
setData(T) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
 
setDateDeposition(Date) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setDBRef(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setDBRef1DBRef2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setDefaultAverageBondLength(double) - Static method in class com.actelion.research.chem.Molecule
When the molecule adds a new bond to a new atom or a new ring, then atoms are positioned such that the lengths of the new bonds are equal to the average length of existing bonds.
setDeletable(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
setDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
Sets the human readable description of this filter.
setDescriptorHandlerFactory(DescriptorHandlerFactory) - Method in class com.actelion.research.chem.io.CompoundFileParser
If a requested descriptor is not available in a particuar compound record, the parser can create one itself, provided its DescriptorHandlerFactory knows the descriptor name.
setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
setDirectionality(Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
setDisableBorder(boolean) - Method in class com.actelion.research.gui.JStructureView
 
setDiscreteFunction(double[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
setDisplayMode(int) - Method in class com.actelion.research.chem.AbstractDepictor
 
setDisplayMode(int) - Method in class com.actelion.research.chem.ExtendedDepictor
 
setDisplayMode(int) - Method in class com.actelion.research.gui.JChemistryView
 
setDisplayMode(int) - Method in class com.actelion.research.gui.JDrawArea
 
setDisplayMode(int) - Method in class com.actelion.research.gui.JStructureView
Sets the display mode for the Depictor.
setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
setDisplayMode(int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
 
setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.Model
 
setDisplaySize(Dimension) - Method in class com.actelion.research.share.gui.editor.Model
 
setDistanceHistogram(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
setDistanceTables(List<double[][]>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
The distance tables which were generated from the conformations.
setDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
setDistHists(byte[], int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
Flat copy
setDouble(double) - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.chem.reaction.Reaction
 
setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.gui.JDrawArea
 
setE0(double) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
setEditable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines, whether the list and individual structures can be edited.
setEditable(boolean) - Method in class com.actelion.research.gui.JChemistryView
 
setEditable(boolean) - Method in class com.actelion.research.gui.JStructureView
 
setEditable(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
setElectronegativity(double) - Method in class com.actelion.research.chem.Element
 
setELUSIVE(boolean) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
 
setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
 
setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
setEnabled(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
setEnabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
 
setEnabled(boolean) - Method in class com.actelion.research.gui.JStructureView
 
setEnabled(boolean) - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
setEnd(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setEnergy(double) - Method in class com.actelion.research.chem.conf.Conformer
 
setErrorColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
 
setESRType(int) - Method in class com.actelion.research.share.gui.editor.Model
 
setExistingSet(long[][]) - Method in class com.actelion.research.chem.DiversitySelector
 
setExpdata(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setExtension(String) - Method in class com.actelion.research.gui.JFileChooserOverwrite
 
setExtensionListInDescription(boolean) - Method in class com.actelion.research.chem.io.CompoundFileFilter
Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setFactorIsomorphSymmetric(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setFactorTextSize(double) - Method in class com.actelion.research.chem.AbstractDepictor
Sets a multiplication factor to the text size of all labels.
setFieldData(String, String) - Method in class com.actelion.research.chem.SDFileMolecule
 
setFileSupport(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines, whether the popup menu contains 'Open' and/or 'Save' items.
setFill(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
setFill(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
setFixedAtoms(int[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
setFixedAtoms(int[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
 
setFlat(double[][]) - Method in class com.actelion.research.calc.Matrix
 
setFlatness(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setFlexible(boolean) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setFont(String, double, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
setFont(String, double, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
setFontEscapement(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
If the foreground color is set, the molecule is drawn in the foreground color except for non carbon atoms, which are drawn in atomicNo specific colors.
setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
 
setForegroundColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
setFragment(boolean) - Method in class com.actelion.research.chem.Molecule
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
setFragment(boolean) - Method in class com.actelion.research.chem.reaction.Reaction
Sets all reactants and products of this reaction to the given fragment state, i.e.
setFragment(boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
setFragment(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setFragment(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setFragment(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
 
setFragment(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
 
setFragment(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
Defines the fragment to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
setFragment(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setFragment(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setFragment(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setFragment(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setFragmentNoColor(long) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
 
setFragmentNoColor(C) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
setFragmentNoColor(Color) - Method in class com.actelion.research.chem.ExtendedDepictor
 
setFragmentNoColor(Color) - Method in class com.actelion.research.gui.JChemistryView
 
setFragments(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
setFragments(StereoMolecule[]) - Method in class com.actelion.research.gui.JDrawArea
 
setFragments(StereoMolecule[]) - Method in class com.actelion.research.share.gui.editor.Model
 
setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
setFrequencyOnePerMol(int) - Method in class com.actelion.research.chem.shredder.Fragment
 
setFrequencySumAll(int) - Method in class com.actelion.research.chem.shredder.Fragment
 
setFunctionalities(int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
setGDIFillBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setGDIFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setGDIFontDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setGDIHollowBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setGDIPen() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setGDIPenDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setGDIPenWidthDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setGrowBoost(double) - Method in class com.actelion.research.chem.Mutator
 
setHash(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
setHash(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
 
setHeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
setHelix(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHelperValidity(int) - Method in class com.actelion.research.chem.Molecule
Use this method with extreme care.
setHet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHetAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
Sets the Hgap attribute of the VerticalFlowLayout object
setHiliteBondSet(int[]) - Method in class com.actelion.research.gui.JDrawArea
 
setHmId_Formula(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHmId_Name(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHmId_Site(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHmId_Synonyms(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setHorizontalFill(boolean) - Method in class com.actelion.research.gui.VerticalFlowLayout
Sets the Hfill attribute of the VerticalFlowLayout object
setHydrogenProtection(boolean) - Method in class com.actelion.research.chem.Molecule
Fragment's query features are checked for consistency and normalized during helper array creation.
setId(int) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
 
setId(long) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
setId(long) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
 
setID(int) - Method in class com.actelion.research.calc.Matrix
 
setID(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setIdcode(String) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
 
setIdCode(String) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
setIDCode(String) - Method in class com.actelion.research.gui.JStructureView
 
setIDCode(String, String) - Method in class com.actelion.research.gui.JStructureView
 
setIdentifier(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
setIdFlexophorePoint1(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
setIdFlexophorePoint2(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
 
setImageProvider(ImageProvider) - Method in class com.actelion.research.share.gui.editor.Model
 
setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setIndex(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
 
setIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
setIndexSphereVisualization(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setInstance(IStructureNameResolver) - Static method in class com.actelion.research.chem.name.StructureNameResolver
 
setInteger(int) - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
setInteractionAtomType(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
setInteractionType(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
setInteractionTypes(Molecule3D) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
 
setInternalDragAndDropIsMove(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines the behaviour for internal drag&drop.
setJrnl(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setKeywords(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setL1(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
setL2(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
setLambda(double) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
setLargestFragmentOnly(boolean) - Method in class com.actelion.research.chem.StructureSearchSpecification
 
setLayouted(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
setLi(List<T>) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
 
setLiConnect(List<int[]>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setLineWidth(double) - Method in class com.actelion.research.chem.AbstractDepictor
 
setLineWidth(double) - Method in class com.actelion.research.chem.Depictor
 
setLineWidth(double) - Method in class com.actelion.research.chem.Depictor2D
 
setLineWidth(double) - Method in class com.actelion.research.chem.SVGDepictor
 
setLineWidth(double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
setLineWidth(double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
setLineWidth(double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
setLink(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setLinkerId(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
setLocaleFormat(Formatter.LocaleFormat) - Static method in class com.actelion.research.util.Formatter
 
setMapMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setMapMode(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setMapper(IReactionMapper) - Method in class com.actelion.research.share.gui.editor.Model
 
setMappingIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setMappingIndex(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setMark(int, boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setMarkAll(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setMarked(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.gui.JDrawArea
 
setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.share.gui.editor.Model
 
setMaster(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setMatchingInfoInQueryAndBase(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
Sets the color information for the visualization of the Flexophore PPPoints.
setMatchLimit(int, int) - Method in class com.actelion.research.chem.reaction.ReactionSearch
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
setMatchLimit(int, int) - Method in class com.actelion.research.chem.StructureSearch
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule
Usually called automatically and hardly needed to be called.
setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule3D
 
setMaxBonds(int) - Method in class com.actelion.research.chem.Molecule
Usually called automatically and hardly needed to be called.
setMaxConfs(int) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
setMaximumTextSize(int) - Method in class com.actelion.research.chem.Depictor
 
setMaxNumSolutions(int) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
setMaxTotalCount(int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
setMdltyp(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setMode(int) - Method in class com.actelion.research.share.gui.editor.Model
 
setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
setModRes(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setMol(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragment
 
setMol(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
Defines fragment and molecule before calling isFragmentInMolecule(...) or findFragmentInMolecule(...).
setMolecule(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setMolecule(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
 
setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
 
setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
 
setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
 
setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
 
setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
 
setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
 
setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
 
setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
Defines the molecule to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
setMolecule(StereoMolecule) - Method in class com.actelion.research.gui.JDrawArea
 
setMolecule(StereoMolecule) - Method in interface com.actelion.research.jfx.gui.chem.IMoleculeView
 
setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
setMolecule(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setMolecule(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setMolecule(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
Deprecated.
setMolecule(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
 
setMoleculeColor(int) - Method in class com.actelion.research.chem.Molecule
Currently, this method only allows to switch the default atomic number dependent atom coloring off by passing cMoleculeColorNeutral.
setMolFile(String) - Method in class com.actelion.research.share.gui.editor.Model
 
setMtrix1(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setMtrix2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setMtrix3(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setName(String) - Method in class com.actelion.research.chem.conf.Conformer
 
setName(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setName(String) - Method in class com.actelion.research.chem.Molecule
 
setName(String) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
setName(String) - Method in class com.actelion.research.chem.reaction.Reaction
 
setNeighbours(List<Integer>) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
setNewMolecule() - Method in class com.actelion.research.share.gui.editor.Model
 
setNodesQuery(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
Only needed for the toString() method.
setNummdl(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setNumRegressionPoints(int) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setObjective(IObjectiveCompleteGraph<T>) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
 
setObjectiveQueryBiased(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
setObsolete(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setOccurencesArray(int[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
setOpaqueBackground(boolean) - Method in class com.actelion.research.gui.JChemistryView
 
setOptimize3D(boolean) - Method in class com.actelion.research.chem.io.AbstractParser
 
setOrigX1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setOrigX2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setOrigX3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
If the overrule color is set, the entire molecule is drawn in the foreground color neglecting any atom color information.
setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
 
setOverruleColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
setOverruleColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
Colors to be passed to Depictor.
setPaint(Paint) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setParities() - Method in class com.actelion.research.chem.Canonizer
Creates parities based on atom indices of original molecule and stores them into the molecule.
setParitiesValid(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Atom stereo parities and bond E/Z-parities are properties that are usually perceived from up/down-bonds and atom coordinates, respectively.
setPartialCharge(int, double) - Method in class com.actelion.research.chem.Molecule3D
 
setPasteAndDropOptions(int) - Method in class com.actelion.research.gui.JChemistryView
fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
setPenStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setPenWidth(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
 
setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setPositionInContainer(int) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
 
setPPP(int, int[]) - Method in class com.actelion.research.chem.Molecule3D
 
setPreferredSize(int, int, int) - Method in class com.actelion.research.chem.Mutator
 
setPreviousAlignment(StereoMolecule[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
setPreviousPheSAResult(double[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
 
setProtAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setQ0(double) - Method in class com.actelion.research.chem.phesa.Quaternion
 
setQ1(double) - Method in class com.actelion.research.chem.phesa.Quaternion
 
setQ2(double) - Method in class com.actelion.research.chem.phesa.Quaternion
 
setQ3(double) - Method in class com.actelion.research.chem.phesa.Quaternion
 
setQuery(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
 
setQuery(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
setQuery(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
This defines the query reaction (or transformation).
setQuery(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
This defines the query reaction (or transformation).
setQuery(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
setRandomSeed(long) - Method in class com.actelion.research.chem.coords.CoordinateInventor
 
setReactant(int, StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reactor
Defines a real world reactant.
setReaction(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
 
setReaction(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
 
setReaction(Reaction) - Method in class com.actelion.research.gui.JDrawArea
 
setReaction(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
 
setReaction(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
This defines the query reaction (or transformation).
setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawArea
 
setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawDialog
 
setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawPanel
 
setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawArea
 
setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawToolbar
 
setRearAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setRect(float, float, float, float) - Method in class com.actelion.research.share.gui.Arrow
 
setRect(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
setReferenceVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
setRemarks(HashMap<Integer, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setRenderingHint(RenderingHints.Key, Object) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setResourcePath(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
Use this method before initializing the TorsionDB, if you want to open the resource files from an external location in the file system rather than from the project resources.
setResSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
setRevdat(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setRMSD(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
Sum of squared distances of the center to the other cluster members
setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.ByteVec
 
setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.IntVec
 
setRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
 
setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.ByteVec
 
setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.IntVec
 
setRNDvalue(double, double) - Method in class com.actelion.research.util.DoubleVec
 
setRole(int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
setROP2(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setROP2(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setRotatableBonds(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setRotationCenters(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setRow(int, double) - Method in class com.actelion.research.calc.Matrix
 
setRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
Deep copy
setRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
 
setRowCoordinates(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Puts the given encoded atom coordinates into the given column.
setRowName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
setRowStructure(StereoMolecule, int, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Calculates the canonical structure representation as idcode from mol and puts it into the given idcodeColumn.
setRowStructure(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Puts the given idcode into the given column.
setRowValue(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Puts the given value into the given column.
setScale1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setScale2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setScale3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setScaling(double) - Method in class com.actelion.research.chem.DepictorTransformation
 
setScore(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setScore(double) - Method in class com.actelion.research.util.datamodel.ScorePoint
 
setSelectable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
setSelected(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
setSelected(boolean) - Method in class com.actelion.research.share.gui.Arrow
 
setSelected(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
 
setSelected(boolean) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
 
setSelectedAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
 
setSelectedBond(int) - Method in class com.actelion.research.share.gui.editor.Model
 
setSelectedDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
 
setSelection(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
May be overridden to act on selection changes
setSeparatorCol(String) - Static method in class com.actelion.research.calc.Matrix
 
setSeparatorRow(String) - Static method in class com.actelion.research.calc.Matrix
 
setSEQADV(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSEQRES(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSheet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setShiftVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
setShowValidationError(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines whether a large red question mark is shown in case of a structure validation error.
setSigma(double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
 
setSim(double) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
setSimilarity(double) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
setSimilarityMappingNodes(float) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setSimilarityMappingNodes(int, float) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
setSingleConformationModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
setSingleUnknownAsRacemicParity() - Method in class com.actelion.research.chem.Canonizer
If the molecule contains exactly one stereo center and if that has unknown configuration, than assume that the configuration is meant to be racemic and update molecule accordingly.
setSize(int) - Method in class com.actelion.research.chem.shredder.Fragment
 
setSize(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setSize(String) - Method in class com.actelion.research.chem.TextDrawingObject
 
setSizes(double[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
 
setSlope(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
 
setSlope(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setSlopeFragments(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setSlopeR2(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
setSmallerSideAtomLists(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setSmiles(String) - Method in class com.actelion.research.share.gui.editor.Model
 
setSource(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSplineFunction(FastSpline) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
 
setSplit(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSprsde(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSSBond(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setSSSearcher(SSSearcher) - Method in class com.actelion.research.chem.mcs.MCS
 
setState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
 
setState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
setState(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
 
setState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
 
setState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
 
setStereoBondFromAtomParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
setStereoBondFromBondParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
In case bond is a BINAP kind of chiral bond with defined parity, then the preferred neighbour single bond is converted into a stereo bond to correctly reflect its defined parity.
setStereoBondsFromParity() - Method in class com.actelion.research.chem.ExtendedMolecule
This converts one single bond per parity into a stereo up/down bond to correctly reflect the given parity.
setStereoCenters() - Method in class com.actelion.research.chem.Canonizer
 
setStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setStroke(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
setStroke(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
setStroke(Stroke) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setStructureSize(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
Defines the width or height of individual structure cells, depending on whether the the CompoundCollectionPane is horizontal or vertical, respectively.
setStyle(String) - Method in class com.actelion.research.chem.TextDrawingObject
 
setTerminalC(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
 
setText(String) - Method in class com.actelion.research.chem.TextDrawingObject
 
setText(String) - Method in class com.actelion.research.gui.JMessageBar
 
setTextAlign(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setTextAlign(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.WMF
 
setTextColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
 
setTextColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setTextColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
 
setTextSize(int) - Method in class com.actelion.research.chem.AbstractDepictor
 
setTextSize(int) - Method in class com.actelion.research.chem.Depictor
 
setTextSize(int) - Method in class com.actelion.research.chem.Depictor2D
 
setTextSize(int) - Method in class com.actelion.research.chem.SVGDepictor
 
setTextSize(int) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
 
setThreadMaster(ThreadMaster) - Method in class com.actelion.research.calc.DataProcessor
 
setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
 
setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
If the conformer generation must be stopped from outside, for instance because of user intervention or because of a defined timeout, the provide a ThreadMaster with this method.
setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
setThreshSimilarityHardMatch(double) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
setTitle(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
setToRacemate() - Method in class com.actelion.research.chem.Molecule
This is for compatibility with old MDL stereo representation that contained a 'chiral' flag to indicate that the molecule is not a racemate.
setTorsionAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setTorsionIDs(String[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
 
setTransform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
 
setTransparent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
setUnique(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
setUniqueFragmentsEstimated(int) - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.Canonizer
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.StereoMolecule
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
setupAtomAndBondFeatures(int) - Method in class com.actelion.research.chem.SSSearcher
 
setUpdateMode(int) - Method in class com.actelion.research.gui.JDrawArea
 
setUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
setUsed(boolean) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
 
setUserData(Object) - Method in class com.actelion.research.chem.Molecule
 
setUseSelfOrganizerIfAllFails(boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
If a molecule has at least one rotatable bond if all permutations of torsions collide beyond a tolerated strain, then the standard behaviour of this class is to return that clashing conformer with the lowest strain.
If passing true to this method, the ConformerGenerator will use the ConformerSelfOrganizer in these cases to generate conformers.
setValue(double) - Method in class com.actelion.research.util.Angle
 
setValue(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
 
setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
setValue(StereoMolecule, boolean) - Method in class com.actelion.research.share.gui.editor.Model
 
setValues(String, double, int) - Method in class com.actelion.research.chem.TextDrawingObject
 
setVerbose(boolean) - Method in class com.actelion.research.calc.DataProcessor
 
setVerbose(boolean) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
 
setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
setVerbose(boolean) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
 
setVgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
Sets the Vgap attribute of the VerticalFlowLayout object
setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
setVolumes(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
setWeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
setWeights(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
setWMF(MetaFile, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setX(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setX(int, double) - Method in class com.actelion.research.chem.conf.Conformer
 
setX(String) - Method in class com.actelion.research.chem.TextDrawingObject
 
setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
setY(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setY(int, double) - Method in class com.actelion.research.chem.conf.Conformer
 
setY(String) - Method in class com.actelion.research.chem.TextDrawingObject
 
setZ(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
setZ(int, double) - Method in class com.actelion.research.chem.conf.Conformer
 
sFactory - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
 
shareSameFragment(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
shear(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
shift(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
shift(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
 
SHIFTJIS_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
shortName - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
 
shortNameToName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
 
showBusyMessage(String) - Method in class com.actelion.research.gui.JMessageBar
 
showErrorMessage(String) - Method in interface com.actelion.research.calc.ProgressListener
 
showErrorMessage(String) - Method in class com.actelion.research.gui.JMessageBar
 
showHelpDialog() - Method in class com.actelion.research.gui.JDrawArea
 
showMessage(String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
 
showMessage(String) - Method in class com.actelion.research.gui.FileHelper
 
showText() - Method in class com.actelion.research.gui.JMessageBar
 
shuffle(int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
shuffle(int[], Random) - Static method in class com.actelion.research.util.ArrayUtils
 
shuffle(IntArray) - Static method in class com.actelion.research.util.datamodel.IntArray
 
shuffle(T[]) - Static method in class com.actelion.research.util.ArrayUtils
 
Sign(double, double) - Static method in class com.actelion.research.calc.Matrix
 
Silicon - Static variable in class com.actelion.research.chem.PeriodicTable
 
SIMILARITY_MODE_CARBON - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
SIMILARITY_MODE_HARD_THRESH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
Hartd thresh means if the similarity of two atom types in a node to node comparison is below a threshold the complete node to node similarity becomes 0.
SIMILARITY_MODE_HARD_THRESH_AVR - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
SIMILARITY_MODE_HARD_THRESH_OPTIMISTIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
SIMILARITY_MODE_SIMPLE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
SIMILARITY_SCALING_SPLIT_SCORE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
SimilarityCalculatorInfo - Class in com.actelion.research.chem.descriptor
 
SimilarityCalculatorInfo(String, String) - Constructor for class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
 
SIMPLE_DATE_FORMAT - Static variable in class com.actelion.research.util.ConstantsDWAR
 
SimpleCanonizer - Class in com.actelion.research.chem
 
SimpleCanonizer(ExtendedMolecule) - Constructor for class com.actelion.research.chem.SimpleCanonizer
 
SimpleMetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
 
SimplePPGaussian - Class in com.actelion.research.chem.phesa.pharmacophore
Differs from the PPGaussian by lacking a directionality vector and is not associated with a molecule Can be used to represent interaction sites in protein binding sites
SimplePPGaussian(Coordinates, IPharmacophorePoint.Functionality) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
SimplePPGaussian(String) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
 
simpleUpdateCoords(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
Returns full transformation that moves/scales original molecule into viewRect.
simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
 
simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.SVGDepictor
 
simpleValidateView(Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
 
sin() - Method in class com.actelion.research.util.Angle
 
SingularValueDecomposition - Class in com.actelion.research.calc
Singular Value Decomposition.
SingularValueDecomposition(double[][], ProgressListener, ThreadMaster) - Constructor for class com.actelion.research.calc.SingularValueDecomposition
Construct the singular value decomposition
SiteParser - Class in com.actelion.research.chem.io.pdb.parser
SiteParser Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other essential sites or environments surrounding ligands present in the structure.
SiteParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.SiteParser
 
size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
size() - Method in class com.actelion.research.chem.coords.InventorFragment
 
size() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Returns the total number of atoms in this force field.
size() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
size() - Static method in class com.actelion.research.chem.PeriodicTable
 
size() - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
 
size() - Method in class com.actelion.research.share.gui.Polygon
 
size() - Method in class com.actelion.research.util.datamodel.ByteVec
 
size() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
size() - Method in class com.actelion.research.util.datamodel.IntVec
 
size() - Method in class com.actelion.research.util.DoubleVec
 
size() - Method in class com.actelion.research.util.hash.HashSetInt
 
size() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
size() - Method in class com.actelion.research.util.SortedList
 
SIZE_RATIO - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
sizeAfterLastBitSet - Variable in class com.actelion.research.chem.properties.complexity.BitArray128
 
sizeBits() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
sizeBits() - Method in class com.actelion.research.util.datamodel.IntVec
 
sizeBytes() - Method in class com.actelion.research.util.datamodel.IntVec
 
sizeContent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
sizeContent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
sizeOf(String) - Static method in class com.actelion.research.util.StringFunctions
https://stackoverflow.com/questions/4385623/bytes-of-a-string-in-java sizeof(string) = 8 + // object header used by the VM 8 + // 64-bit reference to char array (value) 8 + string.length() * 2 + // character array itself (object header + 16-bit chars) 4 + // offset integer 4 + // count integer 4 + // cached hash code
sizeOf(List<String>) - Static method in class com.actelion.research.util.StringFunctions
 
SizeOf - Class in com.actelion.research.util
13.02.2006 MvK
SizeOf() - Constructor for class com.actelion.research.util.SizeOf
 
sizePipe() - Method in class com.actelion.research.util.Pipeline
 
Sketch - Class in com.actelion.research.util
Title: Actelion Java Library
Sketch() - Constructor for class com.actelion.research.util.Sketch
 
skip(Reader) - Static method in class com.actelion.research.io.BOMSkipper
Some text editors (e.g.
skipBytes(int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
 
skipUntilLineMatchesRegEx(StringReadChannel, String) - Static method in class com.actelion.research.io.StringReadChannel
 
skipUntilLineMatchesRegEx(StringReadChannel, String, int) - Static method in class com.actelion.research.io.StringReadChannel
 
skipUntilLineMatchesRegEx(InputStream, String) - Static method in class com.actelion.research.util.IO
 
SlidingWindow - Class in com.actelion.research.calc.filter
SlidingWindow
SlidingWindow(double[]) - Constructor for class com.actelion.research.calc.filter.SlidingWindow
 
SlidingWindowDistHist - Class in com.actelion.research.chem.descriptor.flexophore
SlidingWindowDistHist Created by korffmo1 on 01.03.16.
SlidingWindowDistHist(double[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
 
SmilesCreator - Class in com.actelion.research.chem
 
SmilesCreator() - Constructor for class com.actelion.research.chem.SmilesCreator
 
SmilesParser - Class in com.actelion.research.chem
 
SmilesParser() - Constructor for class com.actelion.research.chem.SmilesParser
 
SmoothingSplineInterpolator - Class in com.actelion.research.util
Smoothing Spline Interpolator based on the algorithm described at http://www.qmw.ac.uk/~ugte133/book/11_tsd/splines.pdf

The Smoothing Spline is used to minimize Sum(sqr((Si-yi)/sigmai)) + lambda*Sum(sqr(S''i)) If lambda=0 (default), this is equivalent to the cubic spline interpolation If lambda=Infinity, this is equivalent to the least square fitting
SmoothingSplineInterpolator() - Constructor for class com.actelion.research.util.SmoothingSplineInterpolator
 
SolubilityPredictor - Class in com.actelion.research.chem.prediction
 
SolubilityPredictor() - Constructor for class com.actelion.research.chem.prediction.SolubilityPredictor
 
SolutionCompleteGraph - Class in com.actelion.research.util.graph.complete
SolutionCompleteGraph
SolutionCompleteGraph() - Constructor for class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
solve(Matrix) - Method in class com.actelion.research.calc.LUDecomposition
Solve A*X = B
SOLVENT_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
 
sort() - Method in class com.actelion.research.util.datamodel.IntArray
 
SortedList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
 
SortedList() - Constructor for class com.actelion.research.util.SortedList
 
SortedList(Comparator) - Constructor for class com.actelion.research.util.SortedList
 
SortedPair - Class in com.actelion.research.chem.forcefield.mmff
SortedPair class is used in the Separation table.
SortedPair(int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.SortedPair
Construct a new SortedPair.
SortedStringList - Class in com.actelion.research.chem
 
SortedStringList() - Constructor for class com.actelion.research.chem.SortedStringList
 
sortInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
SP2_AMINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
SpecialField(String, String, String, String, String) - Constructor for class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
SPECIFIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
SplineFunction - Class in com.actelion.research.chem.interactionstatistics
Class used to represent a Protein Ligand Function
SplineFunction() - Constructor for class com.actelion.research.chem.interactionstatistics.SplineFunction
 
SRC_AND - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
 
SRC_COPY - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
 
SRC_PAINT - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
 
SRCAND - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SRCINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SRCPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SRSearcher - Class in com.actelion.research.chem.reaction
The SRSearcher class handles reaction-sub-structure searches.
SRSearcher() - Constructor for class com.actelion.research.chem.reaction.SRSearcher
 
SSSearcher - Class in com.actelion.research.chem
 
SSSearcher() - Constructor for class com.actelion.research.chem.SSSearcher
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
SSSearcher(int) - Constructor for class com.actelion.research.chem.SSSearcher
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
SSSearcherWithIndex - Class in com.actelion.research.chem
 
SSSearcherWithIndex() - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
 
SSSearcherWithIndex(int) - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
 
STABILIZED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
 
standardize(StereoMolecule, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
 
start() - Method in class com.actelion.research.chem.reaction.ReactionSearch
 
start() - Method in class com.actelion.research.chem.StructureSearch
 
start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
 
start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
 
start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
 
START_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
 
startAnimation(int) - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
In order for a button to support an animation, it need additional images to follow after its normal appearance.
startProgress(String, int, int) - Method in class com.actelion.research.calc.DataProcessor
 
startProgress(String, int, int) - Method in interface com.actelion.research.calc.ProgressListener
 
startWrite(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
 
stateChanged() - Method in interface com.actelion.research.chem.forcefield.ForceFieldChangeListener
 
StatisticalTorsionPotential - Class in com.actelion.research.chem.conf.torsionstrain
 
StatisticalTorsionTerm - Class in com.actelion.research.chem.conf.torsionstrain
Represents a torsion potential as a function of the angle, derived from statistical torsion distributions from the COD/CSD The dihedral angle is defined by a atom sequence of 4 atoms.
stbn - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Stbn - Class in com.actelion.research.chem.forcefield.mmff.table
 
Stbn(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Stbn
 
step() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
 
STEREO_ANGLE_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
 
StereoMolecule - Class in com.actelion.research.chem
 
StereoMolecule() - Constructor for class com.actelion.research.chem.StereoMolecule
 
StereoMolecule(int, int) - Constructor for class com.actelion.research.chem.StereoMolecule
 
StereoMolecule(Molecule) - Constructor for class com.actelion.research.chem.StereoMolecule
 
stopAnimation() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
 
stopProgress() - Method in interface com.actelion.research.calc.ProgressListener
 
stopProgress(String) - Method in class com.actelion.research.calc.DataProcessor
 
stopScrolling() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
 
storeState() - Method in class com.actelion.research.gui.JDrawArea
 
StraightLineRule - Class in org.openmolecules.chem.conf.so
 
StraightLineRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.StraightLineRule
 
StrainTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
knowledge-based term for the internal strain of a ligand, composed of the pair-potentials (only atoms further away than 3 bonds from each other)
StrainTerm(StereoMolecule) - Constructor for class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
 
STRATEGY_ADAPTIVE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
STRATEGY_LIKELY_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
STRATEGY_LIKELY_SYSTEMATIC - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
STRATEGY_PURE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
STRETCH_ANDSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
STRETCH_DELETESCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
STRETCH_ORSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
StretchBend - Class in com.actelion.research.chem.forcefield.mmff
Stretch bending energy term class.
StretchBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.StretchBend
Constructs a new stretch bend object.
stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
 
stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
String2DoubleArray - Class in com.actelion.research.util.convert
 
String2DoubleArray() - Constructor for class com.actelion.research.util.convert.String2DoubleArray
 
StringFunctions - Class in com.actelion.research.util
 
StringFunctions() - Constructor for class com.actelion.research.util.StringFunctions
 
StringReadChannel - Class in com.actelion.research.io
StringReadChannel 2007 MvK: Start implementation 25.06.2009 MvK: implementation changed 12.02.2014 MvK: added charset encoding to handle Umlaute.
StringReadChannel(ReadableByteChannel) - Constructor for class com.actelion.research.io.StringReadChannel
 
stringToColor(String) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
 
stripIsotopInfo() - Method in class com.actelion.research.chem.Molecule
Removes all isotop information, i.e.
stripSmallFragments() - Method in class com.actelion.research.chem.ExtendedMolecule
Removes all unconnected fragments except for the largest one.
stripSmallFragments(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
Removes all unconnected fragments except for the largest one.
stripStereoInformation() - Method in class com.actelion.research.chem.StereoMolecule
Removes defined and implicit stereo information from the molecule.
- up/down-bonds are converted to double bonds
- stereo centers are flagged to be unknown
- double bonds with implicit stereo configurations are converted into cross bonds
- all atom and bond ESR assignments are removed
- parity and CIP helper state is set to invalid, such that stereo calculation is redone, if needed.
strokeLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
 
strokeLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
 
StrokeLineCap<T> - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
StrokeLineJoin - Interface in com.actelion.research.share.gui.editor.geom
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
StrongHasher() - Constructor for class com.actelion.research.chem.CanonizerUtil.StrongHasher
 
StructureAssembler - Class in com.actelion.research.chem.io.pdb.parser
 
StructureAssembler(List<int[]>, List<AtomRecord>, List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.StructureAssembler
 
StructureCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
Utility function based on the molecule's connections (groups, rings,...)
StructureCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
structureChanged() - Method in class com.actelion.research.gui.JStructureView
Should only be called if JStructureView's internal Molecule is changed from outside as: theStructureView.getMolecule().setFragment(false); The caller is responsible to update displayMol also, if it is different from the molecule.
structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.CompoundCollectionPane
 
structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
Updates the molecule used for display, drag & drop and clipboard transfer.
structureChanged(StereoMolecule) - Method in interface com.actelion.research.gui.StructureListener
 
structureChanged(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
Updates both molecules used for display and for drag & drop/clipboard transfer.
StructureInfo - Class in com.actelion.research.chem
 
StructureInfo() - Constructor for class com.actelion.research.chem.StructureInfo
 
StructureInfo(String, String, String, float, String) - Constructor for class com.actelion.research.chem.StructureInfo
 
StructureListener - Interface in com.actelion.research.gui
 
StructureNameResolver - Class in com.actelion.research.chem.name
Created by thomas on 7/13/17.
StructureNameResolver() - Constructor for class com.actelion.research.chem.name.StructureNameResolver
 
StructureSearch - Class in com.actelion.research.chem
 
StructureSearch(StructureSearchSpecification, StructureSearchDataSource, StructureSearchController, ProgressController, DescriptorHandlerFactory) - Constructor for class com.actelion.research.chem.StructureSearch
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
StructureSearchController - Interface in com.actelion.research.chem
 
StructureSearchDataSource - Interface in com.actelion.research.chem
 
StructureSearchSpecification - Class in com.actelion.research.chem
 
StructureSearchSpecification(int, byte[][], Object[], String, float) - Constructor for class com.actelion.research.chem.StructureSearchSpecification
Creates a complete specification for a substructure or similarity search with one or more query fragments or molecules.
StructureTransferData - Class in com.actelion.research.chem
 
StructureTransferData() - Constructor for class com.actelion.research.chem.StructureTransferData
 
StructureTransferData(ExtendedMolecule, StructureInfo) - Constructor for class com.actelion.research.chem.StructureTransferData
 
sub(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
sub(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Subtracts that vector from this vector by component.
sub(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
Substraction
sub(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
Substraction
sub(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
Substraction
subC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
 
SubFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
SubFlexophoreGenerator
SubFlexophoreGenerator(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
 
SubFlexophoreGenerator.ViolatedConditionsCount - Class in com.actelion.research.chem.descriptor.flexophore.generator
 
SubGraphExtractor - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
SubGraphExtractor Creates substructures by fragmentation and summarizes them.
SubGraphExtractor() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
 
SubGraphIndices - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
SubGraphIndices A class to handle indices in a molecular graph.
SubGraphIndices() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
SubStructSearchBondIndex - Class in com.actelion.research.chem.mcs
 
SubStructSearchBondIndex() - Constructor for class com.actelion.research.chem.mcs.SubStructSearchBondIndex
 
SubStructSearchExhaustiveTreeWalker - Class in com.actelion.research.chem.mcs
 
SubStructSearchExhaustiveTreeWalker() - Constructor for class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
 
subtract(double) - Method in class com.actelion.research.calc.Matrix
 
subtract(double) - Method in class com.actelion.research.util.Angle
 
subtract(Matrix) - Method in class com.actelion.research.calc.Matrix
 
subtract(Angle) - Method in class com.actelion.research.util.Angle
 
subtractByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
 
subtractFromCols(Matrix) - Method in class com.actelion.research.calc.Matrix
 
suggestBondType(int, int) - Method in class com.actelion.research.chem.Molecule
Suggests either cBondTypeSingle or cBondTypeMetalLigand whatever seems more appropriate for a new bond between the two atoms.
suggestNewX2AndY2(int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
 
SULFONAMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
SULFONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
SULFONE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
SULFOXIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
Sulfur - Static variable in class com.actelion.research.chem.PeriodicTable
 
sum() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
sum(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
sum(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
sum(double[]) - Static method in class com.actelion.research.util.ArrayUtils
 
sum(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
sum(int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
sum(long[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
summarizeAlkaneCluster(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
Summarizes alkane cluster.
SummaryFragments - Class in com.actelion.research.chem.properties.complexity
 
SummaryFragments(ResultFragmentsStatistic) - Constructor for class com.actelion.research.chem.properties.complexity.SummaryFragments
 
supportsImplicitHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
Whether an atom may be considered to carry implicit hydrogen atoms depends on the atomicNo of that atom.
SVGDepictor - Class in com.actelion.research.chem
 
SVGDepictor(StereoMolecule, int, String) - Constructor for class com.actelion.research.chem.SVGDepictor
 
SVGDepictor(StereoMolecule, String) - Constructor for class com.actelion.research.chem.SVGDepictor
 
swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule
Swaps two atoms' indexes/locations in the atom table.
swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule3D
 
swapBonds(int, int) - Method in class com.actelion.research.chem.Molecule
Swaps two bonds' indexes/locations in the atom table.
swapNodes(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
SWISS - com.actelion.research.util.Formatter.LocaleFormat
 
switchBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
symbol(int) - Static method in class com.actelion.research.chem.PeriodicTable
 
SYMBOL_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
SYMMETRY_C1C1_OR_C1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
 
SYMMETRY_C1D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
 
SYMMETRY_D1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
 
SYMMETRY_D1D2_OR_D2D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
 
SymmetryCalculator - Class in com.actelion.research.chem.properties.complexity
 
SymmetryCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.SymmetryCalculator
 
SymmetryCorrectedRMSDCalculator - Class in com.actelion.research.chem.conf
employing RMSD calculation using a HungarianAlgorithm for the atom assignment to correct for overestimated RMSD values obtained by conventional methods for molecules with symmetric substructures based on: dx.doi.org/10.1021/ci400534h
SymmetryCorrectedRMSDCalculator(Conformer, Conformer) - Constructor for class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
 
systemExec(String[]) - Static method in class com.actelion.research.util.Platform
Wrapper for Runtime.exec() that allows different handling by platform This method fixes forking issues in Windows when starting Mercury (by default new processes do not seem to be forked correctly)

T

TA_BASELINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_BOTTOM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_CENTER - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_LEFT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_NOUPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_RIGHT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_TOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TA_UPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TAB_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
 
table - Variable in class com.actelion.research.chem.forcefield.mmff.Separation
 
table - Variable in class com.actelion.research.chem.forcefield.mmff.table.Def
 
table(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Returns a table given a table name.
TableModelString - Class in com.actelion.research.util.datamodel.table
TableModelText Data model for an only text containing table
TableModelString() - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
 
TableModelString(int, int) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
 
TableModelString(List<String>, List<String>) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
 
Tables - Class in com.actelion.research.chem.forcefield.mmff
A collection of tables with the official parameters of the MMFF94/MMFF94s force field variants.
Tables(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.Tables
Construct a new Tables object.
TAG_AAS_ABBR1 - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
 
TAG_AAS_NAME - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
 
TAG_ACTNO - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_ANISOU - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ATOM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ATOMS - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_AUTHOR - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_BONDS - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_BONDS_AT_MAX_FRAGS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_CAVEAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_CISPEP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_COMPLEXITY - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_COMPND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_CONECT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_CONFORMERSET - Static variable in class com.actelion.research.util.ConstantsDWAR
Contains the idcode and the 3d coordinates.
TAG_COOR - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_COOR2 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_COOR3D - Static variable in class com.actelion.research.util.ConstantsDWAR
Can be one or multiple sets of 3D coordinates.
TAG_CRYST1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_DBREF - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_DBREF1_DBREF2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_END - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ENDMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_EXPDTA - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_FORMUL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_FRACTAL_DIM - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_FREQUENCY - Static variable in class com.actelion.research.chem.shredder.Fragment
 
TAG_FREQUENCY_ONE_PER_MOLECULE - Static variable in class com.actelion.research.chem.shredder.Fragment
 
TAG_HEADER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_HELIX - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_HET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_HETATM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_HETNAM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_HETSYN - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ID - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_ID_QUERY - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_IDCODE - Static variable in class com.actelion.research.util.ConstantsDWAR
Deprecated.
TAG_IDCODE2 - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_JRNL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_KEYWDS - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_LIGAND_EFFICIENCY - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_LINK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MASTER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MAX_NUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_MDLTYP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MESSAGE - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_MODEL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ModelExhaustiveStatistics - Static variable in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
TAG_MODRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MTRIX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MTRIX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MTRIX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_MultipleNonOverlapSolution - Static variable in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
TAG_MW - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_NAME - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_NAMES - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_NUM_BONDS_AT_MAXIMUM_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_NUM_BONDS_AT_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_NUMMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_OBSOLTE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ORIGX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ORIGX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ORIGX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_QUERY_IDENTIFIER - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_RATIO_NON_SYMMETRIC_ATOMS - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_RATIO_USED_BONDS_UP_TO_MAX_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_REACTION_CODE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_REACTION_COORD - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_REACTION_DRAW_OBJ - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_REACTION_MAPPING - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_RECORD_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_RELATIVE_FREQUNCY - Static variable in class com.actelion.research.chem.shredder.Fragment
 
TAG_REMARK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_REMARK_N - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_REMARK0 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_REMARK1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_REMARK2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_REMARK3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_ResultFragmentsStatistic - Static variable in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
TAG_REVDAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SCALE1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SCALE2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SCALE3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SEQADV - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SEQRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SHEET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHelper
 
TAG_SITE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SIZE - Static variable in class com.actelion.research.chem.shredder.Fragment
 
TAG_SMILES - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_SOURCE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SOURCE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_SPLIT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SPRSDE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_SSBOND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_STRUCTURE_EXCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_STRUCTURE_INCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
 
TAG_SUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
TAG_SUM_UNIQUE_FRAGMENTS_UNTIL_MAX - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
 
TAG_TER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_TITLE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
 
TAG_VIZ_INFO_ENCODED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
tan() - Method in class com.actelion.research.util.Angle
 
TANIMOTO - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
TANIMOTO - Static variable in class com.actelion.research.util.DoubleVec
 
TANIMOTO_INV - Static variable in class com.actelion.research.util.datamodel.ByteVec
 
TANIMOTO_INV - Static variable in class com.actelion.research.util.DoubleVec
 
TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
 
TautomerHelper - Class in com.actelion.research.chem
 
TautomerHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.TautomerHelper
 
test() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
test(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
 
test01() - Static method in class com.actelion.research.util.datamodel.ByteVec
 
testChiralDia - Class in com.actelion.research.chem.contrib
 
testChiralDia() - Constructor for class com.actelion.research.chem.contrib.testChiralDia
 
testDiaID - Class in com.actelion.research.chem.contrib
 
testDiaID() - Constructor for class com.actelion.research.chem.contrib.testDiaID
 
testFolder(String, String, String, Sdf.OnMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
Tests an entire pair of folders, one containing SDF files and the other containing reference files.
testHoses - Class in com.actelion.research.chem.contrib
 
testHoses() - Constructor for class com.actelion.research.chem.contrib.testHoses
 
testS1() - Static method in class com.actelion.research.util.datamodel.ByteVec
 
testTakeda1() - Static method in class com.actelion.research.util.datamodel.ByteVec
 
TetrahedralStereoRule - Class in org.openmolecules.chem.conf.so
 
TetrahedralStereoRule(StereoMolecule, int[]) - Constructor for class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
TextClipboardHandler - Class in com.actelion.research.gui.clipboard
TextDrawingObject - Class in com.actelion.research.chem
 
TextDrawingObject() - Constructor for class com.actelion.research.chem.TextDrawingObject
 
TextDrawingObject(String) - Constructor for class com.actelion.research.chem.TextDrawingObject
 
TextDrawingObject(String, double, double) - Constructor for class com.actelion.research.chem.TextDrawingObject
 
TextDrawingObject(String, double, double, double, int) - Constructor for class com.actelion.research.chem.TextDrawingObject
 
textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.MetaFile
 
textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.WMF
 
theta(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
Returns 'theta0' the equilibrium angle for a given index in the table.
theta(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.
theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
 
theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
 
ThreadMaster - Interface in com.actelion.research.calc
 
threadMustDie() - Method in class com.actelion.research.calc.DataProcessor
 
threadMustDie() - Method in interface com.actelion.research.calc.ThreadMaster
 
THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
THRESH_SIMILARITY_COMPARISON_NODE - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
THRESH_SIMILARITY_HARD_MATCH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
Similarity value distribution of the interaction table (April 2020).
TIE_BREAK_FREE_VALENCE_ATOMS - Static variable in class com.actelion.research.chem.Canonizer
 
TINY - Static variable in class com.actelion.research.calc.Matrix
 
TINY_FACTOR - Static variable in class com.actelion.research.calc.histogram.ConstantsHistogram
 
TINY04 - Static variable in class com.actelion.research.calc.Matrix
 
TINY08 - Static variable in class com.actelion.research.calc.Matrix
 
TINY16 - Static variable in class com.actelion.research.calc.Matrix
 
to(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns a vector that points from this vector to that vector.
toArray() - Method in class com.actelion.research.calc.Matrix
 
toArray() - Method in class com.actelion.research.chem.SortedStringList
 
toArray() - Method in class com.actelion.research.chem.UniqueStringList
 
toArray() - Method in class com.actelion.research.util.datamodel.ByteVec
 
toArray() - Method in class com.actelion.research.util.datamodel.IntVec
 
toArray() - Method in class com.actelion.research.util.DoubleVec
 
toArray(List<String>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toArray(T[]) - Method in class com.actelion.research.util.SortedList
 
toArray(T[]) - Method in class com.actelion.research.util.UniqueList
 
toArrayStrStr(List<List<String>>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toBinaryString() - Method in class com.actelion.research.util.datamodel.ByteVec
 
toBinaryStringDense() - Method in class com.actelion.research.util.datamodel.ByteVec
 
toByteArray(double[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toByteArray(int) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toByteArray(int[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toByteArray(long) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toBytes(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
Convenience method to directly decode a String-encoded byte array.
toDegrees() - Method in class com.actelion.research.util.Angle
 
toDoubleArray(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toDoubleArray(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toDoubleBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
 
toIntArray(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toIntArray(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
Converts a List of Integer to an int[]
toIntArray(List<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
Converts a List of Integer to an int[]
toIntByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
 
toInts(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
Convenience method to directly decode a String-encoded int array.
toList() - Method in class com.actelion.research.util.datamodel.IntArray
 
toList() - Method in class com.actelion.research.util.hash.HashSetInt
 
toList(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toList(int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toList(int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
 
toList(int[], List<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
 
toList(String[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toList(T[]) - Static method in class com.actelion.research.util.ArrayUtils
 
TOLX - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
 
toMolecule() - Method in class com.actelion.research.chem.conf.Conformer
Copies this Conformer's atom coordinates to the associated molecule.
toMolecule(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
Copies this Conformer's atom coordinates to the given molecule.
TOOL_CHAINCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_CTEXTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_CURSOR_BASE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_DELETECURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_FISTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_HANDCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_HANDPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_LASSOCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_LASSOPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_POINTERCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_SELECTRECTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_SELECTRECTPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
TOOL_ZOOMCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
 
ToolbarSelectionChange - Interface in com.actelion.research.share.gui.editor.actions
Created by rufenec on 5/3/16.
toolChanged(int) - Method in class com.actelion.research.gui.JDrawArea
 
TOP - Static variable in class com.actelion.research.gui.VerticalFlowLayout
Description of the Field
toRow() - Method in class com.actelion.research.calc.Matrix
 
torsion - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Torsion - Class in com.actelion.research.chem.forcefield.mmff.table
 
Torsion - Class in com.actelion.research.chem.forcefield.mmff.type
The torsion type class provides a static function for getting the torsion type of a torsion angle.
Torsion() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Torsion
 
Torsion(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion
 
TORSION_GREEN - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
TORSION_NOT_FOUND - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
TORSION_RED - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
TORSION_YELLOW - Static variable in class com.actelion.research.chem.conf.TorsionDB
 
Torsion.Kb - Class in com.actelion.research.chem.forcefield.mmff.table
 
TorsionAngle - Class in com.actelion.research.chem.forcefield.mmff
Torsional Angle energy term class.
TorsionAngle(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.TorsionAngle
Construct a new torsion angle energy term.
TorsionConstraint - Class in com.actelion.research.chem.potentialenergy
 
TorsionConstraint(Conformer, int[], double, double) - Constructor for class com.actelion.research.chem.potentialenergy.TorsionConstraint
Term that forces a torsion angle with a harmonic potential to a range of acceptable values (range given by the width)
TorsionDB - Class in com.actelion.research.chem.conf
 
TorsionDescriptor - Class in com.actelion.research.chem.conf
 
TorsionDescriptor(float[], float[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptor
 
TorsionDescriptorHelper - Class in com.actelion.research.chem.conf
 
TorsionDescriptorHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
 
TorsionDescriptorHelper(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
 
TorsionDetail - Class in com.actelion.research.chem.conf
 
TorsionDetail() - Constructor for class com.actelion.research.chem.conf.TorsionDetail
This creates an empty torsion classification detail, which multiply can be used to classify the environment of a rotatable bond.
TorsionPrediction - Class in com.actelion.research.chem.conf
 
TorsionPrediction(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionPrediction
 
TorsionRelevanceHelper - Class in com.actelion.research.chem.conf
 
TorsionRelevanceHelper() - Constructor for class com.actelion.research.chem.conf.TorsionRelevanceHelper
 
TorsionRule - Class in org.openmolecules.chem.conf.so
 
TorsionRule(short[], short[], short[][], int[], int[], int) - Constructor for class org.openmolecules.chem.conf.so.TorsionRule
 
TorsionSet - Class in org.openmolecules.chem.conf.gen
 
TorsionSet(int[], int[], int[], int[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
Creates a new conformer description from torsion and conformer indexes.
TorsionSet(TorsionSet) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
Deep-Copy constructor not including collision intensities
TorsionSetEliminationRule - Class in org.openmolecules.chem.conf.gen
 
TorsionSetEliminationRule(long[], long[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
 
TorsionSetStrategy - Class in org.openmolecules.chem.conf.gen
Knowing all rotatable bonds of an underlying molecule and knowing those rigid fragments that are connected by them, the TorsionSetStrategy provides a mechanism to deliver valid and unique torsion sets, each effectively defining an individual conformer.
TorsionSetStrategy(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategy
 
TorsionSetStrategyAdaptiveRandom - Class in org.openmolecules.chem.conf.gen
 
TorsionSetStrategyAdaptiveRandom(RotatableBond[], RigidFragment[], boolean, boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
This torsion set strategy produces random sets of torsion indices until a torsion set collides.
TorsionSetStrategyLikelySystematic - Class in org.openmolecules.chem.conf.gen
TorsionSetStrategy that systematically creates all possible TorsionSets in batches while keeping a focus on the likelyhood of individual torsions.
TorsionSetStrategyLikelySystematic(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
 
TorsionSetStrategyRandom - Class in org.openmolecules.chem.conf.gen
 
TorsionSetStrategyRandom(RotatableBond[], RigidFragment[], boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
This simple TorsionSetStrategy produces random sets of torsion indexes in a loop.
toShortString(long, int) - Static method in class com.actelion.research.util.DoubleFormat
Converts the value with the given exponent into a short string representation using the scientific notation if it is more compact.
toSortedArray() - Method in class com.actelion.research.chem.UniqueStringList
 
toSortedArray(T[]) - Method in class com.actelion.research.util.UniqueList
 
toSortedString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
 
toString() - Method in class com.actelion.research.calc.histogram.Histogram
First row: bins, upper border.
toString() - Method in class com.actelion.research.calc.Matrix
 
toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
toString() - Method in class com.actelion.research.chem.AbstractDrawingObject
 
toString() - Method in class com.actelion.research.chem.conf.ConformerSet
 
toString() - Method in class com.actelion.research.chem.conf.TorsionDescriptor
 
toString() - Method in class com.actelion.research.chem.Coordinates
 
toString() - Method in class com.actelion.research.chem.DepictorTransformation
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
 
toString() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
 
toString() - Method in class com.actelion.research.chem.DrawingObjectList
 
toString() - Method in class com.actelion.research.chem.Element
 
toString() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
 
toString() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
toString() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Returns a string form of this vector.
toString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
 
toString() - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
 
toString() - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
 
toString() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
 
toString() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
toString() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
 
toString() - Method in class com.actelion.research.chem.Molecule3D
 
toString() - Method in class com.actelion.research.chem.Mutation
 
toString() - Method in class com.actelion.research.chem.PeriodicTable
 
toString() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
toString() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
toString() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
toString() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
 
toString() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
 
toString() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
 
toString() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
toString() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
toString() - Method in class com.actelion.research.chem.SDFileMolecule
 
toString() - Method in class com.actelion.research.chem.StructureSearchSpecification
 
toString() - Method in class com.actelion.research.chem.SVGDepictor
 
toString() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
 
toString() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
 
toString() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
 
toString() - Method in class com.actelion.research.gui.VerticalFlowLayout
Description of the Method
toString() - Method in class com.actelion.research.util.Angle
 
toString() - Method in class com.actelion.research.util.CommandLineParser
 
toString() - Method in class com.actelion.research.util.datamodel.ByteVec
Converts a byte into its decimal.
toString() - Method in class com.actelion.research.util.datamodel.DoubleArray
 
toString() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
 
toString() - Method in class com.actelion.research.util.datamodel.IntArray
 
toString() - Method in class com.actelion.research.util.datamodel.IntegerDouble
 
toString() - Method in class com.actelion.research.util.datamodel.IntVec
 
toString() - Method in class com.actelion.research.util.datamodel.ScorePoint
 
toString() - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
toString() - Method in class com.actelion.research.util.DoubleVec
 
toString() - Method in class com.actelion.research.util.ErrorHashMap
 
toString() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
 
toString() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
 
toString() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
 
toString() - Method in class org.openmolecules.chem.conf.so.ConformationRule
 
toString() - Method in class org.openmolecules.chem.conf.so.DistanceRule
 
toString() - Method in class org.openmolecules.chem.conf.so.PlaneRule
 
toString() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
 
toString() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
 
toString() - Method in class org.openmolecules.chem.conf.so.TorsionRule
 
toString(boolean[]) - Static method in class com.actelion.research.util.StringFunctions
 
toString(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(byte[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toString(byte[]) - Static method in class com.actelion.research.util.StringFunctions
 
toString(byte[], String) - Static method in class com.actelion.research.util.datamodel.ByteVec
 
toString(double) - Static method in class com.actelion.research.util.DoubleFormat
Converts a double value into a String representation in scientific format rounded to 5 significant digits, e.g.
toString(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(double[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(double[]) - Static method in class com.actelion.research.util.StringFunctions
 
toString(double[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(double[], DecimalFormat) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(double[], NumberFormat) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(double[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
 
toString(double, int) - Static method in class com.actelion.research.util.DoubleFormat
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
toString(double, int, boolean) - Static method in class com.actelion.research.util.DoubleFormat
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
toString(float[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(float[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(float[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
 
toString(int) - Method in class com.actelion.research.calc.Matrix
 
toString(int) - Method in class com.actelion.research.util.datamodel.ByteVec
 
toString(int) - Method in class com.actelion.research.util.datamodel.IntVec
 
toString(int) - Method in class com.actelion.research.util.DoubleVec
 
toString(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(int[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(int[][], String) - Static method in class com.actelion.research.util.StringFunctions
 
toString(int[], String) - Static method in class com.actelion.research.util.StringFunctions
 
toString(int, int, int) - Method in class com.actelion.research.calc.Matrix
 
toString(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
toString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
 
toString(ResultFragmentsStatistic) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
 
toString(Exception) - Static method in class com.actelion.research.util.StringFunctions
 
toString(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(Object[]) - Static method in class com.actelion.research.util.ArrayUtils
 
toString(String) - Method in class com.actelion.research.util.datamodel.IntArray
 
toString(String[], String) - Static method in class com.actelion.research.util.StringFunctions
 
toString(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toString(Collection<String>, String) - Static method in class com.actelion.research.util.StringFunctions
 
toString(List<ModelMedianDouble>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
toString(List<ModelMedianFloat>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
toString(List<Double>, NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
 
toString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
 
toStringArray() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
The array part of the object.
toStringArray(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringArray(List<String>) - Static method in class com.actelion.research.util.ArrayUtils
 
toStringBinary() - Method in class com.actelion.research.calc.Matrix
 
toStringBinary() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
toStringBinary() - Method in class com.actelion.research.util.datamodel.IntVec
 
toStringBinary(int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringBinary(int) - Static method in class com.actelion.research.util.datamodel.IntVec
 
toStringBinary(int) - Static method in class com.actelion.research.util.StringFunctions
 
toStringBinary(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringBinary(int, boolean) - Static method in class com.actelion.research.util.datamodel.IntVec
 
toStringBinary(long) - Static method in class com.actelion.research.util.StringFunctions
 
toStringBinaryDense() - Method in class com.actelion.research.util.datamodel.IntVec
 
toStringBytes() - Method in class com.actelion.research.util.datamodel.IntVec
 
toStringFileNameCompatible(double) - Static method in class com.actelion.research.util.StringFunctions
 
toStringFormatted(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringFormatted(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringForValueTable() - Method in class com.actelion.research.chem.Element
 
toStringHeader() - Static method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
 
toStringHex() - Method in class com.actelion.research.util.datamodel.IntVec
 
toStringHex(String) - Static method in class com.actelion.research.util.StringFunctions
 
toStringHists() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
toStringHistsIndexed() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
 
toStringInevitable() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
toStringInt(List<Integer>) - Static method in class com.actelion.research.util.StringFunctions
 
toStringInt(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
 
toStringIntArrays(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringInteger(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
 
toStringIntegerList(List<Integer>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
Writes a list into a string with line terminators.
toStringInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
 
toStringLaTex() - Method in class com.actelion.research.util.datamodel.table.TableModelString
\begin{table}[] \begin{tabular}{lllllllll} & 0.20 & 0.30 & 0.40 & 0.50 & 0.60 & 0.70 & 0.80 & 0.90 \\ Gaussian process regression & 1.3550 & 1.3059 & 1.3818 & 1.4046 & 1.5150 & 1.4804 & 1.4579 & 1.6223 \\ KNN regression & 1.6776 & 1.7294 & 1.8899 & 2.1573 & 2.3484 & 2.6003 & 2.6931 & 2.8232 \\ Median & 1.6730 & 1.7421 & 1.9217 & 2.3378 & 2.7606 & 3.2241 & 3.6768 & 4.5243 \\ PLS & 1.4264 & 1.2870 & 1.2131 & 1.2989 & 1.3866 & 1.3830 & 1.4414 & 1.1730 \\ PLS Power & 1.4886 & 1.3616 & 1.4954 & 1.7442 & 2.2339 & 2.3904 & 2.1669 & 2.6130 \\ Random Forest regression & 1.6746 & 1.6848 & 1.8421 & 2.0106 & 2.2479 & 2.3896 & 2.5420 & 2.6523 \\ SVM regression & 1.5580 & 1.4634 & 1.5879 & 1.6687 & 1.8423 & 1.9769 & 1.8803 & 1.9618 \end{tabular} \end{table}
toStringLong() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
toStringLong(List<Long>, String) - Static method in class com.actelion.research.util.StringFunctions
 
toStringLongHardPPPoint() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
 
toStringLongList(List<Long>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringNoBrackets(Collection<Integer>, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
toStringNoDigits(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringParameter() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
 
toStringPPPoints(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
 
toStringPure(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringPure(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
 
toStringRecentSimilarityResults() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
toStringRow(int, int) - Method in class com.actelion.research.calc.Matrix
 
toStringRowNumber(int, String) - Method in class com.actelion.research.calc.Matrix
 
toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
 
toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
 
toStringShortMessage() - Method in class com.actelion.research.util.ErrorHashMap
 
toStringSpaceDelimited() - Method in class com.actelion.research.chem.Coordinates
 
toStringString() - Method in class com.actelion.research.util.datamodel.ByteVec
Converts the bytes into chars.
toStringTabNL(String[][]) - Static method in class com.actelion.research.util.StringFunctions
Elements are separated by tabs and rows are separated by newline.
toStringValues(IntegerDouble[], NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
 
toStringValues(List<IntegerDouble>, NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
 
toStringVizInfoEncoded(MolDistHistViz) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
Encodes the structure information, that it can be written to an DWAR file.
toStringWithColTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
 
toStringWithRowTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
 
TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
 
TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
 
TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
 
TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
 
ToxicityPredictor - Class in com.actelion.research.chem.prediction
 
ToxicityPredictor() - Constructor for class com.actelion.research.chem.prediction.ToxicityPredictor
 
transform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
transformMolecule(Molecule, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
transformMolecules(Molecule[], double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
transformReaction(Reaction, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
 
transformX(double) - Method in class com.actelion.research.chem.DepictorTransformation
 
transformY(double) - Method in class com.actelion.research.chem.DepictorTransformation
 
translate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
translate(double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
 
translate(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
 
translate(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
translate(double, double, double) - Method in class com.actelion.research.chem.conf.Conformer
Translate this conformer's coordinates by adding the dx,dy,dz shifts to all atom coordinates.
translate(double, double, double) - Method in class com.actelion.research.chem.Molecule
Translate this molecule's 3D-coordinates by adding the dx,dy,dz shifts to all atom coordinates.
translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
 
translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
 
translate(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
Translate a Molecule
translate(StereoMolecule, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
Translate a Molecule
translateCoords(double, double) - Method in class com.actelion.research.chem.Molecule
 
translateFontName(String) - Method in class com.actelion.research.gui.wmf.MetaFile
 
translateFontName(String) - Method in class com.actelion.research.gui.wmf.WMF
 
translateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
translateLigand(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
translateMol(StereoMolecule, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
 
translateRef(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
translateTHParity(int, int[]) - Method in class com.actelion.research.chem.StereoMolecule
This method translates the parity of a stereo center, if its neighbour atoms are assigned new atom indexes, or are assigned to a matching fragment or molecule with different atom indexes.
translateToCOM(Coordinates) - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
TRANSPARENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
TRANSPARENT - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
transpose(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
 
TreeMatcher - Class in com.actelion.research.chem.descriptor.pharmacophoretree
Finds the optimal matching of nodes between two PharmacophoreTrees employing a dynamic programing scheme termed as "match-search" algorithm in the original publication (DOI:10.1023/a:1008068904628).
TreeMatcher(PharmacophoreTree, PharmacophoreTree) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
 
TreeMatcher.FeatureMatch - Class in com.actelion.research.chem.descriptor.pharmacophoretree
TODO: don't add null-matches!
TreeMatcher.TreeMatching - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
TreeMatching() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
 
TreeUtils - Class in com.actelion.research.chem.descriptor.pharmacophoretree
 
TreeUtils() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
 
treeWalkBFS(int, int, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
Walks a subtree of the PharmacophoreTree in breadth-first manner starting from a deleted edge and a designated head node.
Triangle - Class in com.actelion.research.calc.geometry
Triangle Created by korffmo1 on 04.06.17.
Triangle() - Constructor for class com.actelion.research.calc.geometry.Triangle
 
TRUE - com.actelion.research.chem.forcefield.mmff.RingBoolean
 
tryAutoMapReaction() - Method in class com.actelion.research.share.gui.editor.Model
 
TWO_PI - Variable in class com.actelion.research.util.Angle
 
type - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
type - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
TYPE_BACKBONE_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_BRAVAIS_PEARSON - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_CODE - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_HILITE_ATOM_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
 
TYPE_HILITE_BOND_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
 
TYPE_LONG_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_MARKUSH - Static variable in class com.actelion.research.chem.ExtendedDepictor
 
TYPE_MOLECULE_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
 
TYPE_MOLECULES - Static variable in class com.actelion.research.chem.ExtendedDepictor
 
TYPE_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_NO_REACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_NO_STRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_NONE - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_REACTION - Static variable in class com.actelion.research.chem.ExtendedDepictor
 
TYPE_RETRON - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_SELECTION_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
 
TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_SPEARMAN - Static variable in class com.actelion.research.calc.CorrelationCalculator
 
TYPE_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionArrow
 
TYPE_STRING - Static variable in class com.actelion.research.chem.TextDrawingObject
 
TYPE_SUBREACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
 
TYPE_SUBSTRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_TAUTOMER - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 
TYPE_TAUTOMER_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
 

U

UndoAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 3/26/13 Time: 4:39 PM
UndoAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UndoAction
 
undoStep() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
 
UniqueFragmentEstimator - Class in com.actelion.research.chem.properties.complexity
 
UniqueFragmentEstimator() - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
 
UniqueFragmentEstimator(int) - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
 
UniqueList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
 
UniqueList() - Constructor for class com.actelion.research.util.UniqueList
 
UniqueList(Comparator) - Constructor for class com.actelion.research.util.UniqueList
 
UniqueStringList - Class in com.actelion.research.chem
 
UniqueStringList() - Constructor for class com.actelion.research.chem.UniqueStringList
 
unit() - Method in class com.actelion.research.chem.Coordinates
 
unitC() - Method in class com.actelion.research.chem.Coordinates
 
UNKNOWN - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
 
UnknownParityAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 3/26/13 Time: 4:33 PM
UnknownParityAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UnknownParityAction
 
UnparametrizedAtomTypeException - Exception in com.actelion.research.chem.descriptor.flexophore
 
UnparametrizedAtomTypeException() - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
 
UnparametrizedAtomTypeException(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
 
unsetBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
unsetBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
Don't forget to set the hash code!
unsetBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
 
UpBondAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 1/28/13 Time: 1:49 PM
UpBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UpBondAction
 
update(Conformer) - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
update(StereoMolecule) - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
update(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
 
UPDATE_CHECK_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_CHECK_VIEW - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_INVENT_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_NONE - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_REDRAW - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_SCALE_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
 
UPDATE_SCALE_COORDS_USE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
updateAtomIndeces(int[]) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
updateCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
updateCoordinates(Conformer) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.Gaussian3D
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
 
updateCoordinates(StereoMolecule) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
 
updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
 
updateCoords(IDrawContext<T>, Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
 
updateCoords(Graphics, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
Returns full transformation that moves/scales original molecule into viewRect.
updateCoords(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
 
updateCoords(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
updateGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
updates the gradient of the ForceField and returns the gradient scale
updateGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
Minimise the current molecule using default parameter values for the number of iterations, energy tolerance and gradient tolerance.
updateGrid(StereoMolecule) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
 
updateProgress(int) - Method in class com.actelion.research.calc.DataProcessor
 
updateProgress(int) - Method in interface com.actelion.research.calc.ProgressListener
 
updateProgress(int, String) - Method in interface com.actelion.research.calc.ProgressListener
 
updateRenderer(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
 
updateState() - Method in class com.actelion.research.chem.docking.LigandPose
 
updateState() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
 
updateState() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
 
updateState() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
 
updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
 
updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIToggleButton
 
updateWeights(Map<Integer, List<Integer>>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
 
upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
 
upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
 
upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
 
usedMemory() - Static method in class com.actelion.research.util.SizeOf
 
usedMemoryMB() - Static method in class com.actelion.research.util.SizeOf
 

V

v1 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
v1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
v2 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
v2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
v3 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
 
v3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
 
val(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
Returns the VAL type of an atom given its MMFF type.
valid(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
Checks if a Stretch Bend is valid
validate() - Method in class com.actelion.research.chem.ExtendedMolecule
 
validate() - Method in class com.actelion.research.chem.MarkushStructure
Check the validity of a defined Markush structure.
validate() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
Checks, whether this specification is correctly defining a search.
validate() - Method in class com.actelion.research.chem.StereoMolecule
 
validate() - Method in class com.actelion.research.chem.StructureSearchSpecification
Checks, whether this specification is correctly defining a search.
validateBondType(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
 
validateBondType(int, int) - Method in class com.actelion.research.chem.Molecule
 
validateMapping() - Method in class com.actelion.research.chem.reaction.Reaction
Removes mapping numbers that are only used on one side of the reaction.
validateMemberIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
Adds or subtracts the ring size from index to move it into the valid range from 0 to ringSize-1.
validateView(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
A depictor maintains a DepictorTransformation object, which defines translation and scaling of molecule coordinates into the viewRect.
validateView(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
 
validateView(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
 
VALIDATION_ERROR_AMBIGUOUS_CONFIGURATION - Static variable in class com.actelion.research.chem.StereoMolecule
 
VALIDATION_ERROR_ESR_CENTER_UNKNOWN - Static variable in class com.actelion.research.chem.StereoMolecule
 
VALIDATION_ERROR_OVER_UNDER_SPECIFIED - Static variable in class com.actelion.research.chem.StereoMolecule
 
VALIDATION_ERRORS_STEREO - Static variable in class com.actelion.research.chem.StereoMolecule
 
value(double) - Method in class com.actelion.research.util.FastSpline.Polynome
 
value(double) - Method in class com.actelion.research.util.FastSpline
Compute the value for the function.
valueInvalidated() - Method in interface com.actelion.research.share.gui.editor.listeners.IValidationListener
 
valueInvalidated() - Method in class com.actelion.research.share.gui.editor.Model
 
valueOf(String) - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.docking.DockingEngine.StartPosition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.share.gui.DialogResult
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
Returns the enum constant of this type with the specified name.
valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
 
valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
 
values() - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.docking.DockingEngine.StartPosition
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.share.gui.DialogResult
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
Returns an array containing the constants of this enum type, in the order they are declared.
VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff.table
 
VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff
Nonbonded van der Waals energy term class.
VanDerWaals(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.VanDerWaals
Construct a new van der Waals energy term.
VanDerWaals(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
 
VARIABLE_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
VDW_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
VDW Radii indexed by atomic numbers, taken from DOI: 10.1039/c3dt50599e Santiago Alvarez: A cartography of the van der Waals territories Published on 01 May 2013 on http://pubs.rsc.org | doi:10.1039/C3DT50599E (in a few cases no value was given (marked ??), where we use estimated values)
VDW_TOLERANCE_HYDROGEN - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
VDW_TOLERANCE_OTHER - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
VDWRadii - Interface in com.actelion.research.chem.conf
 
vdws - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
 
Vector3 - Class in com.actelion.research.chem.forcefield.mmff
The Vector3 class provides common vector operations used throughout the MMFF codebase.
Vector3() - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector with default coordinates.
Vector3(double[], int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector from three consecutive doubles in a positions array.
Vector3(double[], int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector starting at atom1 position and ending at atom2 position.
Vector3(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector with given x, y and z coordinates.
Vector3(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
Vector3(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
Vector3(MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
Vector3(MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
Vector3(Vector3) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
Copy constructor, copies the x,y,z coordinates from another vector.
VectorSimilarity - Class in com.actelion.research.calc
 
VectorSimilarity() - Constructor for class com.actelion.research.calc.VectorSimilarity
 
VERBOSE - Static variable in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
VERBOSE - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
 
VERBOSE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
 
version - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
 
version - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
 
VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
 
VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
 
VERSION - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered
 
VERSION_INTERACTION_TABLES - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
 
VerticalFlowLayout - Class in com.actelion.research.gui
A vertical flow layout is similar to a flow layuot but it layouts the components vertically instead of horizontally.
VerticalFlowLayout() - Constructor for class com.actelion.research.gui.VerticalFlowLayout
Constructor for the VerticalFlowLayout object
VerticalFlowLayout(int, int) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
Constructor for the VerticalFlowLayout object
VerticalFlowLayout(int, int, int, int, boolean) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
Constructor for the VerticalFlowLayout object
vibrateLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
 
ViolatedConditionsCount() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
 
volume - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
VolumeGaussian - Class in com.actelion.research.chem.phesa
 
VolumeGaussian(int, int, Coordinates, Coordinates, int) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
 
VolumeGaussian(VolumeGaussian) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
 

W

weakCompareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
 
weight - Variable in class com.actelion.research.chem.phesa.Gaussian3D
 
well_depth - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
 
wereAllDataFetched() - Method in interface com.actelion.research.util.IPipeline
Has to be true when all data were fetched.
wereAllDataFetched() - Method in class com.actelion.research.util.Pipeline
Returns true if all data in was set and the queue is empty.
WHITE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
 
WHITENESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
WINDING - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
 
WMF - Class in com.actelion.research.gui.wmf
 
WMF() - Constructor for class com.actelion.research.gui.wmf.WMF
 
WMFConstants - Interface in com.actelion.research.gui.wmf
 
WMFGraphics - Class in com.actelion.research.gui.wmf
 
WMFGraphics(MetaFile, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics
 
WMFGraphics2D - Class in com.actelion.research.gui.wmf
 
WMFGraphics2D(WMF, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics2D
 
write(byte[]) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
write(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
write(double[], int) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
Writes the contents of this vector to the specified positions in a positions array.
write(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCharge
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCIP
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhGroup
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhStereoType
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomIsotope
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomRadical
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondDisplay
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPProducts
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPReactants
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowAtomStereo
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowBondStereo
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowEnhAtomStereo
 
write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPText
 
write(DataOutput, ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
 
write(File) - Method in class com.actelion.research.calc.Matrix
 
write(File, boolean, int) - Method in class com.actelion.research.calc.Matrix
 
write(File, double[]) - Static method in class com.actelion.research.util.IO
 
write(File, int[]) - Static method in class com.actelion.research.util.IO
 
write(File, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
 
write(File, String) - Static method in class com.actelion.research.util.IO
 
write(File, String, boolean) - Static method in class com.actelion.research.util.IO
 
write(File, DecimalFormat, boolean) - Method in class com.actelion.research.calc.Matrix
 
write(File, List<String>) - Static method in class com.actelion.research.util.IO
Writes each string in a separate line
write(OutputStream) - Method in class com.actelion.research.calc.Matrix
 
write(OutputStream, NumberFormat) - Method in class com.actelion.research.calc.Matrix
 
write(String) - Method in class com.actelion.research.calc.Matrix
 
write(String) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
 
write(String, boolean) - Method in class com.actelion.research.calc.Matrix
 
write(String, boolean, int) - Method in class com.actelion.research.calc.Matrix
 
write(String, boolean, int, int) - Method in class com.actelion.research.calc.Matrix
 
write(String, String) - Static method in class com.actelion.research.util.IO
 
write(String, String, boolean) - Static method in class com.actelion.research.util.IO
 
WRITE_DW_FILE - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
 
WRITE_DW_FRAGMENT_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
 
write2Channel(FileChannel, String) - Method in class com.actelion.research.util.IO
 
write2String() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
 
write2String() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
 
write2String() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
 
write2String() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
 
write2String() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
 
write2String() - Method in class com.actelion.research.util.datamodel.IntArray
 
write2String() - Method in class com.actelion.research.util.datamodel.IntVec
 
writeAsLineBase64Encoded() - Method in class com.actelion.research.calc.Matrix
 
writeBitmap(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
writeBitStringDense(File, List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
 
writeBoolean(boolean) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeByte(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeBytes(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeChar(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeChars(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
 
writeContent(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
writeContent(StereoMolecule, ClipboardContent) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
 
writeCTAB(StereoMolecule, double) - Static method in class com.actelion.research.chem.MolfileV3Creator
 
writeCurrentRow() - Method in class com.actelion.research.chem.io.DWARFileCreator
Call this once per row after setting individual cell content with the respective setRowXXXX() methods.
writeDouble(double) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeEnd() - Method in class com.actelion.research.chem.io.DWARFileCreator
 
writeFloat(float) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeHeader(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
Call this after defining columns and specifying column properties
writeHistogram(String, Matrix, boolean, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
 
writeInt(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeInteger(int) - Method in class com.actelion.research.gui.wmf.WMF
 
writeIntegerList(File, List<Integer>) - Static method in class com.actelion.research.util.IO
 
writeL(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
 
writeLong(long) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileCreator
 
writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileV3Creator
 
writeMolSketchFile(Molecule, OutputStream) - Static method in class com.actelion.research.util.Sketch
 
writeMolSketchFile(Molecule, String) - Static method in class com.actelion.research.util.Sketch
 
writeR(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
 
writeReactionSketchFile(Reaction, OutputStream) - Static method in class com.actelion.research.util.Sketch
 
writeReactionSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
 
writeRecordHeader(int, int) - Method in class com.actelion.research.gui.wmf.WMF
 
writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileCreator
 
writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileV3Creator
 
writeSerialized(File) - Method in class com.actelion.research.calc.Matrix
 
writeShort(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeTabDelimitedTable(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
Writes a TAB delimited text file that can be opened for debug or other purposes by DataWarrior containing idcode, idcoords, multiple conformer likelihoods
writeTextFile(String, int) - Method in class com.actelion.research.chem.AtomTypeList
Writes this AtomTypeList into a TAB-delimited text file in human readable form.
writeTypeFile(String) - Method in class com.actelion.research.chem.AtomTypeList
 
writeUTF(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
 
writeWMF(OutputStream) - Method in class com.actelion.research.gui.wmf.WMF
 
writeWord(int) - Method in class com.actelion.research.gui.wmf.WMF
 

X

x - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
 
x - Variable in class com.actelion.research.chem.Coordinates
 
x - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
 
x - Variable in class com.actelion.research.util.datamodel.PointDouble
 
X - com.actelion.research.chem.phesa.PheSAAlignment.axis
 
x1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
 
x2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
 

Y

y - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
 
y - Variable in class com.actelion.research.chem.Coordinates
 
y - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
 
y - Variable in class com.actelion.research.util.datamodel.PointDouble
 
Y - com.actelion.research.chem.phesa.PheSAAlignment.axis
 
y1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
 
y2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
 

Z

z - Variable in class com.actelion.research.chem.Coordinates
 
z - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
 
Z - com.actelion.research.chem.phesa.PheSAAlignment.axis
 
ZERO_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
 
zeroGradient() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
 
zeroGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
zeroes out gradient for fixed atoms
zeroGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
 
zoomAndRotate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
zoomAndRotate(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
 
zoomAndRotate(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
 
zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
 
zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.Molecule
 
zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
 
ZoomRotateAction - Class in com.actelion.research.share.gui.editor.actions
Project: User: rufenec Date: 4/28/2014 Time: 12:39 PM
ZoomRotateAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
 
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