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RDKit
Open-source cheminformatics and machine learning.
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Std stuff. More...
Namespaces | |
AtomPairs | |
Canon | |
common_properties | |
constants | |
Descriptors | |
detail | |
DGeomHelpers | |
Drawing | |
DTags | |
EnumerationStrategyPickler | |
EnumerationTypes | |
FileParserUtils | |
FilterMatchOps | |
FMCS | |
Local | |
MACCSFingerprints | |
MMFF | |
MMPA | |
MolAlign | |
MolDraw2D_detail | |
MolDraw2DUtils | |
MolFragmenter | |
MolHash | |
MolOps | |
Groups a variety of molecular query and transformation operations. | |
MolShapes | |
MorganFingerprints | |
PicklerOps | |
RDTypeTag | |
ReactionRunnerUtils | |
ReducedGraphs | |
RxnOps | |
SLNParse | |
SmartsWrite | |
SmilesWrite | |
StructureCheck | |
Subgraphs | |
UFF | |
Utils | |
Classes | |
class | AromaticAtomIterator_ |
Iterate over aromatic atoms, this is bidirectional. More... | |
class | Atom |
The class for representing atoms. More... | |
class | atomicData |
class | AtomIterator_ |
A general random access iterator. More... | |
class | AtomMonomerInfo |
The abstract base class for atom-level monomer info. More... | |
class | AtomPDBResidueInfo |
Captures atom-level information about peptide residues. More... | |
class | AtomRingQuery |
class | BadFileException |
used by various file parsing classes to indicate a bad file More... | |
class | Bond |
class for representing a bond More... | |
class | BondIterator_ |
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | CachedMolHolder |
Concrete class that holds binary cached molecules in memory. More... | |
class | CachedSmilesMolHolder |
Concrete class that holds smiles strings in memory. More... | |
class | CachedTrustedSmilesMolHolder |
Concrete class that holds trusted smiles strings in memory. More... | |
class | CartesianProductStrategy |
This is a class for enumerating reagents using Cartesian Products of. More... | |
struct | charptr_functor |
functor for comparing two strings More... | |
class | ChemicalReaction |
This is a class for storing and applying general chemical reactions. More... | |
class | ChemicalReactionException |
used to indicate an error in the chemical reaction engine More... | |
class | ChemicalReactionParserException |
used to indicate an error in parsing reaction data More... | |
class | Conformer |
The class for representing 2D or 3D conformation of a molecule. More... | |
class | ConformerException |
used to indicate errors from incorrect confomer access More... | |
class | ConstBondIterator_ |
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More... | |
class | Dict |
The Dict class can be used to store objects of arbitrary type keyed by strings . More... | |
class | DiscreteDistMat |
class | DiscreteValueVect |
a class for efficiently storing vectors of discrete values More... | |
class | EnumerateLibrary |
This is a class for running reactions on sets of reagents. More... | |
class | EnumerateLibraryBase |
Base class for enumerating chemical reactions from collections of. More... | |
struct | EnumerationParams |
This is a class for providing enumeration options that control. More... | |
class | EnumerationStrategyBase |
class | EnumerationStrategyException |
class for flagging enumeration strategy errors More... | |
class | EvenSamplePairsStrategy |
EvenSamplePairsStrategy. More... | |
class | ExclusionList |
class | FeatureFileParseException |
class used to indicate errors in parsing feature definition files. More... | |
class | FileParseException |
used by various file parsing classes to indicate a parse error More... | |
class | FilterCatalog |
class | FilterCatalogEntry |
class | FilterCatalogParams |
struct | FilterData_t |
class | FilterHierarchyMatcher |
struct | FilterMatch |
Holds the atomPairs matched by the underlying matcher. More... | |
class | FilterMatcherBase |
struct | FilterProperty_t |
class | ForwardSDMolSupplier |
class | FPBReader |
class for reading and searching FPB files More... | |
class | FPHolderBase |
Base FPI for the fingerprinter used to rule out impossible matches. More... | |
class | FragCatalogEntry |
class | FragCatGenerator |
class | FragCatParams |
container for user parameters used to create a fragment catalog More... | |
class | FragFPGenerator |
class | GasteigerParams |
class | HasPropQuery |
class | HasPropWithValueQuery |
class | HasPropWithValueQuery< TargetPtr, std::string > |
class | HeteroatomIterator_ |
Iterate over heteroatoms, this is bidirectional. More... | |
struct | larger_of |
functor for returning the larger of two values More... | |
struct | ltDouble |
functor to compare two doubles with a tolerance More... | |
class | MatchingAtomIterator_ |
Iterate over atoms matching a query function. This is bidirectional. More... | |
struct | MCSAtomCompareParameters |
struct | MCSBondCompareParameters |
struct | MCSParameters |
struct | MCSProgressData |
struct | MCSResult |
class | MolBundle |
class | MolCatalogEntry |
This class is used to store ROMol objects in a MolCatalog. More... | |
class | MolCatalogParams |
container for user parameters used to create a mol catalog More... | |
class | MolChemicalFeature |
class | MolChemicalFeatureDef |
class | MolChemicalFeatureFactory |
The class for finding chemical features in molecules. More... | |
class | MolDraw2D |
MolDraw2D is the base class for doing 2D renderings of molecules. More... | |
class | MolDraw2DCairo |
class | MolDraw2DQt |
class | MolDraw2DSVG |
class | MolDraw2Dwx |
struct | MolDrawOptions |
class | MolHolder |
Concrete class that holds molecules in memory. More... | |
class | MolHolderBase |
Base class API for holding molecules so substructure search. More... | |
class | MolPickler |
handles pickling (serializing) molecules More... | |
class | MolPicklerException |
used to indicate exceptions whilst pickling (serializing) molecules More... | |
class | MolSanitizeException |
class for flagging sanitization errors More... | |
class | MolSupplier |
class | MolWriter |
class | MultiFPBReader |
class for reading and searching multiple FPB files More... | |
class | PatternHolder |
Uses the pattern fingerprinter to rule out matches. More... | |
class | PDBMolSupplier |
lazy file parser for PDB files More... | |
class | PDBWriter |
class | PeriodicTable |
singleton class for retrieving information about atoms More... | |
class | QueryAtom |
Class for storing atomic queries. More... | |
class | QueryAtomIterator_ |
Iterate over atoms matching a query. This is bidirectional. More... | |
class | QueryBond |
Class for storing Bond queries. More... | |
class | RandomSampleAllBBsStrategy |
This is a class for randomly enumerating reagents that ensures all reagents. More... | |
class | RandomSampleStrategy |
This is a class for fully randomly sampling reagents. More... | |
struct | RDAny |
class | RDProps |
struct | RDValue |
struct | ReactionFingerprintParams |
class | ReactionPickler |
handles pickling (serializing) reactions More... | |
class | ReactionPicklerException |
used to indicate exceptions whilst pickling (serializing) reactions More... | |
class | RecursiveStructureQuery |
allows use of recursive structure queries (e.g. recursive SMARTS) More... | |
class | ResonanceMolSupplier |
class | RGroupDecomposition |
struct | RGroupDecompositionParameters |
class | RingInfo |
A class to store information about a molecule's rings. More... | |
class | ROMol |
ROMol is a molecule class that is intended to have a fixed topology. More... | |
class | RWMol |
RWMol is a molecule class that is intended to be edited. More... | |
class | RxnSanitizeException |
class for flagging sanitization errors More... | |
class | SDMolSupplier |
class | SDWriter |
class | SLNParseException |
class | SmartsMatcher |
class | SmilesMolSupplier |
lazy file parser for Smiles tables More... | |
class | SmilesParseException |
struct | SmilesParserParams |
class | SmilesWriter |
class | Snapshot |
class | SparseIntVect |
a class for efficiently storing sparse vectors of ints More... | |
class | SubstructLibrary |
Substtructure Search a library of molecules. More... | |
class | TDTMolSupplier |
lazy file parser for TDT files More... | |
class | TDTWriter |
class | Trajectory |
Typedefs | |
typedef boost::shared_ptr< Atom > | ATOM_SPTR |
typedef boost::shared_ptr< ROMol > | ROMOL_SPTR |
typedef boost::shared_ptr< Conformer > | CONFORMER_SPTR |
typedef boost::uint16_t | atomindex_t |
typedef std::vector< RWMOL_SPTR > | RWMOL_SPTR_VECT |
typedef RDCatalog::Catalog< FilterCatalogEntry, FilterCatalogParams > | FCatalog |
typedef std::map< std::string, std::string > | STRING_PROPS |
typedef bool(* | MCSFinalMatchCheckFunction) (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
typedef bool(* | MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* | MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
typedef bool(* | MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > | FragCatalog |
typedef std::vector< boost::shared_ptr< ROMol > > | MOL_SPTR_VECT |
typedef std::vector< std::pair< int, int > > | MatchVectType |
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) More... | |
typedef RDCatalog::HierarchCatalog< MolCatalogEntry, MolCatalogParams, int > | MolCatalog |
a hierarchical catalog for holding molecules More... | |
typedef boost::shared_ptr< MolChemicalFeature > | FeatSPtr |
typedef std::list< FeatSPtr > | FeatSPtrList |
typedef FeatSPtrList::iterator | FeatSPtrList_I |
typedef boost::tuple< float, float, float > | DrawColour |
typedef std::map< int, DrawColour > | ColourPalette |
typedef std::vector< unsigned int > | DashPattern |
typedef std::vector< double > | INVAR_VECT |
typedef INVAR_VECT::iterator | INVAR_VECT_I |
typedef INVAR_VECT::const_iterator | INVAR_VECT_CI |
typedef Queries::Query< bool, Atom const *, true > | ATOM_BOOL_QUERY |
typedef Queries::Query< bool, Bond const *, true > | BOND_BOOL_QUERY |
typedef Queries::AndQuery< int, Atom const *, true > | ATOM_AND_QUERY |
typedef Queries::AndQuery< int, Bond const *, true > | BOND_AND_QUERY |
typedef Queries::OrQuery< int, Atom const *, true > | ATOM_OR_QUERY |
typedef Queries::OrQuery< int, Bond const *, true > | BOND_OR_QUERY |
typedef Queries::XOrQuery< int, Atom const *, true > | ATOM_XOR_QUERY |
typedef Queries::XOrQuery< int, Bond const *, true > | BOND_XOR_QUERY |
typedef Queries::EqualityQuery< int, Atom const *, true > | ATOM_EQUALS_QUERY |
typedef Queries::EqualityQuery< int, Bond const *, true > | BOND_EQUALS_QUERY |
typedef Queries::GreaterQuery< int, Atom const *, true > | ATOM_GREATER_QUERY |
typedef Queries::GreaterQuery< int, Bond const *, true > | BOND_GREATER_QUERY |
typedef Queries::GreaterEqualQuery< int, Atom const *, true > | ATOM_GREATEREQUAL_QUERY |
typedef Queries::GreaterEqualQuery< int, Bond const *, true > | BOND_GREATEREQUAL_QUERY |
typedef Queries::LessQuery< int, Atom const *, true > | ATOM_LESS_QUERY |
typedef Queries::LessQuery< int, Bond const *, true > | BOND_LESS_QUERY |
typedef Queries::LessEqualQuery< int, Atom const *, true > | ATOM_LESSEQUAL_QUERY |
typedef Queries::LessEqualQuery< int, Bond const *, true > | BOND_LESSEQUAL_QUERY |
typedef Queries::RangeQuery< int, Atom const *, true > | ATOM_RANGE_QUERY |
typedef Queries::RangeQuery< int, Bond const *, true > | BOND_RANGE_QUERY |
typedef Queries::SetQuery< int, Atom const *, true > | ATOM_SET_QUERY |
typedef Queries::SetQuery< int, Bond const *, true > | BOND_SET_QUERY |
typedef Queries::Query< int, Bond const *, true > | BOND_NULL_QUERY |
typedef Queries::Query< int, Atom const *, true > | ATOM_NULL_QUERY |
typedef Atom const * | ConstAtomPtr |
typedef Bond const * | ConstBondPtr |
typedef Queries::EqualityQuery< int, Atom const *, true > | ATOM_PROP_QUERY |
typedef Queries::EqualityQuery< int, Bond const *, true > | BOND_PROP_QUERY |
typedef std::map< unsigned int, BondElectrons * > | ConjBondMap |
typedef std::map< unsigned int, AtomElectrons * > | ConjAtomMap |
typedef std::vector< ConjElectrons * > | CEVect |
typedef std::vector< CEVect2 * > | CEVect3 |
typedef std::vector< boost::uint8_t > | ConjFP |
typedef boost::unordered_map< std::size_t, ConjElectrons * > | CEMap |
typedef std::map< std::string, boost::shared_ptr< ROMol > > | RGroupRow |
typedef std::vector< boost::shared_ptr< ROMol > > | RGroupColumn |
typedef std::vector< RGroupRow > | RGroupRows |
typedef std::map< std::string, RGroupColumn > | RGroupColumns |
typedef boost::shared_ptr< Bond > | BOND_SPTR |
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, ATOM_SPTR, BOND_SPTR > | MolGraph |
This is the BGL type used to store the topology: More... | |
typedef std::vector< ROMol > | MOL_VECT |
typedef std::vector< ROMol * > | MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator | MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator | MOL_PTR_VECT_I |
typedef boost::shared_ptr< RWMol > | RWMOL_SPTR |
typedef std::vector< int > | PATH_TYPE |
typedef std::list< PATH_TYPE > | PATH_LIST |
typedef PATH_LIST::const_iterator | PATH_LIST_CI |
typedef std::map< int, PATH_LIST > | INT_PATH_LIST_MAP |
typedef INT_PATH_LIST_MAP::const_iterator | INT_PATH_LIST_MAP_CI |
typedef INT_PATH_LIST_MAP::iterator | INT_PATH_LIST_MAP_I |
typedef std::vector< Snapshot > | SnapshotVect |
typedef std::vector< std::string > | STR_VECT |
typedef RDValue | RDValue_cast_t |
typedef long long int | LONGINT |
typedef unsigned int | UINT |
typedef unsigned short | USHORT |
typedef unsigned char | UCHAR |
typedef std::vector< int > | INT_VECT |
typedef INT_VECT::iterator | INT_VECT_I |
typedef INT_VECT::const_iterator | INT_VECT_CI |
typedef INT_VECT::reverse_iterator | INT_VECT_RI |
typedef INT_VECT::const_reverse_iterator | INT_VECT_CRI |
typedef std::list< int > | INT_LIST |
typedef INT_LIST::iterator | INT_LIST_I |
typedef INT_LIST::const_iterator | INT_LIST_CI |
typedef std::list< INT_VECT > | LIST_INT_VECT |
typedef LIST_INT_VECT::iterator | LIST_INT_VECT_I |
typedef LIST_INT_VECT::const_iterator | LIST_INT_VECT_CI |
typedef std::vector< INT_VECT > | VECT_INT_VECT |
typedef VECT_INT_VECT::iterator | VECT_INT_VECT_I |
typedef VECT_INT_VECT::const_iterator | VECT_INT_VECT_CI |
typedef std::vector< UINT >::const_iterator | UINT_VECT_CI |
typedef std::vector< UINT > | UINT_VECT |
typedef std::vector< std::string >::const_iterator | STR_VECT_CI |
typedef std::vector< std::string >::iterator | STR_VECT_I |
typedef std::vector< double > | DOUBLE_VECT |
typedef DOUBLE_VECT::iterator | DOUBLE_VECT_I |
typedef DOUBLE_VECT::const_iterator | DOUBLE_VECT_CI |
typedef std::vector< DOUBLE_VECT > | VECT_DOUBLE_VECT |
typedef VECT_DOUBLE_VECT::iterator | VECT_DOUBLE_VECT_I |
typedef VECT_DOUBLE_VECT::const_iterator | VECT_DOUBLE_VECT_CI |
typedef std::map< std::string, UINT > | STR_UINT_MAP |
typedef std::map< std::string, UINT >::const_iterator | STR_UINT_MAP_CI |
typedef std::map< int, INT_VECT > | INT_INT_VECT_MAP |
typedef INT_INT_VECT_MAP::const_iterator | INT_INT_VECT_MAP_CI |
typedef std::map< int, int > | INT_MAP_INT |
typedef INT_MAP_INT::iterator | INT_MAP_INT_I |
typedef INT_MAP_INT::const_iterator | INT_MAP_INT_CI |
typedef std::deque< int > | INT_DEQUE |
typedef INT_DEQUE::iterator | INT_DEQUE_I |
typedef INT_DEQUE::const_iterator | INT_DEQUE_CI |
typedef std::map< int, INT_DEQUE > | INT_INT_DEQ_MAP |
typedef INT_INT_DEQ_MAP::const_iterator | INT_INT_DEQ_MAP_CI |
typedef std::set< int > | INT_SET |
typedef INT_SET::iterator | INT_SET_I |
typedef INT_SET::const_iterator | INT_SET_CI |
typedef std::map< double, int, ltDouble > | DOUBLE_INT_MAP |
std::map from double to integer. More... | |
typedef boost::minstd_rand | rng_type |
typedef boost::uniform_int | uniform_int |
typedef boost::uniform_real | uniform_double |
typedef boost::variate_generator< rng_type &, uniform_int > | int_source_type |
typedef boost::variate_generator< rng_type &, uniform_double > | double_source_type |
Enumerations | |
enum | FingerprintType { AtomPairFP = 1, TopologicalTorsion, MorganFP, RDKitFP, PatternFP } |
enum | ReactionMoleculeType { Reactant, Product, Agent } |
enum | Mol2Type { CORINA = 0 } |
enum | AtomComparator { AtomCompareAny, AtomCompareElements, AtomCompareIsotopes } |
enum | BondComparator { BondCompareAny, BondCompareOrder, BondCompareOrderExact } |
enum | RGroupLabels { IsotopeLabels = 0x01, AtomMapLabels = 0x02, AtomIndexLabels = 0x04, RelabelDuplicateLabels = 0x08, AutoDetect = 0x0F } |
enum | RGroupMatching { Greedy = 0x01, GreedyChunks = 0x02, Exhaustive = 0x04 } |
enum | RGroupLabelling { AtomMap = 0x01, Isotope = 0x02, MDLRGroup = 0x04 } |
enum | RGroupCoreAlignment { None = 0x0, MCS = 0x01 } |
enum | EEndian { LITTLE_ENDIAN_ORDER, BIG_ENDIAN_ORDER } |
Functions | |
void | setAtomRLabel (Atom *atm, int rlabel) |
Set the atom's MDL integer RLabel. More... | |
int | getAtomRLabel (const Atom *atm) |
void | setAtomAlias (Atom *atom, const std::string &alias) |
Set the atom's MDL atom alias. More... | |
std::string | getAtomAlias (const Atom *atom) |
void | setAtomValue (Atom *atom, const std::string &value) |
Set the atom's MDL atom value. More... | |
std::string | getAtomValue (const Atom *atom) |
void | setSupplementalSmilesLabel (Atom *atom, const std::string &label) |
Sets the supplemental label that will follow the atom when writing. More... | |
std::string | getSupplementalSmilesLabel (const Atom *atom) |
EnumerationTypes::BBS | removeNonmatchingReagents (const ChemicalReaction &rxn, EnumerationTypes::BBS bbs, const EnumerationParams ¶ms=EnumerationParams()) |
Helper function, remove reagents that are incompatible. More... | |
bool | EnumerateLibraryCanSerialize () |
template<class T > | |
EnumerationTypes::RGROUPS | getSizesFromBBs (const std::vector< std::vector< T > > &bbs) |
Return the number of elements per input vector. More... | |
EnumerationTypes::RGROUPS | getSizesFromReactants (const std::vector< MOL_SPTR_VECT > &bbs) |
MOL_SPTR_VECT | getReactantsFromRGroups (const std::vector< MOL_SPTR_VECT > &bbs, const EnumerationTypes::RGROUPS &rgroups) |
boost::uint64_t | computeNumProducts (const EnumerationTypes::RGROUPS &sizes) |
bool | preprocessReaction (ChemicalReaction &rxn, const std::string &propName=common_properties::molFileValue) |
bool | preprocessReaction (ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors, std::vector< std::vector< std::pair< unsigned int, std::string > > > &reactantLabels, const std::string &propName=common_properties::molFileValue) |
bool | preprocessReaction (ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName=common_properties::molFileValue) |
bool | preprocessReaction (ChemicalReaction &rxn, unsigned int &numWarnings, unsigned int &numErrors, std::vector< std::vector< std::pair< unsigned int, std::string > > > &reactantLabels, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName=common_properties::molFileValue) |
bool | isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeReactantOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
bool | isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeProductOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
bool | isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which) |
bool | isMoleculeAgentOfReaction (const ChemicalReaction &rxn, const ROMol &mol) |
VECT_INT_VECT | getReactingAtoms (const ChemicalReaction &rxn, bool mappedAtomsOnly=false) |
void | addRecursiveQueriesToReaction (ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::vector< std::pair< unsigned int, std::string > > > *reactantLabels=NULL) |
add the recursive queries to the reactants of a reaction More... | |
const ReactionFingerprintParams | DefaultStructuralFPParams (true, 0.2, 1, 1, 4096, PatternFP) |
const ReactionFingerprintParams | DefaultDifferenceFPParams (true, 0.0, 10, 1, 2048, AtomPairFP) |
ExplicitBitVect * | StructuralFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultStructuralFPParams) |
SparseIntVect< boost::uint32_t > * | DifferenceFingerprintChemReaction (const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms=DefaultDifferenceFPParams) |
ChemicalReaction * | RxnBlockToChemicalReaction (const std::string &rxnBlock) |
Parse a text block in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnFileToChemicalReaction (const std::string &fileName) |
Parse a file in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line) |
Parse a text stream in MDL rxn format into a ChemicalReaction. More... | |
ChemicalReaction * | RxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=0, bool useSmiles=false) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction. More... | |
ChemicalReaction * | RxnMolToChemicalReaction (const ROMol &mol) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before. More... | |
std::string | ChemicalReactionToRxnSmarts (const ChemicalReaction &rxn) |
returns the reaction SMARTS for a reaction More... | |
std::string | ChemicalReactionToRxnSmiles (const ChemicalReaction &rxn, bool canonical=true) |
returns the reaction SMILES for a reaction More... | |
std::string | ChemicalReactionToRxnBlock (const ChemicalReaction &rxn, bool separateAgents=false) |
returns an RXN block for a reaction More... | |
ROMol * | ChemicalReactionToRxnMol (const ChemicalReaction &rxn) |
returns a ROMol with RXN roles used to describe the reaction More... | |
std::vector< MOL_SPTR_VECT > | run_Reactants (const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants) |
Runs the reaction on a set of reactants. More... | |
std::vector< MOL_SPTR_VECT > | run_Reactant (const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) |
Runs a single reactant against a single reactant template. More... | |
ROMol * | reduceProductToSideChains (const ROMOL_SPTR &product, bool addDummyAtoms=true) |
Reduce the product generated by run_Reactants or run_Reactant to. More... | |
MOL_SPTR_VECT::const_iterator | getStartIterator (const ChemicalReaction &rxn, ReactionMoleculeType t) |
MOL_SPTR_VECT::const_iterator | getEndIterator (const ChemicalReaction &rxn, ReactionMoleculeType t) |
bool | hasReactantTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasProductTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasAgentTemplateSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn) |
bool | hasReactionSubstructMatch (const ChemicalReaction &rxn, const ChemicalReaction &query_rxn, bool includeAgents=false) |
bool | hasReactionAtomMapping (const ChemicalReaction &rxn) |
bool | isReactionTemplateMoleculeAgent (const ROMol &mol, double agentThreshold) |
void | updateProductsStereochem (ChemicalReaction *rxn) |
void | removeMappingNumbersFromReactions (const ChemicalReaction &rxn) |
ROMol * | deleteSubstructs (const ROMol &mol, const ROMol &query, bool onlyFrags=false, bool useChirality=false) |
Returns a copy of an ROMol with the atoms and bonds that match a pattern removed. More... | |
std::vector< ROMOL_SPTR > | replaceSubstructs (const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false, unsigned int replacementConnectionPoint=0, bool useChirality=false) |
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule. More... | |
ROMol * | replaceSidechains (const ROMol &mol, const ROMol &coreQuery, bool useChirality=false) |
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed. More... | |
ROMol * | replaceCore (const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) |
Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core. More... | |
ROMol * | replaceCore (const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false, bool useChirality=false) |
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed. More... | |
ROMol * | MurckoDecompose (const ROMol &mol) |
Carries out a Murcko decomposition on the molecule provided. More... | |
ROMol * | combineMols (const ROMol &mol1, const ROMol &mol2, RDGeom::Point3D offset=RDGeom::Point3D(0, 0, 0)) |
Combined two molecules to create a new one. More... | |
void | addRecursiveQueries (ROMol &mol, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::pair< unsigned int, std::string > > *reactantLabels=NULL) |
Adds named recursive queries to a molecule's atoms based on atom. More... | |
void | parseQueryDefFile (const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\, const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries() More... | |
void | parseQueryDefFile (std::istream *inStream, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\, const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
void | parseQueryDefText (const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\, const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1) |
equivalent to parseQueryDefFile() but the query definitions are More... | |
std::string | strip (const std::string &orig) |
RWMol * | MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
RWMol * | MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true) |
std::string | MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
void | MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false) |
RWMol * | TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false) |
translate TPL data (BioCad format) into a multi-conf molecule More... | |
RWMol * | TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false) |
construct a multi-conf molecule from a TPL (BioCad format) file More... | |
std::string | MolToTPLText (const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
void | MolToTPLFile (const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) |
RWMol * | Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA) |
RWMol * | PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
RWMol * | PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0) |
std::string | MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0) |
void | MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) |
void | DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf) |
void | DetectBondStereoChemistry (ROMol &mol, const Conformer *conf) |
deprecated, please use MolOps::detectBondStereoChemistry instead More... | |
void | WedgeMolBonds (ROMol &mol, const Conformer *conf) |
INT_MAP_INT | pickBondsToWedge (const ROMol &mol) |
void | ClearSingleBondDirFlags (ROMol &mol) |
Bond::BondDir | DetermineBondWedgeState (const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf) |
void | ConnectTheDots (RWMol *mol, unsigned int flags=0) |
void | StandardPDBResidueBondOrders (RWMol *mol) |
RWMol * | SequenceToMol (const char *seq, bool sanitize, bool lowerD) |
RWMol * | SequenceToMol (const std::string &seq, bool sanitize, bool lowerD) |
RWMol * | SequenceToMol (const char *seq, bool sanitize=true, int flavor=0) |
RWMol * | SequenceToMol (const std::string &seq, bool sanitize=true, int flavor=0) |
RWMol * | FASTAToMol (const char *seq, bool sanitize, bool lowerD) |
RWMol * | FASTAToMol (const std::string &seq, bool sanitize, bool lowerD) |
RWMol * | FASTAToMol (const char *seq, bool sanitize=true, int flavor=0) |
RWMol * | FASTAToMol (const std::string &seq, bool sanitize=true, int flavor=0) |
RWMol * | HELMToMol (const char *helm, bool sanitize=true) |
RWMol * | HELMToMol (const std::string &helm, bool sanitize=true) |
std::string | MolToSequence (const ROMol &mol) |
std::string | MolToFASTA (const ROMol &mol) |
std::string | MolToHELM (const ROMol &mol) |
bool | FilterCatalogCanSerialize () |
unsigned int | GetNumEntries (FilterCatalogParams::FilterCatalogs catalog) |
const FilterData_t * | GetFilterData (FilterCatalogParams::FilterCatalogs catalog) |
unsigned int | GetNumPropertyEntries (FilterCatalogParams::FilterCatalogs catalog) |
const FilterProperty_t * | GetFilterProperties (FilterCatalogParams::FilterCatalogs catalog) |
FilterCatalogEntry * | MakeFilterCatalogEntry (const FilterData_t &, unsigned int num_props=0, const FilterProperty_t *props=0) |
const FilterCatalog & | GetFunctionalGroupHierarchy () |
Return the functional group hierarchy as a FilterCatalog. More... | |
const std::map< std::string, ROMOL_SPTR > & | GetFlattenedFunctionalGroupHierarchy (bool normalized=false) |
ExplicitBitVect * | RDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint32_t > > *atomBits=0, std::map< boost::uint32_t, std::vector< std::vector< int > > > *bitInfo=0) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm. More... | |
ExplicitBitVect * | LayeredFingerprintMol (const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=0, ExplicitBitVect *setOnlyBits=0, bool branchedPaths=true, const std::vector< boost::uint32_t > *fromAtoms=0) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm. More... | |
ExplicitBitVect * | PatternFingerprintMol (const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=0, ExplicitBitVect *setOnlyBits=0) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns. More... | |
SparseIntVect< boost::uint64_t > * | getUnfoldedRDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, bool useHs=true, bool branchedPaths=true, bool useBondOrder=true, std::vector< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint64_t > > *atomBits=0, std::map< boost::uint64_t, std::vector< std::vector< int > > > *bitInfo=0) |
RDKIT_WRAP_DECL bool | MCSAtomCompareAny (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_WRAP_DECL bool | MCSAtomCompareElements (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_WRAP_DECL bool | MCSAtomCompareIsotopes (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
RDKIT_WRAP_DECL bool | MCSBondCompareAny (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
RDKIT_WRAP_DECL bool | MCSBondCompareOrder (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
RDKIT_WRAP_DECL bool | MCSBondCompareOrderExact (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
bool | MCSProgressCallbackTimeout (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
void | parseMCSParametersJSON (const char *json, MCSParameters *params) |
MCSResult | findMCS (const std::vector< ROMOL_SPTR > &mols, const MCSParameters *params=0) |
MCSResult | findMCS_P (const std::vector< ROMOL_SPTR > &mols, const char *params_json) |
MCSResult | findMCS (const std::vector< ROMOL_SPTR > &mols, bool maximizeBonds, double threshold=1.0, unsigned timeout=3600, bool verbose=false, bool matchValences=false, bool ringMatchesRingOnly=false, bool completeRingsOnly=false, bool matchChiralTag=false, AtomComparator atomComp=AtomCompareElements, BondComparator bondComp=BondCompareOrder) |
bool | FinalChiralityCheckFunction (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
MOL_SPTR_VECT | readFuncGroups (std::string fileName) |
MOL_SPTR_VECT | readFuncGroups (std::istream &inStream, int nToRead=-1) |
MatchVectType | findFuncGroupsOnMol (const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds) |
ROMol * | prepareMol (const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap) |
int | parseFeatureData (const std::string &defnText, MolChemicalFeatureDef::CollectionType &featDefs) |
int | parseFeatureData (std::istream &istream, MolChemicalFeatureDef::CollectionType &featDefs) |
int | parseFeatureFile (const std::string &fileName, MolChemicalFeatureDef::CollectionType &featDefs) |
MolChemicalFeatureFactory * | buildFeatureFactory (std::istream &inStream) |
constructs a MolChemicalFeatureFactory from the data in a stream More... | |
MolChemicalFeatureFactory * | buildFeatureFactory (const std::string &featureData) |
constructs a MolChemicalFeatureFactory from the data in a string More... | |
void | assignDefaultPalette (ColourPalette &palette) |
void | assignBWPalette (ColourPalette &palette) |
void | computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false) |
void | computeGasteigerCharges (const ROMol &mol, int nIter=12, bool throwOnParamFailure=false) |
void | computeGasteigerCharges (const ROMol &mol, std::vector< double > &charges, int nIter=12, bool throwOnParamFailure=false) |
std::string | describeQuery (const Atom *atom) |
std::string | describeQuery (const Bond *bond) |
static int | queryAtomAromatic (Atom const *at) |
static int | queryAtomAliphatic (Atom const *at) |
static int | queryAtomExplicitDegree (Atom const *at) |
static int | queryAtomTotalDegree (Atom const *at) |
static int | queryAtomHeavyAtomDegree (Atom const *at) |
static int | queryAtomHCount (Atom const *at) |
static int | queryAtomImplicitHCount (Atom const *at) |
static int | queryAtomHasImplicitH (Atom const *at) |
static int | queryAtomImplicitValence (Atom const *at) |
static int | queryAtomExplicitValence (Atom const *at) |
static int | queryAtomTotalValence (Atom const *at) |
static int | queryAtomUnsaturated (Atom const *at) |
static int | queryAtomNum (Atom const *at) |
static int | queryAtomMass (Atom const *at) |
static int | queryAtomIsotope (Atom const *at) |
static int | queryAtomFormalCharge (Atom const *at) |
static int | queryAtomHybridization (Atom const *at) |
static int | queryAtomNumRadicalElectrons (Atom const *at) |
static int | queryAtomHasChiralTag (Atom const *at) |
static int | queryAtomMissingChiralTag (Atom const *at) |
unsigned int | queryAtomBondProduct (Atom const *at) |
unsigned int | queryAtomAllBondProduct (Atom const *at) |
static int | queryBondOrder (Bond const *bond) |
static int | queryBondDir (Bond const *bond) |
static int | queryIsBondInNRings (Bond const *at) |
static int | queryBondHasStereo (Bond const *bnd) |
static int | queryIsAtomInNRings (Atom const *at) |
static int | queryIsAtomInRing (Atom const *at) |
static int | queryAtomHasRingBond (Atom const *at) |
static int | queryIsBondInRing (Bond const *bond) |
static int | queryAtomMinRingSize (Atom const *at) |
static int | queryBondMinRingSize (Bond const *bond) |
static int | queryAtomRingBondCount (Atom const *at) |
template<int tgt> | |
int | queryAtomIsInRingOfSize (Atom const *at) |
template<int tgt> | |
int | queryBondIsInRingOfSize (Bond const *bond) |
template<class T > | |
T * | makeAtomSimpleQuery (int what, int func(Atom const *), const std::string &description="Atom Simple") |
template<class T > | |
T * | makeAtomNumQuery (int what, const std::string &descr) |
returns a Query for matching atomic number More... | |
ATOM_EQUALS_QUERY * | makeAtomNumQuery (int what) |
template<class T > | |
T * | makeAtomImplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching implicit valence More... | |
ATOM_EQUALS_QUERY * | makeAtomImplicitValenceQuery (int what) |
template<class T > | |
T * | makeAtomExplicitValenceQuery (int what, const std::string &descr) |
returns a Query for matching explicit valence More... | |
ATOM_EQUALS_QUERY * | makeAtomExplicitValenceQuery (int what) |
template<class T > | |
T * | makeAtomTotalValenceQuery (int what, const std::string &descr) |
returns a Query for matching total valence More... | |
ATOM_EQUALS_QUERY * | makeAtomTotalValenceQuery (int what) |
template<class T > | |
T * | makeAtomExplicitDegreeQuery (int what, const std::string &descr) |
returns a Query for matching explicit degree More... | |
ATOM_EQUALS_QUERY * | makeAtomExplicitDegreeQuery (int what) |
template<class T > | |
T * | makeAtomTotalDegreeQuery (int what, const std::string &descr) |
returns a Query for matching atomic degree More... | |
ATOM_EQUALS_QUERY * | makeAtomTotalDegreeQuery (int what) |
template<class T > | |
T * | makeAtomHeavyAtomDegreeQuery (int what, const std::string &descr) |
returns a Query for matching heavy atom degree More... | |
ATOM_EQUALS_QUERY * | makeAtomHeavyAtomDegreeQuery (int what) |
template<class T > | |
T * | makeAtomHCountQuery (int what, const std::string &descr) |
returns a Query for matching hydrogen count More... | |
ATOM_EQUALS_QUERY * | makeAtomHCountQuery (int what) |
template<class T > | |
T * | makeAtomHasImplicitHQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomHasImplicitHQuery () |
template<class T > | |
T * | makeAtomImplicitHCountQuery (int what, const std::string &descr) |
returns a Query for matching implicit hydrogen count More... | |
ATOM_EQUALS_QUERY * | makeAtomImplicitHCountQuery (int what) |
template<class T > | |
T * | makeAtomAromaticQuery (const std::string &descr) |
returns a Query for matching the isAromatic flag More... | |
ATOM_EQUALS_QUERY * | makeAtomAromaticQuery () |
template<class T > | |
T * | makeAtomAliphaticQuery (const std::string &descr) |
returns a Query for matching aliphatic atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomAliphaticQuery () |
template<class T > | |
T * | makeAtomMassQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular mass More... | |
ATOM_EQUALS_QUERY * | makeAtomMassQuery (int what) |
template<class T > | |
T * | makeAtomIsotopeQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular isotope More... | |
ATOM_EQUALS_QUERY * | makeAtomIsotopeQuery (int what) |
template<class T > | |
T * | makeAtomFormalChargeQuery (int what, const std::string &descr) |
returns a Query for matching formal charge More... | |
ATOM_EQUALS_QUERY * | makeAtomFormalChargeQuery (int what) |
template<class T > | |
T * | makeAtomHybridizationQuery (int what, const std::string &descr) |
returns a Query for matching hybridization More... | |
ATOM_EQUALS_QUERY * | makeAtomHybridizationQuery (int what) |
template<class T > | |
T * | makeAtomNumRadicalElectronsQuery (int what, const std::string &descr) |
returns a Query for matching the number of radical electrons More... | |
ATOM_EQUALS_QUERY * | makeAtomNumRadicalElectronsQuery (int what) |
template<class T > | |
T * | makeAtomHasChiralTagQuery (const std::string &descr) |
ATOM_EQUALS_QUERY * | makeAtomHasChiralTagQuery () |
template<class T > | |
T * | makeAtomMissingChiralTagQuery (const std::string &descr) |
ATOM_EQUALS_QUERY * | makeAtomMissingChiralTagQuery () |
template<class T > | |
T * | makeAtomUnsaturatedQuery (const std::string &descr) |
returns a Query for matching atoms with unsaturation: More... | |
ATOM_EQUALS_QUERY * | makeAtomUnsaturatedQuery () |
template<class T > | |
T * | makeAtomInRingQuery (const std::string &descr) |
returns a Query for matching ring atoms More... | |
ATOM_EQUALS_QUERY * | makeAtomInRingQuery () |
template<class T > | |
T * | makeAtomInNRingsQuery (int what, const std::string &descr) |
returns a Query for matching atoms in a particular number of rings More... | |
ATOM_EQUALS_QUERY * | makeAtomInNRingsQuery (int what) |
ATOM_EQUALS_QUERY * | makeAtomInRingOfSizeQuery (int tgt) |
returns a Query for matching atoms in rings of a particular size More... | |
template<class T > | |
T * | makeAtomMinRingSizeQuery (int tgt, const std::string &descr) |
returns a Query for matching an atom's minimum ring size More... | |
ATOM_EQUALS_QUERY * | makeAtomMinRingSizeQuery (int tgt) |
template<class T > | |
T * | makeAtomRingBondCountQuery (int what, const std::string &descr) |
returns a Query for matching atoms with a particular number of ring bonds More... | |
ATOM_EQUALS_QUERY * | makeAtomRingBondCountQuery (int what) |
ATOM_EQUALS_QUERY * | makeAAtomQuery () |
returns a Query for matching generic A atoms (heavy atoms) More... | |
ATOM_EQUALS_QUERY * | makeAHAtomQuery () |
returns a Query for matching generic AH atoms (any atom) More... | |
ATOM_OR_QUERY * | makeQAtomQuery () |
returns a Query for matching generic Q atoms (heteroatoms) More... | |
ATOM_EQUALS_QUERY * | makeQHAtomQuery () |
returns a Query for matching generic QH atoms (heteroatom or H) More... | |
ATOM_OR_QUERY * | makeXAtomQuery () |
returns a Query for matching generic X atoms (halogens) More... | |
ATOM_OR_QUERY * | makeXHAtomQuery () |
returns a Query for matching generic XH atoms (halogen or H) More... | |
ATOM_OR_QUERY * | makeMAtomQuery () |
returns a Query for matching generic M atoms (metals) More... | |
ATOM_OR_QUERY * | makeMHAtomQuery () |
returns a Query for matching generic MH atoms (metals or H) More... | |
template<class T > | |
T * | makeAtomHasRingBondQuery (const std::string &descr) |
returns a Query for matching atoms that have ring bonds More... | |
ATOM_EQUALS_QUERY * | makeAtomHasRingBondQuery () |
BOND_EQUALS_QUERY * | makeBondOrderEqualsQuery (Bond::BondType what) |
returns a Query for matching bond orders More... | |
BOND_EQUALS_QUERY * | makeBondDirEqualsQuery (Bond::BondDir what) |
returns a Query for matching bond directions More... | |
BOND_EQUALS_QUERY * | makeBondHasStereoQuery () |
returns a Query for matching bonds with stereo set More... | |
BOND_EQUALS_QUERY * | makeBondIsInRingQuery () |
returns a Query for matching ring bonds More... | |
BOND_EQUALS_QUERY * | makeBondInRingOfSizeQuery (int what) |
returns a Query for matching bonds in rings of a particular size More... | |
BOND_EQUALS_QUERY * | makeBondMinRingSizeQuery (int what) |
returns a Query for matching a bond's minimum ring size More... | |
BOND_EQUALS_QUERY * | makeBondInNRingsQuery (int tgt) |
returns a Query for matching bonds in a particular number of rings More... | |
BOND_NULL_QUERY * | makeBondNullQuery () |
returns a Query for matching any bond More... | |
ATOM_NULL_QUERY * | makeAtomNullQuery () |
returns a Query for matching any atom More... | |
static int | queryAtomRingMembership (Atom const *at) |
template<typename T > | |
int | nullDataFun (T) |
template<typename T > | |
bool | nullQueryFun (T) |
template<class Target > | |
Queries::EqualityQuery< int, const Target *, true > * | makeHasPropQuery (const std::string &property) |
returns a Query for matching atoms that have a particular property More... | |
template<class Target , class T > | |
Queries::EqualityQuery< int, const Target *, true > * | makePropQuery (const std::string &propname, const T &val, const T &tolerance=T()) |
bool | isComplexQuery (const Bond *b) |
bool | isComplexQuery (const Atom *a) |
bool | isAtomAromatic (const Atom *a) |
unsigned int | RGroupDecompose (const std::vector< ROMOL_SPTR > &cores, const std::vector< ROMOL_SPTR > &mols, RGroupRows &rows, std::vector< unsigned int > *unmatched=0, const RGroupDecompositionParameters &options=RGroupDecompositionParameters()) |
unsigned int | RGroupDecompose (const std::vector< ROMOL_SPTR > &cores, const std::vector< ROMOL_SPTR > &mols, RGroupColumns &columns, std::vector< unsigned int > *unmatched=0, const RGroupDecompositionParameters &options=RGroupDecompositionParameters()) |
RWMol * | SLNToMol (const std::string &smi, bool sanitize=true, int debugParse=0) |
RWMol * | SLNQueryToMol (const std::string &smi, bool mergeHs=true, int debugParse=0) |
std::string | MolToSmarts (ROMol &mol, bool doIsomericSmarts=false) |
returns the SMARTS for a molecule More... | |
RWMol * | SmilesToMol (const std::string &smi, const SmilesParserParams ¶ms) |
RWMol * | SmilesToMol (const std::string &smi, int debugParse=0, bool sanitize=true, std::map< std::string, std::string > *replacements=0) |
Construct a molecule from a SMILES string. More... | |
RWMol * | SmartsToMol (const std::string &sma, int debugParse=0, bool mergeHs=false, std::map< std::string, std::string > *replacements=0) |
Construct a molecule from a SMARTS string. More... | |
std::string | MolToSmiles (const ROMol &mol, bool doIsomericSmiles=false, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) |
returns canonical SMILES for a molecule More... | |
std::string | MolFragmentToSmiles (const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=0, const std::vector< std::string > *atomSymbols=0, const std::vector< std::string > *bondSymbols=0, bool doIsomericSmiles=false, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) |
returns canonical SMILES for part of a molecule More... | |
INT_PATH_LIST_MAP | findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs in a range of sizes More... | |
PATH_LIST | findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs of a particular size More... | |
PATH_LIST | findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true, int rootedAtAtom=-1) |
find unique bond subgraphs of a particular size More... | |
PATH_LIST | findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
find all paths of a particular size More... | |
INT_PATH_LIST_MAP | findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
PATH_TYPE | findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false) |
find bond subgraphs of a particular radius around an atom More... | |
bool | SubstructMatch (const ROMol &mol, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
Find a substructure match for a query in a molecule. More... | |
bool | SubstructMatch (ResonanceMolSupplier &resMolSuppl, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
Find a substructure match for a query in a ResonanceMolSupplier object. More... | |
unsigned int | SubstructMatch (const ROMol &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
Find all substructure matches for a query in a molecule. More... | |
unsigned int | SubstructMatch (ResonanceMolSupplier &resMolSuppl, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=false, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) |
Find all substructure matches for a query in a ResonanceMolSupplier object. More... | |
bool | SubstructMatch (const MolBundle &bundle, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
bool | SubstructMatch (const ROMol &bundle, const MolBundle &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
bool | SubstructMatch (const MolBundle &bundle, const MolBundle &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false) |
unsigned int | SubstructMatch (const MolBundle &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
unsigned int | SubstructMatch (const MolBundle &mol, const MolBundle &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
unsigned int | SubstructMatch (const ROMol &mol, const MolBundle &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000) |
double | toPrime (const MatchVectType &v) |
void | removeDuplicates (std::vector< MatchVectType > &v, unsigned int nAtoms) |
bool | atomCompat (const ATOM_SPTR &a1, const ATOM_SPTR &a2, bool useQueryQueryMatches=false) |
bool | chiralAtomCompat (const ATOM_SPTR &a1, const ATOM_SPTR &a2) |
bool | bondCompat (const BOND_SPTR &b1, const BOND_SPTR &b2, bool useQueryQueryMatches=false) |
unsigned int | readAmberTrajectory (const std::string &fName, Trajectory &traj) |
Reads coordinates from an AMBER trajectory file into the traj Trajectory object. More... | |
unsigned int | readGromosTrajectory (const std::string &fName, Trajectory &traj) |
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object. More... | |
DiscreteDistMat * | getDiscreteDistMat () |
unsigned int | computeL1Norm (const DiscreteValueVect &v1, const DiscreteValueVect &v2) |
DiscreteValueVect | operator+ (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
DiscreteValueVect | operator- (const DiscreteValueVect &p1, const DiscreteValueVect &p2) |
template<typename IndexType , typename SequenceType > | |
void | updateFromSequence (SparseIntVect< IndexType > &vect, const SequenceType &seq) |
template<typename IndexType > | |
double | DiceSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TverskySimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, double a, double b, bool returnDistance=false, double bounds=0.0) |
template<typename IndexType > | |
double | TanimotoSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0) |
template<typename CompareFunc > | |
bool | hanoi (int *base, int nel, int *temp, int *count, int *changed, CompareFunc compar) |
template<typename CompareFunc > | |
void | hanoisort (int *base, int nel, int *count, int *changed, CompareFunc compar) |
template<class T > | |
const T | rdany_cast (const RDAny &d) |
template<class T > | |
T | rdany_cast (RDAny &d) |
template<class T > | |
boost::enable_if< boost::is_arithmetic< T >, T >::type | from_rdany (const RDAny &arg) |
template<class T > | |
boost::disable_if< boost::is_arithmetic< T >, T >::type | from_rdany (const RDAny &arg) |
unsigned int | getNumThreadsToUse (int target) |
void | copy_rdvalue (RDValue &dest, const RDValue &src) |
template<class T > | |
bool | rdvalue_is (RDValue v) |
template<> | |
bool | rdvalue_is< double > (RDValue v) |
template<> | |
bool | rdvalue_is< const double & > (RDValue v) |
template<class T > | |
T | rdvalue_cast (RDValue v) |
template<> | |
double | rdvalue_cast< double > (RDValue v) |
template<> | |
float | rdvalue_cast< float > (RDValue v) |
template<> | |
int | rdvalue_cast< int > (RDValue v) |
template<> | |
unsigned int | rdvalue_cast< unsigned int > (RDValue v) |
template<> | |
bool | rdvalue_cast< bool > (RDValue v) |
template<> | |
std::string | rdvalue_cast< std::string > (RDValue_cast_t v) |
template<> | |
std::string & | rdvalue_cast< std::string & > (RDValue_cast_t v) |
template<> | |
std::vector< double > | rdvalue_cast< std::vector< double > > (RDValue_cast_t v) |
template<> | |
std::vector< double > & | rdvalue_cast< std::vector< double > & > (RDValue_cast_t v) |
template<> | |
std::vector< float > | rdvalue_cast< std::vector< float > > (RDValue_cast_t v) |
template<> | |
std::vector< float > & | rdvalue_cast< std::vector< float > & > (RDValue_cast_t v) |
template<> | |
std::vector< std::string > | rdvalue_cast< std::vector< std::string > > (RDValue_cast_t v) |
template<> | |
std::vector< std::string > & | rdvalue_cast< std::vector< std::string > & > (RDValue_cast_t v) |
template<> | |
std::vector< int > | rdvalue_cast< std::vector< int > > (RDValue_cast_t v) |
template<> | |
std::vector< int > & | rdvalue_cast< std::vector< int > & > (RDValue_cast_t v) |
template<> | |
std::vector< unsigned int > | rdvalue_cast< std::vector< unsigned int > > (RDValue_cast_t v) |
template<> | |
std::vector< unsigned int > & | rdvalue_cast< std::vector< unsigned int > & > (RDValue_cast_t v) |
template<> | |
boost::any | rdvalue_cast< boost::any > (RDValue_cast_t v) |
template<> | |
boost::any & | rdvalue_cast< boost::any & > (RDValue_cast_t v) |
template<> | |
const boost::any & | rdvalue_cast< const boost::any & > (RDValue_cast_t v) |
template<class T > | |
std::string | vectToString (RDValue val) |
bool | rdvalue_tostring (RDValue_cast_t val, std::string &res) |
template<class T > | |
boost::enable_if< boost::is_arithmetic< T >, T >::type | from_rdvalue (RDValue_cast_t arg) |
template<class T > | |
boost::disable_if< boost::is_arithmetic< T >, T >::type | from_rdvalue (RDValue_cast_t arg) |
template<class T , unsigned int size> | |
T | SwapBytes (T value) |
template<EEndian from, EEndian to, class T > | |
T | EndianSwapBytes (T value) |
template<EEndian from, EEndian to> | |
char | EndianSwapBytes (char value) |
template<EEndian from, EEndian to> | |
unsigned char | EndianSwapBytes (unsigned char value) |
template<EEndian from, EEndian to> | |
signed char | EndianSwapBytes (signed char value) |
void | appendPackedIntToStream (std::stringstream &ss, boost::uint32_t num) |
Packs an integer and outputs it to a stream. More... | |
boost::uint32_t | readPackedIntFromStream (std::stringstream &ss) |
Reads an integer from a stream in packed format and returns the result. More... | |
boost::uint32_t | pullPackedIntFromString (const char *&text) |
template<typename T > | |
void | streamWrite (std::ostream &ss, const T &val) |
does a binary write of an object to a stream More... | |
void | streamWrite (std::ostream &ss, const std::string &what) |
special case for string More... | |
template<typename T > | |
void | streamWriteVec (std::ostream &ss, const T &val) |
template<typename T > | |
void | streamRead (std::istream &ss, T &loc) |
does a binary read of an object from a stream More... | |
template<class T > | |
void | streamRead (std::istream &ss, T &obj, int version) |
special case for string More... | |
void | streamRead (std::istream &ss, std::string &what, int version) |
template<class T > | |
void | streamReadVec (std::istream &ss, T &val) |
void | streamReadStringVec (std::istream &ss, std::vector< std::string > &val, int version) |
std::string | getLine (std::istream *inStream) |
grabs the next line from an instream and returns it. More... | |
std::string | getLine (std::istream &inStream) |
grabs the next line from an instream and returns it. More... | |
bool | isSerializable (const Dict::Pair &pair) |
bool | streamWriteProp (std::ostream &ss, const Dict::Pair &pair) |
bool | streamWriteProps (std::ostream &ss, const RDProps &props, bool savePrivate=false, bool saveComputed=false) |
template<class T > | |
void | readRDValue (std::istream &ss, RDValue &value) |
template<class T > | |
void | readRDVecValue (std::istream &ss, RDValue &value) |
void | readRDValueString (std::istream &ss, RDValue &value) |
void | readRDStringVecValue (std::istream &ss, RDValue &value) |
bool | streamReadProp (std::istream &ss, Dict::Pair &pair) |
unsigned int | streamReadProps (std::istream &ss, RDProps &props) |
void | Union (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res) |
calculate the union of two INT_VECTs and put the results in a third vector More... | |
void | Intersect (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res) |
calculate the intersection of two INT_VECTs and put the results in a third vector More... | |
void | Union (const VECT_INT_VECT &rings, INT_VECT &res, const INT_VECT *exclude=NULL) |
calculating the union of the INT_VECT's in a VECT_INT_VECT More... | |
int | nextCombination (INT_VECT &comb, int tot) |
given a current combination of numbers change it to the next possible More... | |
double | round (double v) |
rounds a value to the closest int More... | |
double | computeIntVectPrimesProduct (const INT_VECT &ring) |
compute the product of the set of primes corresponding to the values in an INT_VECT More... | |
bool | feq (double v1, double v2, double tol=1e-4) |
floating point comparison with a tolerance More... | |
rng_type & | getRandomGenerator (int seed=-1) |
Optionally seed and return a reference to the global (Boost) random. More... | |
double | getRandomVal (int seed=-1) |
double_source_type & | getDoubleRandomSource () |
return a reference to the global (Boost) random source More... | |
template<class T > | |
unsigned int | countSwapsToInterconvert (const T &ref, T probe) |
Variables | |
const std::string | periodicTableAtomData |
const std::string | isotopesAtomData [] |
const int | MOLFILE_MAXLINE = 256 |
static int | defaultConfId = -1 |
static unsigned int | ctdIGNORE_H_H_CONTACTS = 0x1 |
static unsigned int | ctdALL_FLAGS = 0xFFFFFFFF |
const char * | DEFAULT_FILTERMATCHERBASE_NAME |
const char * | SMARTS_MATCH_NAME_DEFAULT |
const std::string | RDKFingerprintMolVersion = "2.0.0" |
const unsigned int | maxFingerprintLayers = 10 |
const std::string | LayeredFingerprintMolVersion = "0.7.0" |
const unsigned int | substructLayers = 0x07 |
std::string | paramData |
std::string | additionalParamData |
const double | IONXH = 20.02 |
const double | DAMP_SCALE = 0.5 |
const double | DAMP = 0.5 |
const int | massIntegerConversionFactor = 1000 |
const int | ci_RIGHTMOST_ATOM |
const int | ci_LEADING_BOND |
const int | ci_ATOM_HOLDER |
const int | NUM_PRIMES_AVAIL = 1000 |
the number of primes available and stored More... | |
int | firstThousandPrimes [NUM_PRIMES_AVAIL] |
const unsigned int | BITS_PER_INT = 32 |
const double | MAX_DOUBLE |
const double | EPS_DOUBLE |
const double | SMALL_DOUBLE |
const double | MAX_INT |
const double | MAX_LONGINT |
const int | FILE_MAXLINE |
an assumed maximum length for lines read from files More... | |
const char * | rdkitVersion |
const char * | boostVersion |
const char * | rdkitBuild |
typedef Queries::AndQuery<int, Atom const *, true> RDKit::ATOM_AND_QUERY |
Definition at line 32 of file QueryOps.h.
typedef Queries::Query<bool, Atom const *, true> RDKit::ATOM_BOOL_QUERY |
Definition at line 29 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_EQUALS_QUERY |
Definition at line 41 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Atom const *, true> RDKit::ATOM_GREATER_QUERY |
Definition at line 44 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Atom const *, true> RDKit::ATOM_GREATEREQUAL_QUERY |
Definition at line 48 of file QueryOps.h.
typedef Queries::LessQuery<int, Atom const *, true> RDKit::ATOM_LESS_QUERY |
Definition at line 52 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Atom const *, true> RDKit::ATOM_LESSEQUAL_QUERY |
Definition at line 55 of file QueryOps.h.
typedef Queries::Query<int, Atom const *, true> RDKit::ATOM_NULL_QUERY |
Definition at line 65 of file QueryOps.h.
typedef Queries::OrQuery<int, Atom const *, true> RDKit::ATOM_OR_QUERY |
Definition at line 35 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Atom const *, true> RDKit::ATOM_PROP_QUERY |
Definition at line 623 of file QueryOps.h.
typedef Queries::RangeQuery<int, Atom const *, true> RDKit::ATOM_RANGE_QUERY |
Definition at line 58 of file QueryOps.h.
typedef Queries::SetQuery<int, Atom const *, true> RDKit::ATOM_SET_QUERY |
Definition at line 61 of file QueryOps.h.
typedef boost::shared_ptr< Atom > RDKit::ATOM_SPTR |
typedef Queries::XOrQuery<int, Atom const *, true> RDKit::ATOM_XOR_QUERY |
Definition at line 38 of file QueryOps.h.
typedef boost::uint16_t RDKit::atomindex_t |
typedef Queries::AndQuery<int, Bond const *, true> RDKit::BOND_AND_QUERY |
Definition at line 33 of file QueryOps.h.
typedef Queries::Query<bool, Bond const *, true> RDKit::BOND_BOOL_QUERY |
Definition at line 30 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_EQUALS_QUERY |
Definition at line 42 of file QueryOps.h.
typedef Queries::GreaterQuery<int, Bond const *, true> RDKit::BOND_GREATER_QUERY |
Definition at line 45 of file QueryOps.h.
typedef Queries::GreaterEqualQuery<int, Bond const *, true> RDKit::BOND_GREATEREQUAL_QUERY |
Definition at line 50 of file QueryOps.h.
typedef Queries::LessQuery<int, Bond const *, true> RDKit::BOND_LESS_QUERY |
Definition at line 53 of file QueryOps.h.
typedef Queries::LessEqualQuery<int, Bond const *, true> RDKit::BOND_LESSEQUAL_QUERY |
Definition at line 56 of file QueryOps.h.
typedef Queries::Query<int, Bond const *, true> RDKit::BOND_NULL_QUERY |
Definition at line 64 of file QueryOps.h.
typedef Queries::OrQuery<int, Bond const *, true> RDKit::BOND_OR_QUERY |
Definition at line 36 of file QueryOps.h.
typedef Queries::EqualityQuery<int, Bond const *, true> RDKit::BOND_PROP_QUERY |
Definition at line 624 of file QueryOps.h.
typedef Queries::RangeQuery<int, Bond const *, true> RDKit::BOND_RANGE_QUERY |
Definition at line 59 of file QueryOps.h.
typedef Queries::SetQuery<int, Bond const *, true> RDKit::BOND_SET_QUERY |
Definition at line 62 of file QueryOps.h.
typedef boost::shared_ptr< Bond > RDKit::BOND_SPTR |
typedef Queries::XOrQuery<int, Bond const *, true> RDKit::BOND_XOR_QUERY |
Definition at line 39 of file QueryOps.h.
typedef boost::unordered_map<std::size_t, ConjElectrons *> RDKit::CEMap |
Definition at line 31 of file Resonance.h.
typedef std::vector<ConjElectrons *> RDKit::CEVect |
Definition at line 28 of file Resonance.h.
typedef std::vector<CEVect2 *> RDKit::CEVect3 |
Definition at line 29 of file Resonance.h.
typedef std::map<int, DrawColour> RDKit::ColourPalette |
Definition at line 39 of file MolDraw2D.h.
typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR |
Definition at line 135 of file Conformer.h.
typedef std::map<unsigned int, AtomElectrons *> RDKit::ConjAtomMap |
Definition at line 27 of file Resonance.h.
typedef std::map<unsigned int, BondElectrons *> RDKit::ConjBondMap |
Definition at line 25 of file Resonance.h.
typedef std::vector<boost::uint8_t> RDKit::ConjFP |
Definition at line 30 of file Resonance.h.
typedef Atom const* RDKit::ConstAtomPtr |
Definition at line 476 of file QueryOps.h.
typedef Bond const* RDKit::ConstBondPtr |
Definition at line 586 of file QueryOps.h.
typedef std::vector<unsigned int> RDKit::DashPattern |
Definition at line 40 of file MolDraw2D.h.
typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP |
typedef boost::variate_generator<rng_type &, uniform_double> RDKit::double_source_type |
typedef std::vector<double> RDKit::DOUBLE_VECT |
typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI |
typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I |
typedef boost::tuple<float, float, float> RDKit::DrawColour |
Definition at line 38 of file MolDraw2D.h.
Definition at line 109 of file FilterCatalog.h.
typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr |
Definition at line 18 of file MolChemicalFeatureFactory.h.
typedef std::list<FeatSPtr> RDKit::FeatSPtrList |
Definition at line 20 of file MolChemicalFeatureFactory.h.
typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I |
Definition at line 21 of file MolChemicalFeatureFactory.h.
typedef RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > RDKit::FragCatalog |
Definition at line 19 of file FragCatGenerator.h.
typedef std::deque<int> RDKit::INT_DEQUE |
typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI |
typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I |
typedef std::map<int, INT_DEQUE> RDKit::INT_INT_DEQ_MAP |
typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI |
typedef std::map<int, INT_VECT> RDKit::INT_INT_VECT_MAP |
typedef INT_INT_VECT_MAP::const_iterator RDKit::INT_INT_VECT_MAP_CI |
typedef std::list<int> RDKit::INT_LIST |
typedef INT_LIST::const_iterator RDKit::INT_LIST_CI |
typedef INT_LIST::iterator RDKit::INT_LIST_I |
typedef std::map<int, int> RDKit::INT_MAP_INT |
typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI |
typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I |
typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP |
Definition at line 44 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI |
Definition at line 45 of file Subgraphs.h.
typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I |
Definition at line 46 of file Subgraphs.h.
typedef std::set<int> RDKit::INT_SET |
typedef INT_SET::const_iterator RDKit::INT_SET_CI |
typedef INT_SET::iterator RDKit::INT_SET_I |
typedef boost::variate_generator<rng_type &, uniform_int> RDKit::int_source_type |
typedef std::vector<int> RDKit::INT_VECT |
typedef INT_VECT::const_iterator RDKit::INT_VECT_CI |
typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI |
typedef INT_VECT::iterator RDKit::INT_VECT_I |
typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI |
typedef std::vector<double> RDKit::INVAR_VECT |
typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI |
typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I |
typedef std::list<INT_VECT> RDKit::LIST_INT_VECT |
typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI |
typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I |
typedef long long int RDKit::LONGINT |
typedef std::vector< std::pair< int, int > > RDKit::MatchVectType |
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
Definition at line 23 of file FragFPGenerator.h.
typedef bool(* RDKit::MCSAtomCompareFunction) (const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData) |
typedef bool(* RDKit::MCSBondCompareFunction) (const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData) |
typedef bool(* RDKit::MCSFinalMatchCheckFunction) (const short unsigned c1[], const short unsigned c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p) |
typedef bool(* RDKit::MCSProgressCallback) (const MCSProgressData &stat, const MCSParameters ¶ms, void *userData) |
typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT |
typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI |
typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I |
typedef std::vector< ROMOL_SPTR > RDKit::MOL_SPTR_VECT |
Definition at line 19 of file FragCatParams.h.
typedef std::vector<ROMol> RDKit::MOL_VECT |
a hierarchical catalog for holding molecules
Definition at line 16 of file MolCatalog.h.
typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, ATOM_SPTR, BOND_SPTR> RDKit::MolGraph |
typedef std::list<PATH_TYPE> RDKit::PATH_LIST |
Definition at line 41 of file Subgraphs.h.
typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI |
Definition at line 42 of file Subgraphs.h.
typedef std::vector<int> RDKit::PATH_TYPE |
Definition at line 36 of file Subgraphs.h.
typedef RDValue RDKit::RDValue_cast_t |
Definition at line 359 of file RDValue-doublemagic.h.
typedef std::vector<boost::shared_ptr<ROMol> > RDKit::RGroupColumn |
Definition at line 87 of file RGroupDecomp.h.
typedef std::map<std::string, RGroupColumn> RDKit::RGroupColumns |
Definition at line 90 of file RGroupDecomp.h.
typedef std::map<std::string, boost::shared_ptr<ROMol> > RDKit::RGroupRow |
Definition at line 86 of file RGroupDecomp.h.
typedef std::vector<RGroupRow> RDKit::RGroupRows |
Definition at line 89 of file RGroupDecomp.h.
typedef boost::minstd_rand RDKit::rng_type |
typedef boost::shared_ptr< ROMol > RDKit::ROMOL_SPTR |
Definition at line 21 of file ChemTransforms.h.
typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR |
typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT |
Definition at line 30 of file FileParsers.h.
typedef std::vector<Snapshot> RDKit::SnapshotVect |
Definition at line 18 of file Snapshot.h.
typedef std::map<std::string, UINT> RDKit::STR_UINT_MAP |
typedef std::map<std::string, UINT>::const_iterator RDKit::STR_UINT_MAP_CI |
typedef std::vector< std::string > RDKit::STR_VECT |
typedef std::vector<std::string>::const_iterator RDKit::STR_VECT_CI |
typedef std::vector<std::string>::iterator RDKit::STR_VECT_I |
typedef std::map<std::string, std::string> RDKit::STRING_PROPS |
Definition at line 52 of file FilterCatalogEntry.h.
typedef unsigned char RDKit::UCHAR |
typedef unsigned int RDKit::UINT |
typedef std::vector<UINT> RDKit::UINT_VECT |
typedef std::vector<UINT>::const_iterator RDKit::UINT_VECT_CI |
typedef boost::uniform_real RDKit::uniform_double |
typedef boost::uniform_int RDKit::uniform_int |
typedef unsigned short RDKit::USHORT |
typedef std::vector<DOUBLE_VECT> RDKit::VECT_DOUBLE_VECT |
typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI |
typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I |
typedef std::vector<INT_VECT> RDKit::VECT_INT_VECT |
typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI |
typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I |
enum RDKit::EEndian |
Enumerator | |
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LITTLE_ENDIAN_ORDER | |
BIG_ENDIAN_ORDER |
Definition at line 26 of file StreamOps.h.
Enumerator | |
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AtomPairFP | |
TopologicalTorsion | |
MorganFP | |
RDKitFP | |
PatternFP |
Definition at line 42 of file ReactionFingerprints.h.
enum RDKit::Mol2Type |
Enumerator | |
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CORINA |
Definition at line 159 of file FileParsers.h.
Enumerator | |
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Reactant | |
Product | |
Agent |
Definition at line 40 of file ReactionUtils.h.
Enumerator | |
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None | |
MCS |
Definition at line 47 of file RGroupDecomp.h.
Enumerator | |
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AtomMap | |
Isotope | |
MDLRGroup |
Definition at line 41 of file RGroupDecomp.h.
enum RDKit::RGroupLabels |
Compute the isomporphic degenerative points in the molecule. These are points that are symmetrically equivalent.
mol | Molecule to compute the degenerative points |
Enumerator | |
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IsotopeLabels | |
AtomMapLabels | |
AtomIndexLabels | |
RelabelDuplicateLabels | |
AutoDetect |
Definition at line 27 of file RGroupDecomp.h.
Enumerator | |
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Greedy | |
GreedyChunks | |
Exhaustive |
Definition at line 35 of file RGroupDecomp.h.
void RDKit::addRecursiveQueries | ( | ROMol & | mol, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName, | ||
std::vector< std::pair< unsigned int, std::string > > * | reactantLabels = NULL |
||
) |
Adds named recursive queries to a molecule's atoms based on atom.
mol | - the molecule to be modified |
queries | - the dictionary of named queries to add |
propName | - the atom property to use to get query names |
reactantLabels | - to store pairs of (atom index, query string) |
NOTES:
queries
void RDKit::addRecursiveQueriesToReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > * | reactantLabels = NULL |
||
) |
add the recursive queries to the reactants of a reaction
This does its work using RDKit::addRecursiveQueries()
rxn | the reaction we are interested in |
queries | - the dictionary of named queries to add |
propName | - the atom property to use to get query names optional: |
reactantLabels | - to store pairs of (atom index, query string) per reactant |
NOTES:
queries
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
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inline |
Packs an integer and outputs it to a stream.
Definition at line 95 of file StreamOps.h.
References CHECK_INVARIANT.
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Definition at line 57 of file MolDraw2D.h.
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Definition at line 42 of file MolDraw2D.h.
Referenced by RDKit::MolDrawOptions::MolDrawOptions().
bool RDKit::atomCompat | ( | const ATOM_SPTR & | a1, |
const ATOM_SPTR & | a2, | ||
bool | useQueryQueryMatches = false |
||
) |
bool RDKit::bondCompat | ( | const BOND_SPTR & | b1, |
const BOND_SPTR & | b2, | ||
bool | useQueryQueryMatches = false |
||
) |
MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | std::istream & | inStream | ) |
constructs a MolChemicalFeatureFactory from the data in a stream
Referenced by RDKit::MolChemicalFeatureFactory::addFeatureDef().
MolChemicalFeatureFactory* RDKit::buildFeatureFactory | ( | const std::string & | featureData | ) |
constructs a MolChemicalFeatureFactory from the data in a string
std::string RDKit::ChemicalReactionToRxnBlock | ( | const ChemicalReaction & | rxn, |
bool | separateAgents = false |
||
) |
returns an RXN block for a reaction
rxn | chemical reaction |
separateAgents | flag to decide if agents were put in a seperate block, otherwise they were included in the reactants block (default) |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ROMol* RDKit::ChemicalReactionToRxnMol | ( | const ChemicalReaction & | rxn | ) |
returns a ROMol with RXN roles used to describe the reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
std::string RDKit::ChemicalReactionToRxnSmarts | ( | const ChemicalReaction & | rxn | ) |
returns the reaction SMARTS for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
std::string RDKit::ChemicalReactionToRxnSmiles | ( | const ChemicalReaction & | rxn, |
bool | canonical = true |
||
) |
returns the reaction SMILES for a reaction
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
void RDKit::ClearSingleBondDirFlags | ( | ROMol & | mol | ) |
ROMol* RDKit::combineMols | ( | const ROMol & | mol1, |
const ROMol & | mol2, | ||
RDGeom::Point3D | offset = RDGeom::Point3D(0, 0, 0) |
||
) |
Combined two molecules to create a new one.
mol1 | - the first ROMol to be combined |
mol2 | - the second ROMol to be combined |
offset | - a constant offset to be added to every atom position in mol2 |
void RDKit::computeGasteigerCharges | ( | const ROMol * | mol, |
int | nIter = 12 , |
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bool | throwOnParamFailure = false |
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) |
void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
void RDKit::computeGasteigerCharges | ( | const ROMol & | mol, |
std::vector< double > & | charges, | ||
int | nIter = 12 , |
||
bool | throwOnParamFailure = false |
||
) |
double RDKit::computeIntVectPrimesProduct | ( | const INT_VECT & | ring | ) |
compute the product of the set of primes corresponding to the values in an INT_VECT
unsigned int RDKit::computeL1Norm | ( | const DiscreteValueVect & | v1, |
const DiscreteValueVect & | v2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
boost::uint64_t RDKit::computeNumProducts | ( | const EnumerationTypes::RGROUPS & | sizes | ) |
computeNumProducts Returns the number of possible product combination from The given numbers of building blocks for each rgroup or EnumerationStrategyBase::EnumerationOverflow if the number will not fit into the machines integer type. n.b. An overflow simply means there are a lot of products not that they cannot be enumerated
Referenced by getSizesFromBBs(), RDKit::EnumerationStrategyBase::initialize(), and RDKit::EnumerationStrategyBase::internalInitialize().
void RDKit::ConnectTheDots | ( | RWMol * | mol, |
unsigned int | flags = 0 |
||
) |
Definition at line 289 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::AnyTag, RDKit::RDValue::destroy(), RDKit::RDValue::getTag(), RDKit::RDValue::ptrCast(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by RDKit::RDValue::cleanup_rdvalue(), RDKit::Dict::Dict(), RDKit::RDAny::operator=(), RDKit::Dict::operator=(), RDKit::RDAny::RDAny(), and RDKit::Dict::update().
unsigned int RDKit::countSwapsToInterconvert | ( | const T & | ref, |
T | probe | ||
) |
Definition at line 53 of file utils.h.
References CHECK_INVARIANT, and PRECONDITION.
const ReactionFingerprintParams RDKit::DefaultDifferenceFPParams | ( | true | , |
0. | 0, | ||
10 | , | ||
1 | , | ||
2048 | , | ||
AtomPairFP | |||
) |
const ReactionFingerprintParams RDKit::DefaultStructuralFPParams | ( | true | , |
0. | 2, | ||
1 | , | ||
1 | , | ||
4096 | , | ||
PatternFP | |||
) |
ROMol* RDKit::deleteSubstructs | ( | const ROMol & | mol, |
const ROMol & | query, | ||
bool | onlyFrags = false , |
||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.
mol | the ROMol of interest |
query | the query ROMol |
onlyFrags | if this is set, atoms will only be removed if the entire fragment in which they are found is matched by the query. |
useChirality | - if set, match the coreQuery using chirality |
mol
with the matching atoms and bonds (if any) removed.
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Definition at line 98 of file QueryAtom.h.
References RDKit::Atom::getQuery(), RDKit::Atom::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
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Definition at line 109 of file QueryBond.h.
References RDKit::Bond::getQuery(), RDKit::Bond::hasQuery(), PRECONDITION, and RDKit::detail::qhelper().
deprecated, please use MolOps::detectBondStereoChemistry instead
Bond::BondDir RDKit::DetermineBondWedgeState | ( | const Bond * | bond, |
const INT_MAP_INT & | wedgeBonds, | ||
const Conformer * | conf | ||
) |
double RDKit::DiceSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 469 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDKit::SparseIntVect< IndexType >::getTotalVal().
SparseIntVect<boost::uint32_t>* RDKit::DifferenceFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultDifferenceFPParams |
||
) |
Generates a difference fingerprint for a reaction to use in similarity search of reactions
A difference fingerprint is generated as a SparseIntVect to use for similarity search of reactions. By default the fingerprint is generated as 2048 bit hashed fingerprint subtracting AtompairFP of the reactants from the products' AtompairFP and tentatively the agent AtompairFP is added
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result
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Definition at line 66 of file StreamOps.h.
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Definition at line 81 of file StreamOps.h.
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Definition at line 85 of file StreamOps.h.
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Definition at line 89 of file StreamOps.h.
bool RDKit::EnumerateLibraryCanSerialize | ( | ) |
Referenced by RDKit::EnumerateLibrary::getReagents().
RWMol* RDKit::FASTAToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
lowerD | - if set, lower case letters will be parsed as the d form of the corresponding amino acid |
RWMol* RDKit::FASTAToMol | ( | const std::string & | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RWMol* RDKit::FASTAToMol | ( | const char * | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
flavor | - 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps |
RWMol* RDKit::FASTAToMol | ( | const std::string & | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
bool RDKit::feq | ( | double | v1, |
double | v2, | ||
double | tol = 1e-4 |
||
) |
floating point comparison with a tolerance
bool RDKit::FilterCatalogCanSerialize | ( | ) |
Referenced by RDKit::FilterCatalog::getNumEntries().
bool RDKit::FinalChiralityCheckFunction | ( | const short unsigned | c1[], |
const short unsigned | c2[], | ||
const ROMol & | mol1, | ||
const FMCS::Graph & | query, | ||
const ROMol & | mol2, | ||
const FMCS::Graph & | target, | ||
const MCSParameters * | p | ||
) |
PATH_LIST RDKit::findAllPathsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
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) |
find all paths of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the paths to be returned |
useBonds | - if set, the path indices will be bond indices, not atom indices |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
INT_PATH_LIST_MAP RDKit::findAllPathsOfLengthsMtoN | ( | const ROMol & | mol, |
unsigned int | lowerLen, | ||
unsigned int | upperLen, | ||
bool | useBonds = true , |
||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
PATH_LIST RDKit::findAllSubgraphsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
find all bond subgraphs of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the subgraphs to be returned |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
INT_PATH_LIST_MAP RDKit::findAllSubgraphsOfLengthsMtoN | ( | const ROMol & | mol, |
unsigned int | lowerLen, | ||
unsigned int | upperLen, | ||
bool | useHs = false , |
||
int | rootedAtAtom = -1 |
||
) |
find all bond subgraphs in a range of sizes
mol | - the molecule to be considered |
lowerLen | - the minimum subgraph size to find |
upperLen | - the maximum subgraph size to find |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a map from subgraph size -> list of paths (i.e. list of list of bond indices)
PATH_TYPE RDKit::findAtomEnvironmentOfRadiusN | ( | const ROMol & | mol, |
unsigned int | radius, | ||
unsigned int | rootedAtAtom, | ||
bool | useHs = false |
||
) |
find bond subgraphs of a particular radius around an atom
mol | - the molecule to be considered |
radius | - the radius of the subgraphs to be considered |
rootedAtAtom | - the atom to consider |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
The result is a path (a vector of bond indices)
MatchVectType RDKit::findFuncGroupsOnMol | ( | const ROMol & | mol, |
const FragCatParams * | params, | ||
INT_VECT & | fgBonds | ||
) |
MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
const MCSParameters * | params = 0 |
||
) |
Referenced by RDKit::MCSResult::isCompleted().
MCSResult RDKit::findMCS | ( | const std::vector< ROMOL_SPTR > & | mols, |
bool | maximizeBonds, | ||
double | threshold = 1.0 , |
||
unsigned | timeout = 3600 , |
||
bool | verbose = false , |
||
bool | matchValences = false , |
||
bool | ringMatchesRingOnly = false , |
||
bool | completeRingsOnly = false , |
||
bool | matchChiralTag = false , |
||
AtomComparator | atomComp = AtomCompareElements , |
||
BondComparator | bondComp = BondCompareOrder |
||
) |
MCSResult RDKit::findMCS_P | ( | const std::vector< ROMOL_SPTR > & | mols, |
const char * | params_json | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
PATH_LIST RDKit::findUniqueSubgraphsOfLengthN | ( | const ROMol & | mol, |
unsigned int | targetLen, | ||
bool | useHs = false , |
||
bool | useBO = true , |
||
int | rootedAtAtom = -1 |
||
) |
find unique bond subgraphs of a particular size
mol | - the molecule to be considered |
targetLen | - the length of the subgraphs to be returned |
useHs | - if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph. |
useBO | - if set, bond orders will be considered when uniquifying the paths |
rootedAtAtom | - if non-negative, only subgraphs that start at this atom will be returned. |
The result is a list of paths (i.e. list of list of bond indices)
boost::enable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 192 of file RDAny.h.
References RDKit::RDValue::getTag(), RDKit::RDAny::m_value, rdany_cast(), and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdany | ( | const RDAny & | arg | ) |
Definition at line 213 of file RDAny.h.
References rdany_cast().
boost::enable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 229 of file RDValue.h.
References RDKit::RDValue::getTag(), rdvalue_cast(), and RDKit::RDTypeTag::StringTag.
boost::disable_if<boost::is_arithmetic<T>, T>::type RDKit::from_rdvalue | ( | RDValue_cast_t | arg | ) |
Definition at line 250 of file RDValue.h.
References rdvalue_cast().
std::string RDKit::getAtomAlias | ( | const Atom * | atom | ) |
int RDKit::getAtomRLabel | ( | const Atom * | atm | ) |
std::string RDKit::getAtomValue | ( | const Atom * | atom | ) |
DiscreteDistMat* RDKit::getDiscreteDistMat | ( | ) |
Referenced by RDKit::DiscreteDistMat::~DiscreteDistMat().
double_source_type& RDKit::getDoubleRandomSource | ( | ) |
return a reference to the global (Boost) random source
MOL_SPTR_VECT::const_iterator RDKit::getEndIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
const FilterData_t* RDKit::GetFilterData | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
const FilterProperty_t* RDKit::GetFilterProperties | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
const std::map<std::string, ROMOL_SPTR>& RDKit::GetFlattenedFunctionalGroupHierarchy | ( | bool | normalized = false | ) |
Return the flattened functional group hierarchy as a string->ROMOL_SPTR map The label is the name of the functional group in the hiearchy e.g. Halogen.Bromine.Aliphatic
const FilterCatalog& RDKit::GetFunctionalGroupHierarchy | ( | ) |
Return the functional group hierarchy as a FilterCatalog.
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grabs the next line from an instream and returns it.
Definition at line 288 of file StreamOps.h.
Referenced by getLine().
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grabs the next line from an instream and returns it.
Definition at line 297 of file StreamOps.h.
References getLine().
unsigned int RDKit::GetNumEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
unsigned int RDKit::GetNumPropertyEntries | ( | FilterCatalogParams::FilterCatalogs | catalog | ) |
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Definition at line 38 of file RDThreads.h.
References RDUNUSED_PARAM.
Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), and RDKit::UFF::UFFOptimizeMoleculeConfs().
rng_type& RDKit::getRandomGenerator | ( | int | seed = -1 | ) |
Optionally seed and return a reference to the global (Boost) random.
double RDKit::getRandomVal | ( | int | seed = -1 | ) |
Return a random double value between 0.0 and 1.0 Optionally seed the random number generator
MOL_SPTR_VECT RDKit::getReactantsFromRGroups | ( | const std::vector< MOL_SPTR_VECT > & | bbs, |
const EnumerationTypes::RGROUPS & | rgroups | ||
) |
getReactantsFromRGroups Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >
Referenced by getSizesFromBBs().
VECT_INT_VECT RDKit::getReactingAtoms | ( | const ChemicalReaction & | rxn, |
bool | mappedAtomsOnly = false |
||
) |
returns indices of the atoms in each reactant that are changed in the reaction
rxn | the reaction we are interested in |
mappedAtomsOnly | if set, atoms that are not mapped will not be included in the list of changed atoms (otherwise they are automatically included) |
How are changed atoms recognized? 1) Atoms whose degree changes 2) Atoms whose bonding pattern changes 3) unmapped atoms (unless the mappedAtomsOnly flag is set) 4) Atoms connected to unmapped atoms 5) Atoms whose atomic number changes (unless the corresponding product atom is a dummy) 6) Atoms with more than one atomic number query (unless the corresponding product atom is a dummy)
Note that the atomic number of a query atom depends on how it's constructed. When coming from SMARTS: if the first query is an atomic label/number that sets the atomic number, otherwise it's zero. For example [O;] is atomic number 8 while [;O] is atomic number 0. When coming from RXN: the atomic number of the atom in the rxn file sets the value.
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
EnumerationTypes::RGROUPS RDKit::getSizesFromBBs | ( | const std::vector< std::vector< T > > & | bbs | ) |
Return the number of elements per input vector.
bbs | vector<vector<T> > |
Definition at line 70 of file EnumerationStrategyBase.h.
References computeNumProducts(), getReactantsFromRGroups(), and getSizesFromReactants().
Referenced by RDKit::EnumerationStrategyBase::initialize().
EnumerationTypes::RGROUPS RDKit::getSizesFromReactants | ( | const std::vector< MOL_SPTR_VECT > & | bbs | ) |
getSizesFromReactants Helper function for enumeration, bbs are stored in a std::vector< std::vector<boost:shared_ptr<ROMol> >
Referenced by getSizesFromBBs().
MOL_SPTR_VECT::const_iterator RDKit::getStartIterator | ( | const ChemicalReaction & | rxn, |
ReactionMoleculeType | t | ||
) |
std::string RDKit::getSupplementalSmilesLabel | ( | const Atom * | atom | ) |
SparseIntVect<boost::uint64_t>* RDKit::getUnfoldedRDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
bool | useHs = true , |
||
bool | branchedPaths = true , |
||
bool | useBondOrder = true , |
||
std::vector< boost::uint32_t > * | atomInvariants = 0 , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 , |
||
std::vector< std::vector< boost::uint64_t > > * | atomBits = 0 , |
||
std::map< boost::uint64_t, std::vector< std::vector< int > > > * | bitInfo = 0 |
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) |
bool RDKit::hanoi | ( | int * | base, |
int | nel, | ||
int * | temp, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
void RDKit::hanoisort | ( | int * | base, |
int | nel, | ||
int * | count, | ||
int * | changed, | ||
CompareFunc | compar | ||
) |
Definition at line 140 of file hanoiSort.h.
References hanoi().
Referenced by RDKit::Canon::RefinePartitions().
bool RDKit::hasAgentTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasProductTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasReactantTemplateSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn | ||
) |
bool RDKit::hasReactionAtomMapping | ( | const ChemicalReaction & | rxn | ) |
bool RDKit::hasReactionSubstructMatch | ( | const ChemicalReaction & | rxn, |
const ChemicalReaction & | query_rxn, | ||
bool | includeAgents = false |
||
) |
RWMol* RDKit::HELMToMol | ( | const char * | helm, |
bool | sanitize = true |
||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
RWMol* RDKit::HELMToMol | ( | const std::string & | helm, |
bool | sanitize = true |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
calculate the intersection of two INT_VECTs and put the results in a third vector
Referenced by RDKit::charptr_functor::operator()().
bool RDKit::isAtomAromatic | ( | const Atom * | a | ) |
Referenced by makePropQuery().
bool RDKit::isComplexQuery | ( | const Bond * | b | ) |
Referenced by makePropQuery().
bool RDKit::isComplexQuery | ( | const Atom * | a | ) |
bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's agents the which
argument is used to return which of the agents the molecule matches. If there's no match, it is equal to the number of agents on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
bool RDKit::isMoleculeAgentOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's products the which
argument is used to return which of the products the molecule matches. If there's no match, it is equal to the number of products on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
bool RDKit::isMoleculeProductOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol, | ||
unsigned int & | which | ||
) |
tests whether or not the molecule has a substructure match to any of the reaction's reactants the which
argument is used to return which of the reactants the molecule matches. If there's no match, it is equal to the number of reactants on return
Referenced by RDKit::ChemicalReaction::setImplicitPropertiesFlag().
bool RDKit::isMoleculeReactantOfReaction | ( | const ChemicalReaction & | rxn, |
const ROMol & | mol | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
bool RDKit::isReactionTemplateMoleculeAgent | ( | const ROMol & | mol, |
double | agentThreshold | ||
) |
|
inline |
Definition at line 319 of file StreamOps.h.
References RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by streamWriteProp(), and streamWriteProps().
ExplicitBitVect* RDKit::LayeredFingerprintMol | ( | const ROMol & | mol, |
unsigned int | layerFlags = 0xFFFFFFFF , |
||
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 , |
||
bool | branchedPaths = true , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using a layer-based hashing algorithm.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
layerFlags | the layers to be included (see below) |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
Notes:
delete
ing the resultLayer definitions:
ATOM_EQUALS_QUERY* RDKit::makeAAtomQuery | ( | ) |
returns a Query for matching generic A atoms (heavy atoms)
Referenced by makeAtomRingBondCountQuery().
ATOM_EQUALS_QUERY* RDKit::makeAHAtomQuery | ( | ) |
returns a Query for matching generic AH atoms (any atom)
Referenced by makeAtomRingBondCountQuery().
T* RDKit::makeAtomAliphaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching aliphatic atoms
Definition at line 314 of file QueryOps.h.
References queryAtomAliphatic().
ATOM_EQUALS_QUERY* RDKit::makeAtomAliphaticQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomAromaticQuery | ( | const std::string & | descr | ) |
returns a Query for matching the isAromatic
flag
Definition at line 306 of file QueryOps.h.
References queryAtomAromatic().
ATOM_EQUALS_QUERY* RDKit::makeAtomAromaticQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomExplicitDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit degree
Definition at line 258 of file QueryOps.h.
References queryAtomExplicitDegree().
ATOM_EQUALS_QUERY* RDKit::makeAtomExplicitDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomExplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching explicit valence
Definition at line 242 of file QueryOps.h.
References queryAtomExplicitValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomExplicitValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomFormalChargeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching formal charge
Definition at line 339 of file QueryOps.h.
References queryAtomFormalCharge().
ATOM_EQUALS_QUERY* RDKit::makeAtomFormalChargeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHasChiralTagQuery | ( | const std::string & | descr | ) |
returns a Query for matching whether or not chirality has been set on the atom
Definition at line 364 of file QueryOps.h.
References queryAtomHasChiralTag().
ATOM_EQUALS_QUERY* RDKit::makeAtomHasChiralTagQuery | ( | ) |
T* RDKit::makeAtomHasImplicitHQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 290 of file QueryOps.h.
References queryAtomHasImplicitH().
ATOM_EQUALS_QUERY* RDKit::makeAtomHasImplicitHQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHasRingBondQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms that have ring bonds
Definition at line 441 of file QueryOps.h.
References makeAtomNullQuery(), makeBondDirEqualsQuery(), makeBondHasStereoQuery(), makeBondInNRingsQuery(), makeBondInRingOfSizeQuery(), makeBondIsInRingQuery(), makeBondMinRingSizeQuery(), makeBondNullQuery(), makeBondOrderEqualsQuery(), and queryAtomHasRingBond().
ATOM_EQUALS_QUERY* RDKit::makeAtomHasRingBondQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hydrogen count
Definition at line 282 of file QueryOps.h.
References queryAtomHCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomHCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHeavyAtomDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching heavy atom degree
Definition at line 274 of file QueryOps.h.
References queryAtomHeavyAtomDegree().
ATOM_EQUALS_QUERY* RDKit::makeAtomHeavyAtomDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomHybridizationQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching hybridization
Definition at line 347 of file QueryOps.h.
References queryAtomHybridization().
ATOM_EQUALS_QUERY* RDKit::makeAtomHybridizationQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomImplicitHCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit hydrogen count
Definition at line 298 of file QueryOps.h.
References queryAtomImplicitHCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomImplicitHCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomImplicitValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching implicit valence
Definition at line 234 of file QueryOps.h.
References queryAtomImplicitValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomImplicitValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomInNRingsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms in a particular number of rings
Definition at line 397 of file QueryOps.h.
References makeAtomInRingOfSizeQuery(), and queryIsAtomInNRings().
ATOM_EQUALS_QUERY* RDKit::makeAtomInNRingsQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
ATOM_EQUALS_QUERY* RDKit::makeAtomInRingOfSizeQuery | ( | int | tgt | ) |
returns a Query for matching atoms in rings of a particular size
Referenced by makeAtomInNRingsQuery().
T* RDKit::makeAtomInRingQuery | ( | const std::string & | descr | ) |
returns a Query for matching ring atoms
Definition at line 389 of file QueryOps.h.
References queryIsAtomInRing().
ATOM_EQUALS_QUERY* RDKit::makeAtomInRingQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomIsotopeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular isotope
Definition at line 331 of file QueryOps.h.
References queryAtomIsotope().
ATOM_EQUALS_QUERY* RDKit::makeAtomIsotopeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomMassQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular mass
Definition at line 322 of file QueryOps.h.
References queryAtomMass().
ATOM_EQUALS_QUERY* RDKit::makeAtomMassQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomMinRingSizeQuery | ( | int | tgt, |
const std::string & | descr | ||
) |
returns a Query for matching an atom's minimum ring size
Definition at line 408 of file QueryOps.h.
References queryAtomMinRingSize().
ATOM_EQUALS_QUERY* RDKit::makeAtomMinRingSizeQuery | ( | int | tgt | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomMissingChiralTagQuery | ( | const std::string & | descr | ) |
returns a Query for matching whether or not a potentially chiral atom is missing a chiral tag
Definition at line 373 of file QueryOps.h.
References queryAtomMissingChiralTag().
ATOM_EQUALS_QUERY* RDKit::makeAtomMissingChiralTagQuery | ( | ) |
ATOM_NULL_QUERY* RDKit::makeAtomNullQuery | ( | ) |
returns a Query for matching any atom
Referenced by makeAtomHasRingBondQuery().
T* RDKit::makeAtomNumQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic number
Definition at line 226 of file QueryOps.h.
References queryAtomNum().
ATOM_EQUALS_QUERY* RDKit::makeAtomNumQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomNumRadicalElectronsQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching the number of radical electrons
Definition at line 355 of file QueryOps.h.
References queryAtomNumRadicalElectrons().
ATOM_EQUALS_QUERY* RDKit::makeAtomNumRadicalElectronsQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomRingBondCountQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atoms with a particular number of ring bonds
Definition at line 416 of file QueryOps.h.
References makeAAtomQuery(), makeAHAtomQuery(), makeMAtomQuery(), makeMHAtomQuery(), makeQAtomQuery(), makeQHAtomQuery(), makeXAtomQuery(), makeXHAtomQuery(), and queryAtomRingBondCount().
ATOM_EQUALS_QUERY* RDKit::makeAtomRingBondCountQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomSimpleQuery | ( | int | what, |
int | funcAtom const *, | ||
const std::string & | description = "Atom Simple" |
||
) |
Definition at line 215 of file QueryOps.h.
T* RDKit::makeAtomTotalDegreeQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching atomic degree
Definition at line 266 of file QueryOps.h.
References queryAtomTotalDegree().
ATOM_EQUALS_QUERY* RDKit::makeAtomTotalDegreeQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomTotalValenceQuery | ( | int | what, |
const std::string & | descr | ||
) |
returns a Query for matching total valence
Definition at line 250 of file QueryOps.h.
References queryAtomTotalValence().
ATOM_EQUALS_QUERY* RDKit::makeAtomTotalValenceQuery | ( | int | what | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
T* RDKit::makeAtomUnsaturatedQuery | ( | const std::string & | descr | ) |
returns a Query for matching atoms with unsaturation:
Definition at line 381 of file QueryOps.h.
References queryAtomUnsaturated().
ATOM_EQUALS_QUERY* RDKit::makeAtomUnsaturatedQuery | ( | ) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
BOND_EQUALS_QUERY* RDKit::makeBondDirEqualsQuery | ( | Bond::BondDir | what | ) |
returns a Query for matching bond directions
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondHasStereoQuery | ( | ) |
returns a Query for matching bonds with stereo set
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondInNRingsQuery | ( | int | tgt | ) |
returns a Query for matching bonds in a particular number of rings
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondInRingOfSizeQuery | ( | int | what | ) |
returns a Query for matching bonds in rings of a particular size
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondIsInRingQuery | ( | ) |
returns a Query for matching ring bonds
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondMinRingSizeQuery | ( | int | what | ) |
returns a Query for matching a bond's minimum ring size
Referenced by makeAtomHasRingBondQuery().
BOND_NULL_QUERY* RDKit::makeBondNullQuery | ( | ) |
returns a Query for matching any bond
Referenced by makeAtomHasRingBondQuery().
BOND_EQUALS_QUERY* RDKit::makeBondOrderEqualsQuery | ( | Bond::BondType | what | ) |
returns a Query for matching bond orders
Referenced by makeAtomHasRingBondQuery().
FilterCatalogEntry* RDKit::MakeFilterCatalogEntry | ( | const FilterData_t & | , |
unsigned int | num_props = 0 , |
||
const FilterProperty_t * | props = 0 |
||
) |
Queries::EqualityQuery<int, const Target *, true>* RDKit::makeHasPropQuery | ( | const std::string & | property | ) |
returns a Query for matching atoms that have a particular property
Definition at line 628 of file QueryOps.h.
ATOM_OR_QUERY* RDKit::makeMAtomQuery | ( | ) |
returns a Query for matching generic M atoms (metals)
Referenced by makeAtomRingBondCountQuery().
ATOM_OR_QUERY* RDKit::makeMHAtomQuery | ( | ) |
returns a Query for matching generic MH atoms (metals or H)
Referenced by makeAtomRingBondCountQuery().
Queries::EqualityQuery<int, const Target *, true>* RDKit::makePropQuery | ( | const std::string & | propname, |
const T & | val, | ||
const T & | tolerance = T() |
||
) |
Definition at line 767 of file QueryOps.h.
References isAtomAromatic(), and isComplexQuery().
ATOM_OR_QUERY* RDKit::makeQAtomQuery | ( | ) |
returns a Query for matching generic Q atoms (heteroatoms)
Referenced by makeAtomRingBondCountQuery().
ATOM_EQUALS_QUERY* RDKit::makeQHAtomQuery | ( | ) |
returns a Query for matching generic QH atoms (heteroatom or H)
Referenced by makeAtomRingBondCountQuery().
ATOM_OR_QUERY* RDKit::makeXAtomQuery | ( | ) |
returns a Query for matching generic X atoms (halogens)
Referenced by makeAtomRingBondCountQuery().
ATOM_OR_QUERY* RDKit::makeXHAtomQuery | ( | ) |
returns a Query for matching generic XH atoms (halogen or H)
Referenced by makeAtomRingBondCountQuery().
RDKIT_WRAP_DECL bool RDKit::MCSAtomCompareAny | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_WRAP_DECL bool RDKit::MCSAtomCompareElements | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_WRAP_DECL bool RDKit::MCSAtomCompareIsotopes | ( | const MCSAtomCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | atom1, | ||
const ROMol & | mol2, | ||
unsigned int | atom2, | ||
void * | userData | ||
) |
RDKIT_WRAP_DECL bool RDKit::MCSBondCompareAny | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
RDKIT_WRAP_DECL bool RDKit::MCSBondCompareOrder | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
RDKIT_WRAP_DECL bool RDKit::MCSBondCompareOrderExact | ( | const MCSBondCompareParameters & | p, |
const ROMol & | mol1, | ||
unsigned int | bond1, | ||
const ROMol & | mol2, | ||
unsigned int | bond2, | ||
void * | userData | ||
) |
bool RDKit::MCSProgressCallbackTimeout | ( | const MCSProgressData & | stat, |
const MCSParameters & | params, | ||
void * | userData | ||
) |
RWMol* RDKit::Mol2BlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
molBlock | - string containing the mol block |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
inStream | - stream containing the data |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
RWMol* RDKit::Mol2DataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
RWMol* RDKit::Mol2FileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
Mol2Type | variant = CORINA |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
variant | - the atom type definitions to use |
RWMol* RDKit::MolBlockToMol | ( | const std::string & | molBlock, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
molBlock | - string containing the mol block |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
RWMol* RDKit::MolDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
inStream | - stream containing the data |
line | - current line number (used for error reporting) |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
line | - current line number (used for error reporting) |
strictParsing | - if not set, the parser is more lax about correctness of the contents. |
RWMol* RDKit::MolDataStreamToMol | ( | std::istream & | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
RWMol* RDKit::MolFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
bool | strictParsing = true |
||
) |
fName | - string containing the file name |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
removeHs | - toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized |
strictParsing | - if set, the parser is more lax about correctness of the contents. |
std::string RDKit::MolFragmentToSmiles | ( | const ROMol & | mol, |
const std::vector< int > & | atomsToUse, | ||
const std::vector< int > * | bondsToUse = 0 , |
||
const std::vector< std::string > * | atomSymbols = 0 , |
||
const std::vector< std::string > * | bondSymbols = 0 , |
||
bool | doIsomericSmiles = false , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
returns canonical SMILES for part of a molecule
mol | : the molecule in question. |
atomsToUse | : indices of the atoms in the fragment |
bondsToUse | : indices of the bonds in the fragment. If this is not provided, all bonds between the atoms in atomsToUse will be included |
atomSymbols | : symbols to use for the atoms in the output SMILES |
bondSymbols | : sybmols to use for the bonds in the output SMILES |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
NOTE: the bondSymbols are not currently used in the canonicalization.
std::string RDKit::MolToFASTA | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures std::string RDKit::MolToHELM | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures std::string RDKit::MolToMolBlock | ( | const ROMol & | mol, |
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
mol | - the molecule in question |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
forceV3000 | - force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds) |
void RDKit::MolToMolFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
bool | includeStereo = true , |
||
int | confId = -1 , |
||
bool | kekulize = true , |
||
bool | forceV3000 = false |
||
) |
mol | - the molecule in question |
fName | - the name of the file to use |
includeStereo | - toggles inclusion of stereochemistry information |
confId | - selects the conformer to be used |
kekulize | - triggers kekulization of the molecule before it is written |
forceV3000 | - force generation a V3000 mol block (happens automatically with more than 999 atoms or bonds) |
std::string RDKit::MolToPDBBlock | ( | const ROMol & | mol, |
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write any CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
void RDKit::MolToPDBFile | ( | const ROMol & | mol, |
const std::string & | fname, | ||
int | confId = -1 , |
||
unsigned int | flavor = 0 |
||
) |
mol | - the molecule in question |
fName | - the name of the file to use |
confId | - selects the conformer to be used |
flavor | - controls what gets written: flavor & 1 : Write MODEL/ENDMDL lines around each record flavor & 2 : Don't write any CONECT records flavor & 4 : Write CONECT records in both directions flavor & 8 : Don't use multiple CONECTs to encode bond order flavor & 16 : Write MASTER record flavor & 32 : Write TER record |
std::string RDKit::MolToSequence | ( | const ROMol & | mol | ) |
mol | - the molecule to work with |
mol
should contain monomer information in AtomMonomerInfo
structures std::string RDKit::MolToSmarts | ( | ROMol & | mol, |
bool | doIsomericSmarts = false |
||
) |
returns the SMARTS for a molecule
std::string RDKit::MolToSmiles | ( | const ROMol & | mol, |
bool | doIsomericSmiles = false , |
||
bool | doKekule = false , |
||
int | rootedAtAtom = -1 , |
||
bool | canonical = true , |
||
bool | allBondsExplicit = false , |
||
bool | allHsExplicit = false |
||
) |
returns canonical SMILES for a molecule
mol | : the molecule in question. |
doIsomericSmiles | : include stereochemistry and isotope information in the SMILES |
doKekule | : do Kekule smiles (i.e. don't use aromatic bonds) |
rootedAtAtom | : make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical. |
canonical | : if false, no attempt will be made to canonicalize the SMILES |
allBondsExplicit | : if true, symbols will be included for all bonds. |
allHsExplicit | : if true, hydrogen counts will be provided for every atom. |
Referenced by RDKit::CachedSmilesMolHolder::addMol(), and RDKit::CachedTrustedSmilesMolHolder::addMol().
void RDKit::MolToTPLFile | ( | const ROMol & | mol, |
const std::string & | fName, | ||
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
std::string RDKit::MolToTPLText | ( | const ROMol & | mol, |
const std::string & | partialChargeProp = "_GasteigerCharge" , |
||
bool | writeFirstConfTwice = false |
||
) |
int RDKit::nextCombination | ( | INT_VECT & | comb, |
int | tot | ||
) |
given a current combination of numbers change it to the next possible
comb | the sorted vector to consider |
tot | the maximum number possible in the vector |
Referenced by RDKit::charptr_functor::operator()().
int RDKit::nullDataFun | ( | T | ) |
Definition at line 578 of file QueryOps.h.
bool RDKit::nullQueryFun | ( | T | ) |
Definition at line 582 of file QueryOps.h.
DiscreteValueVect RDKit::operator+ | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
DiscreteValueVect RDKit::operator- | ( | const DiscreteValueVect & | p1, |
const DiscreteValueVect & | p2 | ||
) |
Referenced by RDKit::DiscreteValueVect::getNumInts().
int RDKit::parseFeatureData | ( | const std::string & | defnText, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
int RDKit::parseFeatureData | ( | std::istream & | istream, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
int RDKit::parseFeatureFile | ( | const std::string & | fileName, |
MolChemicalFeatureDef::CollectionType & | featDefs | ||
) |
void RDKit::parseMCSParametersJSON | ( | const char * | json, |
MCSParameters * | params | ||
) |
Referenced by RDKit::MCSResult::isCompleted().
void RDKit::parseQueryDefFile | ( | const std::string & | filename, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true |
||
) |
parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries()
filename | - the name of the file to be read |
queryDefs | - the dictionary of named queries (return value) |
standardize | - if true, query names will be converted to lower case |
delimiter | - the line delimiter in the file |
comment | - text used to recognize comment lines |
nameColumn | - column with the names of queries |
smartsColumn | - column with the SMARTS definitions of the queries |
void RDKit::parseQueryDefFile | ( | std::istream * | inStream, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
void RDKit::parseQueryDefText | ( | const std::string & | queryDefText, |
std::map< std::string, ROMOL_SPTR > & | queryDefs, | ||
bool | standardize = true |
||
) |
equivalent to parseQueryDefFile() but the query definitions are
ExplicitBitVect* RDKit::PatternFingerprintMol | ( | const ROMol & | mol, |
unsigned int | fpSize = 2048 , |
||
std::vector< unsigned int > * | atomCounts = 0 , |
||
ExplicitBitVect * | setOnlyBits = 0 |
||
) |
Generates a topological fingerprint for a molecule using a series of pre-defined structural patterns.
Experimental: This function is experimental. The API or results may change from release to release.
mol | the molecule to be fingerprinted |
fpSize | the size of the fingerprint |
atomCounts | if provided, this will be used to provide the count of the number of paths that set bits each atom is involved in. The vector should have at least as many entries as the molecule has atoms and is not zeroed out here. |
setOnlyBits | if provided, only bits that are set in this bit vector will be set in the result. This is essentially the same as doing: (*res) &= (*setOnlyBits); but also has an impact on the atomCounts (if being used) |
Notes:
delete
ing the result Referenced by RDKit::PatternHolder::makeFingerprint().
RWMol* RDKit::PDBBlockToMol | ( | const char * | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBBlockToMol | ( | const std::string & | str, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBDataStreamToMol | ( | std::istream * | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBDataStreamToMol | ( | std::istream & | inStream, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
RWMol* RDKit::PDBFileToMol | ( | const std::string & | fname, |
bool | sanitize = true , |
||
bool | removeHs = true , |
||
unsigned int | flavor = 0 |
||
) |
INT_MAP_INT RDKit::pickBondsToWedge | ( | const ROMol & | mol | ) |
ROMol* RDKit::prepareMol | ( | const ROMol & | mol, |
const FragCatParams * | fparams, | ||
MatchVectType & | aToFmap | ||
) |
bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::string & | propName = common_properties::molFileValue |
||
) |
bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
unsigned int & | numWarnings, | ||
unsigned int & | numErrors, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > & | reactantLabels, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
bool RDKit::preprocessReaction | ( | ChemicalReaction & | rxn, |
unsigned int & | numWarnings, | ||
unsigned int & | numErrors, | ||
std::vector< std::vector< std::pair< unsigned int, std::string > > > & | reactantLabels, | ||
const std::map< std::string, ROMOL_SPTR > & | queries, | ||
const std::string & | propName = common_properties::molFileValue |
||
) |
|
inline |
Reads an integer from a char * in packed format and returns the result. The argument is advanced
Definition at line 177 of file StreamOps.h.
|
inlinestatic |
Definition at line 73 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAliphaticQuery().
unsigned int RDKit::queryAtomAllBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomMissingChiralTag().
|
inlinestatic |
Definition at line 70 of file QueryOps.h.
References RDKit::Atom::getIsAromatic().
Referenced by makeAtomAromaticQuery().
unsigned int RDKit::queryAtomBondProduct | ( | Atom const * | at | ) |
Referenced by queryAtomMissingChiralTag().
|
inlinestatic |
Definition at line 76 of file QueryOps.h.
References RDKit::Atom::getDegree().
Referenced by makeAtomExplicitDegreeQuery().
|
inlinestatic |
Definition at line 97 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getNumExplicitHs().
Referenced by makeAtomExplicitValenceQuery().
|
inlinestatic |
Definition at line 114 of file QueryOps.h.
References RDKit::Atom::getFormalCharge().
Referenced by makeAtomFormalChargeQuery().
|
inlinestatic |
Definition at line 123 of file QueryOps.h.
References RDKit::Atom::CHI_UNSPECIFIED, and RDKit::Atom::getChiralTag().
Referenced by makeAtomHasChiralTagQuery().
|
inlinestatic |
Definition at line 91 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHasImplicitHQuery().
|
inlinestatic |
Definition at line 159 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomHasRingBondQuery().
|
inlinestatic |
Definition at line 85 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHCountQuery().
|
inlinestatic |
Definition at line 82 of file QueryOps.h.
References RDKit::Atom::getTotalDegree(), and RDKit::Atom::getTotalNumHs().
Referenced by makeAtomHeavyAtomDegreeQuery().
|
inlinestatic |
Definition at line 117 of file QueryOps.h.
References RDKit::Atom::getHybridization().
Referenced by makeAtomHybridizationQuery().
|
inlinestatic |
Definition at line 88 of file QueryOps.h.
References RDKit::Atom::getTotalNumHs().
Referenced by makeAtomImplicitHCountQuery().
|
inlinestatic |
Definition at line 94 of file QueryOps.h.
References RDKit::Atom::getImplicitValence().
Referenced by makeAtomImplicitValenceQuery().
int RDKit::queryAtomIsInRingOfSize | ( | Atom const * | at | ) |
Definition at line 197 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isAtomInRingOfSize().
|
inlinestatic |
Definition at line 111 of file QueryOps.h.
References RDKit::Atom::getIsotope().
Referenced by makeAtomIsotopeQuery().
|
inlinestatic |
Definition at line 108 of file QueryOps.h.
References RDKit::Atom::getMass(), and round().
Referenced by makeAtomMassQuery().
|
inlinestatic |
Definition at line 174 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().
Referenced by makeAtomMinRingSizeQuery().
|
inlinestatic |
Definition at line 126 of file QueryOps.h.
References RDKit::common_properties::_ChiralityPossible, RDKit::Atom::CHI_UNSPECIFIED, RDKit::Atom::getChiralTag(), RDKit::RDProps::hasProp(), queryAtomAllBondProduct(), and queryAtomBondProduct().
Referenced by makeAtomMissingChiralTagQuery().
|
inlinestatic |
Definition at line 106 of file QueryOps.h.
References RDKit::Atom::getAtomicNum().
Referenced by makeAtomNumQuery().
|
inlinestatic |
Definition at line 120 of file QueryOps.h.
References RDKit::Atom::getNumRadicalElectrons().
Referenced by makeAtomNumRadicalElectronsQuery().
|
inlinestatic |
Definition at line 181 of file QueryOps.h.
References RDKit::ROMol::getAtomBonds(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), RDKit::ROMol::getTopology(), and RDKit::RingInfo::numBondRings().
Referenced by makeAtomRingBondCountQuery().
|
inlinestatic |
Definition at line 467 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by RDKit::AtomRingQuery::AtomRingQuery().
|
inlinestatic |
Definition at line 79 of file QueryOps.h.
References RDKit::Atom::getTotalDegree().
Referenced by makeAtomTotalDegreeQuery().
|
inlinestatic |
Definition at line 100 of file QueryOps.h.
References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getImplicitValence().
Referenced by makeAtomTotalValenceQuery().
|
inlinestatic |
Definition at line 103 of file QueryOps.h.
References RDKit::Atom::getDegree(), and RDKit::Atom::getExplicitValence().
Referenced by makeAtomUnsaturatedQuery().
|
inlinestatic |
Definition at line 140 of file QueryOps.h.
References RDKit::Bond::getBondDir().
|
inlinestatic |
Definition at line 146 of file QueryOps.h.
References RDKit::Bond::getStereo(), and RDKit::Bond::STEREONONE.
int RDKit::queryBondIsInRingOfSize | ( | Bond const * | bond | ) |
Definition at line 205 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isBondInRingOfSize().
|
inlinestatic |
Definition at line 177 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().
|
inlinestatic |
Definition at line 137 of file QueryOps.h.
References RDKit::Bond::getBondType().
|
inlinestatic |
Definition at line 153 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInNRingsQuery().
|
inlinestatic |
Definition at line 156 of file QueryOps.h.
References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().
Referenced by makeAtomInRingQuery().
|
inlinestatic |
Definition at line 143 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
|
inlinestatic |
Definition at line 171 of file QueryOps.h.
References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().
const T RDKit::rdany_cast | ( | const RDAny & | d | ) |
Definition at line 181 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
Referenced by from_rdany().
T RDKit::rdany_cast | ( | RDAny & | d | ) |
Definition at line 187 of file RDAny.h.
References RDKit::RDAny::m_value, and rdvalue_cast().
ExplicitBitVect* RDKit::RDKFingerprintMol | ( | const ROMol & | mol, |
unsigned int | minPath = 1 , |
||
unsigned int | maxPath = 7 , |
||
unsigned int | fpSize = 2048 , |
||
unsigned int | nBitsPerHash = 2 , |
||
bool | useHs = true , |
||
double | tgtDensity = 0.0 , |
||
unsigned int | minSize = 128 , |
||
bool | branchedPaths = true , |
||
bool | useBondOrder = true , |
||
std::vector< boost::uint32_t > * | atomInvariants = 0 , |
||
const std::vector< boost::uint32_t > * | fromAtoms = 0 , |
||
std::vector< std::vector< boost::uint32_t > > * | atomBits = 0 , |
||
std::map< boost::uint32_t, std::vector< std::vector< int > > > * | bitInfo = 0 |
||
) |
Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.
mol | the molecule to be fingerprinted |
minPath | the minimum path length (in bonds) to be included |
maxPath | the minimum path length (in bonds) to be included |
fpSize | the size of the fingerprint |
nBitsPerHash | the number of bits to be set by each path |
useHs | toggles inclusion of Hs in paths (if the molecule has explicit Hs) |
tgtDensity | if the generated fingerprint is below this density, it will be folded until the density is reached. |
minSize | the minimum size to which the fingerprint will be folded |
branchedPaths | toggles generation of branched subgraphs, not just linear paths |
useBondOrders | toggles inclusion of bond orders in the path hashes |
atomInvariants | a vector of atom invariants to use while hashing the paths |
fromAtoms | only paths starting at these atoms will be included |
atomBits | used to return the bits that each atom is involved in (should be at least mol.numAtoms long) |
Notes:
delete
ing the result
|
inline |
Definition at line 362 of file RDValue-doublemagic.h.
References RDKit::RDValue::ptrCast().
Referenced by RDKit::RDValue::cleanup_rdvalue(), from_rdvalue(), rdany_cast(), rdvalue_tostring(), streamWriteProp(), and vectToString().
|
inline |
Definition at line 412 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::BoolTag.
Referenced by streamWriteProp().
|
inline |
|
inline |
|
inline |
|
inline |
Definition at line 381 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
Referenced by streamWriteProp().
|
inline |
Definition at line 387 of file RDValue-doublemagic.h.
Referenced by streamWriteProp().
|
inline |
Definition at line 399 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::IntTag.
Referenced by streamWriteProp().
|
inline |
|
inline |
|
inline |
Definition at line 65 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 58 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 79 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 72 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 107 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 100 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 93 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 86 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 121 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 114 of file RDValue.h.
References rdvalue_is().
|
inline |
Definition at line 405 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::UnsignedIntTag.
Referenced by streamWriteProp().
|
inline |
Definition at line 323 of file RDValue-doublemagic.h.
References RDKit::RDValue::getTag().
Referenced by RDKit::RDValue::cleanup_rdvalue(), rdvalue_cast< std::vector< double > & >(), rdvalue_cast< std::vector< double > >(), rdvalue_cast< std::vector< float > & >(), rdvalue_cast< std::vector< float > >(), rdvalue_cast< std::vector< int > & >(), rdvalue_cast< std::vector< int > >(), rdvalue_cast< std::vector< std::string > & >(), rdvalue_cast< std::vector< std::string > >(), rdvalue_cast< std::vector< unsigned int > & >(), and rdvalue_cast< std::vector< unsigned int > >().
|
inline |
Definition at line 334 of file RDValue-doublemagic.h.
References rdvalue_is< double >().
|
inline |
Definition at line 328 of file RDValue-doublemagic.h.
References RDKit::RDTypeTag::MaxDouble, and RDKit::RDTypeTag::NaN.
Referenced by RDKit::RDValue::cleanup_rdvalue(), rdvalue_cast< double >(), and rdvalue_is< const double & >().
|
inline |
Definition at line 166 of file RDValue.h.
References RDKit::RDTypeTag::AnyTag, RDKit::RDTypeTag::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, rdvalue_cast(), RDKit::RDTypeTag::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::RDTypeTag::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::RDTypeTag::VecStringTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
unsigned int RDKit::readAmberTrajectory | ( | const std::string & | fName, |
Trajectory & | traj | ||
) |
Reads coordinates from an AMBER trajectory file into the traj Trajectory object.
Referenced by RDKit::Trajectory::clear().
MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::string | fileName | ) |
MOL_SPTR_VECT RDKit::readFuncGroups | ( | std::istream & | inStream, |
int | nToRead = -1 |
||
) |
unsigned int RDKit::readGromosTrajectory | ( | const std::string & | fName, |
Trajectory & | traj | ||
) |
Reads coordinates from a GROMOS trajectory file into the traj Trajectory object.
Referenced by RDKit::Trajectory::clear().
|
inline |
Reads an integer from a stream in packed format and returns the result.
Definition at line 139 of file StreamOps.h.
|
inline |
Definition at line 456 of file StreamOps.h.
References streamReadStringVec().
Referenced by streamReadProp().
void RDKit::readRDValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 435 of file StreamOps.h.
References streamRead().
|
inline |
Definition at line 448 of file StreamOps.h.
References streamRead().
Referenced by streamReadProp().
void RDKit::readRDVecValue | ( | std::istream & | ss, |
RDValue & | value | ||
) |
Definition at line 442 of file StreamOps.h.
References streamReadVec().
ROMol* RDKit::reduceProductToSideChains | ( | const ROMOL_SPTR & | product, |
bool | addDummyAtoms = true |
||
) |
Reduce the product generated by run_Reactants or run_Reactant to.
addDummyAtoms | If true, add dummy atoms to the sidechains for the non-reagent parts of the sidechain. Dummy atoms are annotated with the atom maps from the reaction. If False, then any sidechain atom where a bond was cleaved is annotated with: _rgroupAtomMaps property which indicates the scaffold atommaps that where bonded _rgroupBonds property which indicates the bondtype for each atommap bonded |
void RDKit::removeDuplicates | ( | std::vector< MatchVectType > & | v, |
unsigned int | nAtoms | ||
) |
void RDKit::removeMappingNumbersFromReactions | ( | const ChemicalReaction & | rxn | ) |
EnumerationTypes::BBS RDKit::removeNonmatchingReagents | ( | const ChemicalReaction & | rxn, |
EnumerationTypes::BBS | bbs, | ||
const EnumerationParams & | params = EnumerationParams() |
||
) |
Helper function, remove reagents that are incompatible.
Referenced by RDKit::EnumerationParams::EnumerationParams().
ROMol* RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | core, | ||
const MatchVectType & | matchVect, | ||
bool | replaceDummies = true , |
||
bool | labelByIndex = false , |
||
bool | requireDummyMatch = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core.
dummy atoms are left to indicate attachment points. These dummy atoms can be labeled either by the matching index in the query or by an arbitrary "first match" found. Additional matching options are given below.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
core | - the core being matched against |
matchVect | - a matchVect of the type returned by Substructure Matching |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. ROMol* RDKit::replaceCore | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | replaceDummies = true , |
||
bool | labelByIndex = false , |
||
bool | requireDummyMatch = false , |
||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that do match the query.
mol | - the ROMol of interest |
coreQuery | - a query ROMol to be used to match the core |
replaceDummies | - if set, atoms matching dummies in the core will also be replaced |
labelByIndex | - if set, the dummy atoms at attachment points are labelled with the index+1 of the corresponding atom in the core |
requireDummyMatch | - if set, only side chains that are connected to atoms in the core that have attached dummies will be considered. Molecules that have sidechains that are attached at other points will be rejected (NULL returned). |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule. If the core query is not matched, NULL is returned. ROMol* RDKit::replaceSidechains | ( | const ROMol & | mol, |
const ROMol & | coreQuery, | ||
bool | useChirality = false |
||
) |
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.
dummy atoms are left to indicate attachment points.
mol | the ROMol of interest |
coreQuery | a query ROMol to be used to match the core |
useChirality | - if set, match the coreQuery using chirality |
mol
with the non-matching atoms and bonds (if any) removed and dummies at the connection points. std::vector<ROMOL_SPTR> RDKit::replaceSubstructs | ( | const ROMol & | mol, |
const ROMol & | query, | ||
const ROMol & | replacement, | ||
bool | replaceAll = false , |
||
unsigned int | replacementConnectionPoint = 0 , |
||
bool | useChirality = false |
||
) |
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.
Bonds are created between the joining atom in the existing molecule and the atoms in the new molecule. So, using SMILES instead of molecules: replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') -> ['[X]NCCNC(=O)O','OC(=O)NCCN[X]'] replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) -> ['[X]NCCN[X]'] Chains should be handled "correctly": replaceSubstructs('CC(=O)C','C(=O)','[X]') -> ['C[X]C'] As should rings: replaceSubstructs('C1C(=O)C1','C(=O)','[X]') -> ['C1[X]C1'] And higher order branches: replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') -> ['C[X](C)C'] Note that the client is responsible for making sure that the resulting molecule actually makes sense - this function does not perform sanitization.
mol | the ROMol of interest |
query | the query ROMol |
replacement | the ROMol to be inserted |
replaceAll | if this is true, only a single result, with all |
useChirality | - if set, match the coreQuery using chirality |
occurances of the substructure replaced, will be returned.
replacementConnectionPoint | index of the atom in the replacement that the bond should made to |
mol
with the matching atoms and bonds (if any) replaced unsigned int RDKit::RGroupDecompose | ( | const std::vector< ROMOL_SPTR > & | cores, |
const std::vector< ROMOL_SPTR > & | mols, | ||
RGroupRows & | rows, | ||
std::vector< unsigned int > * | unmatched = 0 , |
||
const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
||
) |
unsigned int RDKit::RGroupDecompose | ( | const std::vector< ROMOL_SPTR > & | cores, |
const std::vector< ROMOL_SPTR > & | mols, | ||
RGroupColumns & | columns, | ||
std::vector< unsigned int > * | unmatched = 0 , |
||
const RGroupDecompositionParameters & | options = RGroupDecompositionParameters() |
||
) |
double RDKit::round | ( | double | v | ) |
rounds a value to the closest int
Referenced by RDKit::charptr_functor::operator()(), and queryAtomMass().
std::vector<MOL_SPTR_VECT> RDKit::run_Reactant | ( | const ChemicalReaction & | rxn, |
const ROMOL_SPTR & | reactant, | ||
unsigned int | reactantIdx | ||
) |
Runs a single reactant against a single reactant template.
reactant | The single reactant to use |
reactantTemplateIdx | the reactant template to target in the reaction |
We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.
std::vector<MOL_SPTR_VECT> RDKit::run_Reactants | ( | const ChemicalReaction & | rxn, |
const MOL_SPTR_VECT & | reactants | ||
) |
Runs the reaction on a set of reactants.
rxn | the template reaction we are interested |
reactants | the reactants to be used. The length of this must be equal to rxn->getNumReactantTemplates() Caution: The order of the reactant templates determines the order of the reactants! |
We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.
ChemicalReaction* RDKit::RxnBlockToChemicalReaction | ( | const std::string & | rxnBlock | ) |
Parse a text block in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnDataStreamToChemicalReaction | ( | std::istream & | rxnStream, |
unsigned int & | line | ||
) |
Parse a text stream in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnFileToChemicalReaction | ( | const std::string & | fileName | ) |
Parse a file in MDL rxn format into a ChemicalReaction.
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnMolToChemicalReaction | ( | const ROMol & | mol | ) |
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
Alternative to build a reaction from a molecule (fragments) which have RXN roles set as atom properties: common_properties::molRxnRole (1=reactant, 2=product, 3=agent)
mol | ROMol with RXN roles set |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
ChemicalReaction* RDKit::RxnSmartsToChemicalReaction | ( | const std::string & | text, |
std::map< std::string, std::string > * | replacements = 0 , |
||
bool | useSmiles = false |
||
) |
Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
Our definition of Reaction SMARTS is something that looks a lot like reaction SMILES, except that SMARTS queries are allowed on the reactant side and that atom-map numbers are required (at least for now)
text | the SMARTS to convert |
replacements | a string->string map of replacement strings. |
useSmiles | if set, the SMILES parser will be used instead of the SMARTS parserfor the individual components |
Referenced by RDKit::ChemicalReactionParserException::~ChemicalReactionParserException().
RWMol* RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
lowerD | - if set, lower case letters will be parsed as the d form of the corresponding amino acid |
RWMol* RDKit::SequenceToMol | ( | const std::string & | seq, |
bool | sanitize, | ||
bool | lowerD | ||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RWMol* RDKit::SequenceToMol | ( | const char * | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
seq | - the string to be processed |
sanitize | - toggles sanitization and stereochemistry perception of the molecule |
flavor | - 0 Protein, L amino acids (default) 1 Protein, D amino acids 2 RNA, no cap 3 RNA, 5' cap 4 RNA, 3' cap 5 RNA, both caps 6 DNA, no cap 7 DNA, 5' cap 8 DNA, 3' cap 9 DNA, both caps |
RWMol* RDKit::SequenceToMol | ( | const std::string & | seq, |
bool | sanitize = true , |
||
int | flavor = 0 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
void RDKit::setAtomAlias | ( | Atom * | atom, |
const std::string & | alias | ||
) |
Set the atom's MDL atom alias.
void RDKit::setAtomRLabel | ( | Atom * | atm, |
int | rlabel | ||
) |
Set the atom's MDL integer RLabel.
void RDKit::setAtomValue | ( | Atom * | atom, |
const std::string & | value | ||
) |
Set the atom's MDL atom value.
void RDKit::setSupplementalSmilesLabel | ( | Atom * | atom, |
const std::string & | label | ||
) |
Sets the supplemental label that will follow the atom when writing.
RWMol* RDKit::SLNQueryToMol | ( | const std::string & | smi, |
bool | mergeHs = true , |
||
int | debugParse = 0 |
||
) |
RWMol* RDKit::SLNToMol | ( | const std::string & | smi, |
bool | sanitize = true , |
||
int | debugParse = 0 |
||
) |
RWMol* RDKit::SmartsToMol | ( | const std::string & | sma, |
int | debugParse = 0 , |
||
bool | mergeHs = false , |
||
std::map< std::string, std::string > * | replacements = 0 |
||
) |
Construct a molecule from a SMARTS string.
sma | the SMARTS to convert |
debugParse | toggles verbose debugging information from the parser |
mergeHs | toggles merging H atoms in the SMARTS into neighboring atoms |
replacements | a string->string map of replacement strings. |
Referenced by SmilesToMol().
RWMol* RDKit::SmilesToMol | ( | const std::string & | smi, |
const SmilesParserParams & | params | ||
) |
|
inline |
Construct a molecule from a SMILES string.
smi | the SMILES to convert |
debugParse | toggles verbose debugging information from the parser |
sanitize | toggles H removal and sanitization of the molecule |
replacements | a string->string map of replacement strings. See below for more information about replacements. |
The optional replacements map can be used to do string substitution of abbreviations in the input SMILES. The set of substitutions is repeatedly looped through until the string no longer changes. It is the responsiblity of the caller to make sure that substitutions results in legal and sensible SMILES.
Examples of substitutions:
Definition at line 66 of file SmilesParse.h.
References RDKit::SmilesParserParams::debugParse, RDKit::SmilesParserParams::removeHs, RDKit::SmilesParserParams::replacements, RDKit::SmilesParserParams::sanitize, SmartsToMol(), and SmilesToMol().
void RDKit::StandardPDBResidueBondOrders | ( | RWMol * | mol | ) |
void RDKit::streamRead | ( | std::istream & | ss, |
T & | loc | ||
) |
does a binary read of an object from a stream
Definition at line 243 of file StreamOps.h.
Referenced by RDKit::SparseIntVect< IndexType >::fromString(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream(), readRDValue(), readRDValueString(), streamRead(), streamReadProp(), streamReadProps(), streamReadStringVec(), and streamReadVec().
void RDKit::streamRead | ( | std::istream & | ss, |
T & | obj, | ||
int | version | ||
) |
special case for string
Definition at line 251 of file StreamOps.h.
References RDUNUSED_PARAM, and streamRead().
|
inline |
Definition at line 256 of file StreamOps.h.
References RDUNUSED_PARAM.
|
inline |
Definition at line 464 of file StreamOps.h.
References RDKit::DTags::BoolTag, RDKit::DTags::DoubleTag, RDKit::DTags::FloatTag, RDKit::DTags::IntTag, RDKit::Dict::Pair::key, readRDStringVecValue(), readRDValueString(), streamRead(), RDKit::DTags::StringTag, RDKit::DTags::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::DTags::VecDoubleTag, RDKit::DTags::VecFloatTag, RDKit::DTags::VecIntTag, RDKit::DTags::VecStringTag, and RDKit::DTags::VecUIntTag.
Referenced by streamReadProps().
|
inline |
Definition at line 490 of file StreamOps.h.
References CHECK_INVARIANT, RDKit::Dict::getData(), RDKit::RDProps::getDict(), streamRead(), and streamReadProp().
|
inline |
Definition at line 278 of file StreamOps.h.
References streamRead().
Referenced by readRDStringVecValue().
void RDKit::streamReadVec | ( | std::istream & | ss, |
T & | val | ||
) |
Definition at line 269 of file StreamOps.h.
References streamRead().
Referenced by readRDVecValue().
void RDKit::streamWrite | ( | std::ostream & | ss, |
const T & | val | ||
) |
does a binary write of an object to a stream
Definition at line 222 of file StreamOps.h.
Referenced by streamWriteProp(), streamWriteProps(), streamWriteVec(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream(), and RDKit::SparseIntVect< IndexType >::toString().
|
inline |
special case for string
Definition at line 228 of file StreamOps.h.
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inline |
Definition at line 340 of file StreamOps.h.
References RDKit::RDTypeTag::BoolTag, RDKit::DTags::BoolTag, RDKit::RDTypeTag::DoubleTag, RDKit::DTags::DoubleTag, RDKit::RDTypeTag::FloatTag, RDKit::DTags::FloatTag, RDKit::RDValue::getTag(), RDKit::RDTypeTag::IntTag, RDKit::DTags::IntTag, isSerializable(), RDKit::Dict::Pair::key, rdvalue_cast(), rdvalue_cast< bool >(), rdvalue_cast< double >(), rdvalue_cast< float >(), rdvalue_cast< int >(), rdvalue_cast< unsigned int >(), streamWrite(), streamWriteVec(), RDKit::RDTypeTag::StringTag, RDKit::DTags::StringTag, RDKit::RDTypeTag::UnsignedIntTag, RDKit::DTags::UnsignedIntTag, RDKit::Dict::Pair::val, RDKit::RDTypeTag::VecDoubleTag, RDKit::DTags::VecDoubleTag, RDKit::RDTypeTag::VecFloatTag, RDKit::DTags::VecFloatTag, RDKit::RDTypeTag::VecIntTag, RDKit::DTags::VecIntTag, RDKit::RDTypeTag::VecStringTag, RDKit::DTags::VecStringTag, RDKit::DTags::VecUIntTag, and RDKit::RDTypeTag::VecUnsignedIntTag.
Referenced by streamWriteProps().
|
inline |
Definition at line 399 of file StreamOps.h.
References RDKit::RDProps::getDict(), RDKit::RDProps::getPropList(), isSerializable(), POSTCONDITION, streamWrite(), and streamWriteProp().
void RDKit::streamWriteVec | ( | std::ostream & | ss, |
const T & | val | ||
) |
Definition at line 235 of file StreamOps.h.
References streamWrite().
Referenced by streamWriteProp().
std::string RDKit::strip | ( | const std::string & | orig | ) |
ExplicitBitVect* RDKit::StructuralFingerprintChemReaction | ( | const ChemicalReaction & | rxn, |
const ReactionFingerprintParams & | params = DefaultStructuralFPParams |
||
) |
Generates a structural fingerprint for a reaction to use in screening
A structural fingerprint is generated as an ExplicitBitVect to use for searching e.g. substructure in reactions. By default the fingerprint is generated as 4096 BitVect using a PatternFP for reactants and products and tentatively agents which were finally concatenated
rxn | the reaction to be fingerprinted |
params | specific settings to manipulate fingerprint generation |
Notes:
delete
ing the result bool RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
Find a substructure match for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
matchVect | Used to return the match (pre-existing contents will be deleted) |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
bool RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSuppl, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
Find a substructure match for a query in a ResonanceMolSupplier object.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
matchVect | Used to return the match (pre-existing contents will be deleted) |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
unsigned int RDKit::SubstructMatch | ( | const ROMol & | mol, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
Find all substructure matches for a query in a molecule.
mol | The ROMol to be searched |
query | The query ROMol |
matchVect | Used to return the matches (pre-existing contents will be deleted) |
uniquify | Toggles uniquification (by atom index) of the results |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
maxMatches | The maximum number of matches that will be returned. In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences |
unsigned int RDKit::SubstructMatch | ( | ResonanceMolSupplier & | resMolSuppl, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = false , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 , |
||
int | numThreads = 1 |
||
) |
Find all substructure matches for a query in a ResonanceMolSupplier object.
resMolSuppl | The ResonanceMolSupplier object to be searched |
query | The query ROMol |
matchVect | Used to return the matches (pre-existing contents will be deleted) |
uniquify | Toggles uniquification (by atom index) of the results |
recursionPossible | flags whether or not recursive matches are allowed |
useChirality | use atomic CIP codes as part of the comparison |
useQueryQueryMatches | if set, the contents of atom and bond queries will be used as part of the matching |
maxMatches | The maximum number of matches that will be returned. In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences |
numThreads | The number of threads used during the search (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware) |
bool RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const ROMol & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
bool RDKit::SubstructMatch | ( | const ROMol & | bundle, |
const MolBundle & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
bool RDKit::SubstructMatch | ( | const MolBundle & | bundle, |
const MolBundle & | query, | ||
MatchVectType & | matchVect, | ||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds the first match in the bundle
unsigned int RDKit::SubstructMatch | ( | const MolBundle & | mol, |
const ROMol & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches in the first molecule of the bundle that matches the query
unsigned int RDKit::SubstructMatch | ( | const MolBundle & | mol, |
const MolBundle & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches in the first molecule of the bundle that matches
unsigned int RDKit::SubstructMatch | ( | const ROMol & | mol, |
const MolBundle & | query, | ||
std::vector< MatchVectType > & | matchVect, | ||
bool | uniquify = true , |
||
bool | recursionPossible = true , |
||
bool | useChirality = false , |
||
bool | useQueryQueryMatches = false , |
||
unsigned int | maxMatches = 1000 |
||
) |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. finds all matches against the first molecule of the query bundle that matches
|
inline |
Definition at line 41 of file StreamOps.h.
double RDKit::TanimotoSimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 540 of file SparseIntVect.h.
References TverskySimilarity().
double RDKit::toPrime | ( | const MatchVectType & | v | ) |
RWMol* RDKit::TPLDataStreamToMol | ( | std::istream * | inStream, |
unsigned int & | line, | ||
bool | sanitize = true , |
||
bool | skipFirstConf = false |
||
) |
translate TPL data (BioCad format) into a multi-conf molecule
inStream | the stream from which to read |
line | used to track the line number of errors |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
RWMol* RDKit::TPLFileToMol | ( | const std::string & | fName, |
bool | sanitize = true , |
||
bool | skipFirstConf = false |
||
) |
construct a multi-conf molecule from a TPL (BioCad format) file
fName | the name of the file from which to read |
sanitize | toggles sanitization and stereochemistry perception of the molecule |
skipFirstConf | according to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set. |
double RDKit::TverskySimilarity | ( | const SparseIntVect< IndexType > & | v1, |
const SparseIntVect< IndexType > & | v2, | ||
double | a, | ||
double | b, | ||
bool | returnDistance = false , |
||
double | bounds = 0.0 |
||
) |
Definition at line 513 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), and RDUNUSED_PARAM.
Referenced by TanimotoSimilarity().
calculate the union of two INT_VECTs and put the results in a third vector
Referenced by RDKit::charptr_functor::operator()().
void RDKit::Union | ( | const VECT_INT_VECT & | rings, |
INT_VECT & | res, | ||
const INT_VECT * | exclude = NULL |
||
) |
calculating the union of the INT_VECT's in a VECT_INT_VECT
rings | the INT_VECT's to consider |
res | used to return results |
exclude | any values in this optional INT_VECT will be excluded from the union. |
void RDKit::updateFromSequence | ( | SparseIntVect< IndexType > & | vect, |
const SequenceType & | seq | ||
) |
Definition at line 403 of file SparseIntVect.h.
References RDKit::SparseIntVect< IndexType >::getLength(), RDKit::SparseIntVect< IndexType >::getNonzeroElements(), RDKit::SparseIntVect< IndexType >::getVal(), and RDKit::SparseIntVect< IndexType >::setVal().
void RDKit::updateProductsStereochem | ( | ChemicalReaction * | rxn | ) |
std::string RDKit::vectToString | ( | RDValue | val | ) |
Definition at line 155 of file RDValue.h.
References rdvalue_cast().
std::string RDKit::additionalParamData |
const unsigned int RDKit::BITS_PER_INT = 32 |
Definition at line 20 of file DiscreteValueVect.h.
const char* RDKit::boostVersion |
const int RDKit::ci_ATOM_HOLDER |
const int RDKit::ci_LEADING_BOND |
const int RDKit::ci_RIGHTMOST_ATOM |
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static |
Definition at line 16 of file ProximityBonds.h.
|
static |
Definition at line 15 of file ProximityBonds.h.
const double RDKit::DAMP = 0.5 |
Definition at line 27 of file GasteigerParams.h.
const double RDKit::DAMP_SCALE = 0.5 |
Definition at line 26 of file GasteigerParams.h.
const char* RDKit::DEFAULT_FILTERMATCHERBASE_NAME |
Referenced by RDKit::FilterMatch::operator!=().
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static |
Definition at line 22 of file MolWriters.h.
const double RDKit::EPS_DOUBLE |
const int RDKit::FILE_MAXLINE |
const double RDKit::IONXH = 20.02 |
Definition at line 24 of file GasteigerParams.h.
const std::string RDKit::isotopesAtomData[] |
const std::string RDKit::LayeredFingerprintMolVersion = "0.7.0" |
Definition at line 111 of file Fingerprints.h.
const int RDKit::massIntegerConversionFactor = 1000 |
Definition at line 107 of file QueryOps.h.
const double RDKit::MAX_DOUBLE |
const double RDKit::MAX_INT |
const double RDKit::MAX_LONGINT |
const unsigned int RDKit::maxFingerprintLayers = 10 |
Definition at line 110 of file Fingerprints.h.
const int RDKit::MOLFILE_MAXLINE = 256 |
Definition at line 24 of file FileParsers.h.
const int RDKit::NUM_PRIMES_AVAIL = 1000 |
std::string RDKit::paramData |
const std::string RDKit::periodicTableAtomData |
const std::string RDKit::RDKFingerprintMolVersion = "2.0.0" |
Definition at line 61 of file Fingerprints.h.
const char* RDKit::rdkitBuild |
const char* RDKit::rdkitVersion |
const double RDKit::SMALL_DOUBLE |
const char* RDKit::SMARTS_MATCH_NAME_DEFAULT |
Referenced by RDKit::FilterMatchOps::Not::copy().
const unsigned int RDKit::substructLayers = 0x07 |
Definition at line 112 of file Fingerprints.h.