Package org.jmol.adapter.readers.simple
Class InputReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.simple.InputReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
MopacArchiveReader
public class InputReader extends AtomSetCollectionReader
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Field Summary
Fields Modifier and Type Field Description protected int
ac
private java.util.Map<java.lang.String,java.lang.Integer>
atomMap
private boolean
firstLine
private boolean
isHeader
private boolean
isJmolZformat
private boolean
isMopac
private javajs.util.Lst<java.lang.String[]>
lineBuffer
private javajs.util.P4
plane1
private javajs.util.P4
plane2
private javajs.util.P3
pt0
private java.util.Map<java.lang.String,java.lang.Float>
symbolicMap
private java.lang.String[]
tokens
private javajs.util.V3
v1
private javajs.util.V3
v2
protected javajs.util.Lst<Atom>
vAtoms
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description InputReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
private java.lang.String
cleanLine()
protected void
finalizeSubclassReader()
optional reader-specific method run first.private Atom
getAtom()
private Atom
getAtomGeneral(Atom atom, int ia, int bondOrder)
private int
getAtomIndex(int i)
private void
getSymbolic()
private float
getSymbolic(java.lang.String key)
private float
getValue(int i)
private void
parseAtomTokens(Atom atom, java.lang.String element)
private boolean
readBlock(java.lang.String strEnd)
private void
readCFI()
private void
readConFile()
private boolean
readVFI()
protected Atom
setAtom(Atom atom, int ia, int ib, int ic, float d, float theta1, float theta2)
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
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Field Detail
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ac
protected int ac
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vAtoms
protected javajs.util.Lst<Atom> vAtoms
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atomMap
private java.util.Map<java.lang.String,java.lang.Integer> atomMap
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tokens
private java.lang.String[] tokens
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isJmolZformat
private boolean isJmolZformat
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lineBuffer
private javajs.util.Lst<java.lang.String[]> lineBuffer
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symbolicMap
private java.util.Map<java.lang.String,java.lang.Float> symbolicMap
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isMopac
private boolean isMopac
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isHeader
private boolean isHeader
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firstLine
private boolean firstLine
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pt0
private final javajs.util.P3 pt0
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v1
private final javajs.util.V3 v1
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v2
private final javajs.util.V3 v2
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plane1
private final javajs.util.P4 plane1
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plane2
private final javajs.util.P4 plane2
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Method Detail
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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readConFile
private void readConFile() throws java.lang.Exception
- Throws:
java.lang.Exception
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readCFI
private void readCFI() throws java.lang.Exception
- Throws:
java.lang.Exception
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readVFI
private boolean readVFI() throws java.lang.Exception
- Throws:
java.lang.Exception
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readBlock
private boolean readBlock(java.lang.String strEnd) throws java.lang.Exception
- Throws:
java.lang.Exception
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cleanLine
private java.lang.String cleanLine()
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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getSymbolic
private void getSymbolic()
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getAtom
private Atom getAtom() throws java.lang.Exception
- Throws:
java.lang.Exception
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parseAtomTokens
private void parseAtomTokens(Atom atom, java.lang.String element) throws java.lang.Exception
- Throws:
java.lang.Exception
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getAtomGeneral
private Atom getAtomGeneral(Atom atom, int ia, int bondOrder) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSymbolic
private float getSymbolic(java.lang.String key)
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getValue
private float getValue(int i) throws java.lang.Exception
- Throws:
java.lang.Exception
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getAtomIndex
private int getAtomIndex(int i)
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