Package org.jmol.adapter.readers.simple
Class InputReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.simple.InputReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
MopacArchiveReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
private boolean
private boolean
private boolean
private boolean
private javajs.util.Lst
<String[]> private final javajs.util.P4
private final javajs.util.P4
private final javajs.util.P3
private String[]
private final javajs.util.V3
private final javajs.util.V3
protected javajs.util.Lst
<Atom> 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, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
private String
protected void
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
private float
getSymbolic
(String key) private float
getValue
(int i) private void
parseAtomTokens
(Atom atom, String element) private boolean
private void
readCFI()
private void
private boolean
readVFI()
protected Atom
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 Details
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ac
protected int ac -
vAtoms
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atomMap
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tokens
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isJmolZformat
private boolean isJmolZformat -
lineBuffer
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symbolicMap
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isMopac
private boolean isMopac -
isHeader
private boolean isHeader -
firstLine
private boolean firstLine -
pt0
private final javajs.util.P3 pt0 -
v1
private final javajs.util.V3 v1 -
v2
private final javajs.util.V3 v2 -
plane1
private final javajs.util.P4 plane1 -
plane2
private final javajs.util.P4 plane2
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Constructor Details
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InputReader
public InputReader()
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Method Details
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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readConFile
- Throws:
Exception
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readCFI
- Throws:
Exception
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readVFI
- Throws:
Exception
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readBlock
- Throws:
Exception
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cleanLine
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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getSymbolic
private void getSymbolic() -
getAtom
- Throws:
Exception
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parseAtomTokens
- Throws:
Exception
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getAtomGeneral
- Throws:
Exception
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getSymbolic
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getValue
- Throws:
Exception
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getAtomIndex
private int getAtomIndex(int i) -
setAtom
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