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 Map<String,Integer>
atomMap
private boolean
firstLine
private boolean
isHeader
private boolean
isJmolZformat
private boolean
isMopac
private javajs.util.Lst<String[]>
lineBuffer
private javajs.util.P4
plane1
private javajs.util.P4
plane2
private javajs.util.P3
pt0
private Map<String,Float>
symbolicMap
private 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, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, 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, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, 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 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(String key)
private float
getValue(int i)
private void
parseAtomTokens(Atom atom, String element)
private boolean
readBlock(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, 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, 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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tokens
private String[] tokens
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isJmolZformat
private boolean isJmolZformat
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lineBuffer
private javajs.util.Lst<String[]> lineBuffer
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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 Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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cleanLine
private String cleanLine()
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finalizeSubclassReader
protected void finalizeSubclassReader() throws Exception
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()
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parseAtomTokens
private void parseAtomTokens(Atom atom, String element) throws Exception
- Throws:
Exception
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getAtomGeneral
private Atom getAtomGeneral(Atom atom, int ia, int bondOrder) throws Exception
- Throws:
Exception
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getSymbolic
private float getSymbolic(String key)
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getAtomIndex
private int getAtomIndex(int i)
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