Package org.jmol.adapter.readers.xtal
Class DmolReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.DmolReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class DmolReader extends AtomSetCollectionReader
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Field Summary
Fields Modifier and Type Field Description private booleangeomOptprivate java.lang.DoubletotEprivate float[]unitCellData-
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description DmolReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected booleancheckLine()private voidnewAtomSet()private voidreadCellParam()private voidreadCoord()private voidreadEnergy()private voidreadFreq()private voidsetEnergy()-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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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Method Detail
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checkLine
protected boolean checkLine() throws java.lang.Exception- Overrides:
checkLinein classAtomSetCollectionReader- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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readCellParam
private void readCellParam() throws java.lang.Exception- Throws:
java.lang.Exception
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newAtomSet
private void newAtomSet() throws java.lang.Exception- Throws:
java.lang.Exception
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readCoord
private void readCoord() throws java.lang.Exception- Throws:
java.lang.Exception
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readEnergy
private void readEnergy() throws java.lang.Exception- Throws:
java.lang.Exception
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setEnergy
private void setEnergy()
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readFreq
private void readFreq() throws java.lang.Exception- Throws:
java.lang.Exception
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