Package org.jmol.adapter.readers.xtal
Class EspressoReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.EspressoReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class EspressoReader extends AtomSetCollectionReader
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Field Summary
Fields Modifier and Type Field Description private floataParprivate float[]cellParamsprivate booleanendFlagprivate java.lang.DoubletotEnergy-
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 EspressoReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected booleancheckLine()protected voidinitializeReader()private voidnewAtomSet()private voidreadAparam()private voidreadAtoms()private voidreadCellParam(boolean andAPar)private voidreadEnergy()private voidsetCellParams()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, 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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initializeReader
protected void initializeReader()
- Overrides:
initializeReaderin classAtomSetCollectionReader
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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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readAparam
private void readAparam() throws java.lang.Exception- Throws:
java.lang.Exception
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readCellParam
private void readCellParam(boolean andAPar) 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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setCellParams
private void setCellParams() throws java.lang.Exception- Throws:
java.lang.Exception
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readAtoms
private void readAtoms() 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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