Package org.jmol.adapter.readers.xtal
Class GulpReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.GulpReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class GulpReader extends AtomSetCollectionReader
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional. Default right now is to read conventional cell, not primitive celll -- Frequency data number of atoms does not correspond to initial atom count. It looks like there is a missing report of symmetry-generated atoms. see https://projects.ivec.org/gulp/- Version:
- 1.0
- Author:
- Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom, pc229@kent.ac.uk
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Field Summary
Fields Modifier and Type Field Description private float
a
private float
alpha
private java.util.Map<java.lang.String,java.lang.Float>
atomCharges
private float
b
private float
beta
private boolean
bTest
private float
c
private boolean
coordinatesArePrimitive
private java.lang.String
energyUnits
private float
gamma
private boolean
isPolymer
private boolean
isPrimitive
private boolean
isSlab
private float[]
primitiveData
private java.lang.String
sep
private static java.lang.String[]
tags
private java.lang.Double
totEnergy
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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, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, 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, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description GulpReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
applySymmetryAndSetTrajectory()
protected boolean
checkLine()
protected void
finalizeSubclassReader()
optional reader-specific method run first.protected void
initializeReader()
private void
newAtomSet(boolean doSetUnitCell)
private static int
parameterIndex(java.lang.String key)
private void
readAtomicPos(boolean finalizeSymmetry)
private void
readCellParameters(boolean isLatticeVectors)
private boolean
readDimensionality()
private void
readEnergy()
private void
readFinalCell()
private void
readPartialCharges()
private void
readSpaceGroup()
private void
scalePrimitiveData(int i, float value)
private void
setEnergy()
private void
setModelParameters(boolean isPrimitive)
private void
setParameter(java.lang.String key, float value)
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, 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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Field Detail
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isSlab
private boolean isSlab
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isPolymer
private boolean isPolymer
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isPrimitive
private boolean isPrimitive
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sep
private java.lang.String sep
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coordinatesArePrimitive
private boolean coordinatesArePrimitive
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atomCharges
private java.util.Map<java.lang.String,java.lang.Float> atomCharges
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bTest
private boolean bTest
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a
private float a
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b
private float b
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c
private float c
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alpha
private float alpha
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beta
private float beta
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gamma
private float gamma
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primitiveData
private float[] primitiveData
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tags
private static final java.lang.String[] tags
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totEnergy
private java.lang.Double totEnergy
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energyUnits
private java.lang.String energyUnits
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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finalizeSubclassReader
protected void finalizeSubclassReader()
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
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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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readDimensionality
private boolean readDimensionality() throws java.lang.Exception
- Throws:
java.lang.Exception
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readSpaceGroup
private void readSpaceGroup() throws java.lang.Exception
- Throws:
java.lang.Exception
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parameterIndex
private static int parameterIndex(java.lang.String key)
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setParameter
private void setParameter(java.lang.String key, float value)
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newAtomSet
private void newAtomSet(boolean doSetUnitCell)
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setModelParameters
private void setModelParameters(boolean isPrimitive)
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readCellParameters
private void readCellParameters(boolean isLatticeVectors) throws java.lang.Exception
- Throws:
java.lang.Exception
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readFinalCell
private void readFinalCell() throws java.lang.Exception
- Throws:
java.lang.Exception
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scalePrimitiveData
private void scalePrimitiveData(int i, float value)
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applySymmetryAndSetTrajectory
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
- Overrides:
applySymmetryAndSetTrajectory
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readAtomicPos
private void readAtomicPos(boolean finalizeSymmetry) throws java.lang.Exception
- Throws:
java.lang.Exception
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readPartialCharges
private void readPartialCharges() 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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