org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.GulpReader

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

Field Summary

Fields

Modifier and Type

Field

Description

private float

a

private float

alpha

private Map<String,Float>

atomCharges

private float

b

private float

beta

private boolean

bTest

private float

c

private boolean

coordinatesArePrimitive

private String

energyUnits

private float

gamma

private boolean

isPolymer

private boolean

isPrimitive

private boolean

isSlab

private float[]

primitiveData

private String

sep

private static final String[]

tags

private Double

totEnergy

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, 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
Constructor Summary

Constructors

Constructor

Description

GulpReader()
Method Summary

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(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(String key, float value)

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, getFilterWithCase, 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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- isSlab
  
  private boolean isSlab
- isPolymer
  
  private boolean isPolymer
- isPrimitive
  
  private boolean isPrimitive
- sep
  
  private String sep
- coordinatesArePrimitive
  
  private boolean coordinatesArePrimitive
- atomCharges
  
  private Map<String,Float> atomCharges
- bTest
  
  private boolean bTest
- a
  
  private float a
- b
  
  private float b
- c
  
  private float c
- alpha
  
  private float alpha
- beta
  
  private float beta
- gamma
  
  private float gamma
- primitiveData
  
  private float[] primitiveData
- tags
  
  private static final String[] tags
- totEnergy
  
  private Double totEnergy
- energyUnits
  
  private String energyUnits
Constructor Details
- GulpReader
  
  public GulpReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  protected void finalizeSubclassReader()
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readDimensionality
  
  private boolean readDimensionality() throws Exception
  
  Throws:
  
  Exception
- readSpaceGroup
  
  private void readSpaceGroup() throws Exception
  
  Throws:
  
  Exception
- parameterIndex
  
  private static int parameterIndex(String key)
- setParameter
  
  private void setParameter(String key, float value)
- newAtomSet
  
  private void newAtomSet(boolean doSetUnitCell)
- setModelParameters
  
  private void setModelParameters(boolean isPrimitive)
- readCellParameters
  
  private void readCellParameters(boolean isLatticeVectors) throws Exception
  
  Throws:
  
  Exception
- readFinalCell
  
  private void readFinalCell() throws Exception
  
  Throws:
  
  Exception
- scalePrimitiveData
  
  private void scalePrimitiveData(int i, float value)
- applySymmetryAndSetTrajectory
  
  public void applySymmetryAndSetTrajectory() throws Exception
  
  Overrides:
  
  applySymmetryAndSetTrajectory in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readAtomicPos
  
  private void readAtomicPos(boolean finalizeSymmetry) throws Exception
  
  Throws:
  
  Exception
- readPartialCharges
  
  private void readPartialCharges() throws Exception
  
  Throws:
  
  Exception
- readEnergy
  
  private void readEnergy() throws Exception
  
  Throws:
  
  Exception
- setEnergy
  
  private void setEnergy()

Class GulpReader

Field Summary

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

isSlab

isPolymer

isPrimitive

sep

coordinatesArePrimitive

atomCharges

bTest

a

b

c

alpha

beta

gamma

primitiveData

tags

totEnergy

energyUnits

Constructor Details

GulpReader

Method Details

initializeReader

finalizeSubclassReader

checkLine

readDimensionality

readSpaceGroup

parameterIndex

setParameter

newAtomSet

setModelParameters

readCellParameters

readFinalCell

scalePrimitiveData

applySymmetryAndSetTrajectory

readAtomicPos

readPartialCharges

readEnergy

setEnergy