Package org.jmol.adapter.readers.xtal

Class GulpReader

java.lang.Object

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 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, 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, 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, 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, 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail

GulpReader

public GulpReader()

Method Detail

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()