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
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
FieldsModifier and TypeFieldDescriptionprivate float
private float
private float
private float
private boolean
private float
private boolean
private String
private float
private boolean
private boolean
private boolean
private float[]
private String
private static final String[]
private Double
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
protected boolean
protected void
optional reader-specific method run first.protected void
private void
newAtomSet
(boolean doSetUnitCell) private static int
parameterIndex
(String key) private void
readAtomicPos
(boolean finalizeSymmetry) private void
readCellParameters
(boolean isLatticeVectors) private boolean
private void
private void
private void
private void
private void
scalePrimitiveData
(int i, float value) private void
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
-
Field Details
-
isSlab
private boolean isSlab -
isPolymer
private boolean isPolymer -
isPrimitive
private boolean isPrimitive -
sep
-
coordinatesArePrimitive
private boolean coordinatesArePrimitive -
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
-
totEnergy
-
energyUnits
-
-
Constructor Details
-
GulpReader
public GulpReader()
-
-
Method Details
-
initializeReader
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
-
finalizeSubclassReader
protected void finalizeSubclassReader()Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
-
checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
-
readDimensionality
- Throws:
Exception
-
readSpaceGroup
- Throws:
Exception
-
parameterIndex
-
setParameter
-
newAtomSet
private void newAtomSet(boolean doSetUnitCell) -
setModelParameters
private void setModelParameters(boolean isPrimitive) -
readCellParameters
- Throws:
Exception
-
readFinalCell
- Throws:
Exception
-
scalePrimitiveData
private void scalePrimitiveData(int i, float value) -
applySymmetryAndSetTrajectory
- Overrides:
applySymmetryAndSetTrajectory
in classAtomSetCollectionReader
- Throws:
Exception
-
readAtomicPos
- Throws:
Exception
-
readPartialCharges
- Throws:
Exception
-
readEnergy
- Throws:
Exception
-
setEnergy
private void setEnergy()
-