public class GulpReader extends AtomSetCollectionReader
Modifier and Type | Field and 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 |
isMolecular |
private boolean |
isPolymer |
private boolean |
isPrimitive |
private boolean |
isSlab |
private float[] |
primitiveData |
private String |
sep |
private static String[] |
tags |
private Double |
totEnergy |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
GulpReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
protected boolean |
checkLine() |
protected void |
finalizeReader()
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) |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private boolean isSlab
private boolean isPolymer
private boolean isMolecular
private boolean isPrimitive
private String sep
private boolean coordinatesArePrimitive
private boolean bTest
private float a
private float b
private float c
private float alpha
private float beta
private float gamma
private float[] primitiveData
private static String[] tags
private Double totEnergy
private String energyUnits
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected void finalizeReader()
AtomSetCollectionReader
finalizeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private static int parameterIndex(String key)
private void setParameter(String key, float value)
private void newAtomSet(boolean doSetUnitCell)
private void setModelParameters(boolean isPrimitive)
private void readCellParameters(boolean isLatticeVectors) throws Exception
Exception
private void scalePrimitiveData(int i, float value)
public void applySymmetryAndSetTrajectory() throws Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
Exception
private void readAtomicPos(boolean finalizeSymmetry) throws Exception
Exception
private void setEnergy()