public class CrystalReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
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private int |
atomCount |
private int[] |
atomFrag |
private int |
atomIndexLast |
private javax.vecmath.Vector3f[] |
directLatticeVectors |
private java.lang.Double |
energy |
private boolean |
getLastConventional |
private boolean |
haveCharges |
private boolean |
havePrimitiveMapping |
private boolean |
inputOnly |
private boolean |
isFreqCalc |
private boolean |
isLongMode |
private boolean |
isMolecular |
private boolean |
isPolymer |
private boolean |
isPrimitive |
private boolean |
isProperties |
private boolean |
isSlab |
private boolean |
isVersion3 |
private float[] |
nuclearCharges |
private javax.vecmath.Matrix3f |
primitiveToCryst |
private int[] |
primitiveToIndex |
private javax.vecmath.Point3f |
ptOriginShift |
private java.lang.String |
spaceGroupName |
private java.util.List<java.lang.String> |
vInputCoords |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
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CrystalReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
protected void |
finalizeReader() |
private float |
fraction(java.lang.String f) |
private int |
getAtomicNumber(java.lang.String token) |
private int |
getAtomIndexFromPrimitiveIndex(int iPrim) |
private java.lang.String |
getAtomName(java.lang.String s) |
private boolean |
getPropertyTensors() |
protected void |
initializeReader() |
private void |
newAtomSet() |
private void |
processInputCoords() |
private boolean |
readAtoms() |
private void |
readCellParams(boolean isNewSet) |
private void |
readCrystallographicCoords() |
private void |
readEnergy() |
private boolean |
readFragments() |
private boolean |
readFrequencies() |
private boolean |
readGradient() |
private boolean |
readHeader() |
private boolean |
readMagneticMoments() |
private boolean |
readPartialCharges() |
private boolean |
readPrimitiveMapping()
create arrays that maps primitive atoms to conventional atoms in a 1:1
fashion.
|
private boolean |
readShift() |
private boolean |
readSpins() |
private boolean |
readTotalAtomicCharges() |
private void |
readTransformationMatrix() |
private boolean |
readVolumePrimCell() |
private void |
setData(java.lang.String name,
java.lang.String data,
int pt,
int dp) |
private boolean |
setDirect() |
private void |
setEnergy() |
private void |
setFreqValue(float freq,
java.lang.String[] data) |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private boolean isVersion3
private boolean isPrimitive
private boolean isPolymer
private boolean isSlab
private boolean isMolecular
private boolean haveCharges
private boolean isFreqCalc
private boolean inputOnly
private boolean isLongMode
private boolean getLastConventional
private boolean havePrimitiveMapping
private boolean isProperties
private int atomCount
private int atomIndexLast
private int[] atomFrag
private int[] primitiveToIndex
private float[] nuclearCharges
private java.util.List<java.lang.String> vInputCoords
private java.lang.Double energy
private javax.vecmath.Point3f ptOriginShift
private javax.vecmath.Matrix3f primitiveToCryst
private javax.vecmath.Vector3f[] directLatticeVectors
private java.lang.String spaceGroupName
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeReader() throws java.lang.Exception
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private boolean setDirect() throws java.lang.Exception
java.lang.Exception
private void readTransformationMatrix() throws java.lang.Exception
java.lang.Exception
private boolean readShift()
private float fraction(java.lang.String f)
private boolean readGradient() throws java.lang.Exception
java.lang.Exception
private boolean readVolumePrimCell()
private boolean readSpins() throws java.lang.Exception
java.lang.Exception
private boolean readMagneticMoments() throws java.lang.Exception
java.lang.Exception
private void setData(java.lang.String name, java.lang.String data, int pt, int dp) throws java.lang.Exception
java.lang.Exception
private boolean readHeader() throws java.lang.Exception
java.lang.Exception
private void readCellParams(boolean isNewSet) throws java.lang.Exception
java.lang.Exception
private boolean readPrimitiveMapping() throws java.lang.Exception
java.lang.Exception
private boolean readAtoms() throws java.lang.Exception
java.lang.Exception
private java.lang.String getAtomName(java.lang.String s)
private int getAtomicNumber(java.lang.String token)
private void readCrystallographicCoords() throws java.lang.Exception
java.lang.Exception
private void processInputCoords() throws java.lang.Exception
java.lang.Exception
private void newAtomSet() throws java.lang.Exception
java.lang.Exception
private void readEnergy()
private void setEnergy()
private boolean readPartialCharges() throws java.lang.Exception
java.lang.Exception
private boolean readTotalAtomicCharges() throws java.lang.Exception
java.lang.Exception
private int getAtomIndexFromPrimitiveIndex(int iPrim)
private boolean readFragments() throws java.lang.Exception
java.lang.Exception
private boolean readFrequencies() throws java.lang.Exception
java.lang.Exception
private void setFreqValue(float freq, java.lang.String[] data)
private boolean getPropertyTensors() throws java.lang.Exception
java.lang.Exception