org.jmol.adapter.readers.xtal
public class CrystalReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private int[] |
atomFrag |
private int |
atomIndexLast |
private Vector3f[] |
directLatticeVectors |
private 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 Matrix3f |
primitiveToCryst |
private int[] |
primitiveToIndex |
private Point3f |
ptOriginShift |
private String |
spaceGroupName |
private List<String> |
vInputCoords |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, 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(String f) |
private int |
getAtomicNumber(String token) |
private int |
getAtomIndexFromPrimitiveIndex(int iPrim) |
private String |
getAtomName(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(String name,
String data,
int pt,
int dp) |
private boolean |
setDirect() |
private void |
setEnergy() |
private void |
setFreqValue(float freq,
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, 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, 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 Double energy
private Point3f ptOriginShift
private Matrix3f primitiveToCryst
private Vector3f[] directLatticeVectors
private String spaceGroupName
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
protected void finalizeReader() throws Exception
finalizeReader
in class AtomSetCollectionReader
Exception
private boolean readShift()
private float fraction(String f)
private boolean readVolumePrimCell()
private void setData(String name, String data, int pt, int dp) throws Exception
Exception
private boolean readPrimitiveMapping() throws Exception
Exception
private int getAtomicNumber(String token)
private void readCrystallographicCoords() throws Exception
Exception
private void readEnergy()
private void setEnergy()
private int getAtomIndexFromPrimitiveIndex(int iPrim)
private void setFreqValue(float freq, String[] data)