public class CrystalReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private int[] |
atomFrag |
private int |
atomIndexLast |
private boolean |
checkModelTrigger |
private int |
cpno |
private static java.lang.String[] |
crtypes |
private javajs.util.V3[] |
directLatticeVectors |
private boolean |
directLatticeVectorsFirst
CRYSTAL 17 moves directLatticeVectors before LATTICE PARAMETERS
|
private java.lang.Double |
energy |
private float[] |
f14 |
private float[] |
f16 |
private java.lang.String |
firstLine |
private boolean |
fullSymmetry |
private boolean |
getLastConventional |
private boolean |
haveCharges |
private boolean |
havePrimitiveMapping |
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> |
htCriticalPoints |
private boolean |
inputOnly |
private boolean |
isLongMode |
private boolean |
isPolymer |
private boolean |
isProperties |
private boolean |
isSlab |
private boolean |
isVersion3 |
private javajs.util.Lst<java.lang.String> |
lstCoords |
private float[] |
nuclearCharges |
private float |
primitiveDensity |
private int[] |
primitiveToIndex |
private float |
primitiveVolume |
private javajs.util.P3 |
ptOriginShift |
private static int[] |
smap |
private java.lang.String |
spaceGroupName |
private int |
state |
private static int |
STATE_FREQ |
private static int |
STATE_INPUT |
private static int |
STATE_INPUT_FROM |
private static int |
STATE_NONE |
private static int |
STATE_OPT_FINAL |
private static int |
STATE_OPT_POINT |
private static int |
STATE_WAVEFUNCTION |
private javajs.util.Lst<java.lang.String> |
symops |
addedData, addedDataKey, addVibrations, 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, isPrimitive, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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CrystalReader() |
Modifier and Type | Method and Description |
---|---|
private boolean |
addModel() |
void |
applySymmetryAndSetTrajectory() |
protected boolean |
checkLine() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private static java.lang.String |
fixAtomName(java.lang.String s)
MN33 becomes Mn33
|
private int |
getAtomicNumber(java.lang.String token) |
private int |
getAtomIndexFromPrimitiveIndex(int iPrim)
Get the atom index from a primitive index.
|
private java.lang.String |
getCPAtomInfo(java.lang.String line,
javajs.util.Lst<java.lang.Object> list)
Process a CP data line
|
private void |
getDirect() |
private int |
getModelForMode(int i0,
int mode) |
private boolean |
getQuadrupoleTensors() |
protected void |
initializeReader() |
private void |
newAtomSet() |
private void |
newLattice(boolean isConv) |
private void |
processCoordLines()
Now create atoms from the coordinate lines.
|
private void |
processNextCriticalPoint() |
private boolean |
readAtoms() |
private boolean |
readBornChargeTensors() |
private void |
readCoordLines()
Read coordinates, either input or crystallographic, just saving their lines
in a vector for now.
|
private boolean |
readData(java.lang.String name,
int nfields)
For spin and magnetic moment data, read the data block and save it as
property_spin or propert_magneticMoment.
|
private void |
readFreqFragments()
Select only specific atoms for frequency generation.
|
private void |
readFrequencies() |
private boolean |
readGradient()
Read minimization measures
|
private boolean |
readHeader() |
private void |
readLatticeParams(boolean isPrimitive)
Read the lattice parameters.
|
private boolean |
readPartialCharges() |
private void |
readPrimitiveLatticeVectors()
Read transform matrix primitive to conventional.
|
private javajs.util.Lst<java.lang.String> |
readRaman(javajs.util.Lst<java.lang.String> ramanData) |
private boolean |
readShift()
Read the origin shift
|
private void |
readSymmetryOperators() |
private boolean |
readTotalAtomicCharges() |
private void |
setEnergy() |
private void |
setFreqValue(float freq,
java.lang.String[] data) |
private void |
setSymmOps() |
private void |
setUnitCellOrientation() |
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
private boolean isVersion3
private boolean isPolymer
private boolean isSlab
private boolean haveCharges
private boolean inputOnly
private boolean isLongMode
private boolean getLastConventional
private boolean havePrimitiveMapping
private boolean isProperties
private static final int STATE_NONE
private static final int STATE_INPUT
private static final int STATE_INPUT_FROM
private static final int STATE_WAVEFUNCTION
private static final int STATE_OPT_POINT
private static final int STATE_OPT_FINAL
private static final int STATE_FREQ
private int state
private int ac
private int atomIndexLast
private int[] atomFrag
private int[] primitiveToIndex
private float[] nuclearCharges
private javajs.util.Lst<java.lang.String> lstCoords
private java.lang.Double energy
private javajs.util.P3 ptOriginShift
private javajs.util.V3[] directLatticeVectors
private java.lang.String spaceGroupName
private boolean checkModelTrigger
private boolean fullSymmetry
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> htCriticalPoints
private boolean directLatticeVectorsFirst
private int cpno
private static final java.lang.String[] crtypes
private javajs.util.Lst<java.lang.String> symops
private final float[] f14
private final float[] f16
private static final int[] smap
private float primitiveVolume
private float primitiveDensity
private java.lang.String firstLine
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
private void processNextCriticalPoint() throws java.lang.Exception
java.lang.Exception
private java.lang.String getCPAtomInfo(java.lang.String line, javajs.util.Lst<java.lang.Object> list)
line
- full TOPOND data linelist
- entries to fill with informationprivate void newLattice(boolean isConv) throws java.lang.Exception
java.lang.Exception
private boolean addModel() throws java.lang.Exception
java.lang.Exception
private void readSymmetryOperators() throws java.lang.Exception
java.lang.Exception
private void setSymmOps()
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
private void getDirect() throws java.lang.Exception
java.lang.Exception
private void setUnitCellOrientation()
private void readPrimitiveLatticeVectors() throws java.lang.Exception
java.lang.Exception
private boolean readShift()
private boolean readHeader() throws java.lang.Exception
java.lang.Exception
private void readLatticeParams(boolean isPrimitive) throws java.lang.Exception
isNewSet
- java.lang.Exception
private int getAtomIndexFromPrimitiveIndex(int iPrim)
iPrim
- private boolean readAtoms() throws java.lang.Exception
java.lang.Exception
private static java.lang.String fixAtomName(java.lang.String s)
s
- private int getAtomicNumber(java.lang.String token)
private void readCoordLines() throws java.lang.Exception
java.lang.Exception
private void processCoordLines() throws java.lang.Exception
java.lang.Exception
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
java.lang.Exception
private void newAtomSet() throws java.lang.Exception
java.lang.Exception
private void setEnergy()
private boolean readPartialCharges() throws java.lang.Exception
java.lang.Exception
private boolean readTotalAtomicCharges() throws java.lang.Exception
java.lang.Exception
private void readFreqFragments() throws java.lang.Exception
java.lang.Exception
private void readFrequencies() throws java.lang.Exception
java.lang.Exception
private void setFreqValue(float freq, java.lang.String[] data)
private javajs.util.Lst<java.lang.String> readRaman(javajs.util.Lst<java.lang.String> ramanData) throws java.lang.Exception
java.lang.Exception
private int getModelForMode(int i0, int mode)
private boolean readGradient() throws java.lang.Exception
java.lang.Exception
private boolean readData(java.lang.String name, int nfields) throws java.lang.Exception
name
- nfields
- java.lang.Exception
private boolean getQuadrupoleTensors() throws java.lang.Exception
java.lang.Exception
private boolean readBornChargeTensors() throws java.lang.Exception
java.lang.Exception