public class CsfReader extends MopacSlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorterBasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
private static byte |
ANUM |
private static byte[] |
atomFieldMap |
private static java.lang.String[] |
atomFields |
private static byte |
BFXN_ANGL |
private static byte[] |
bondFieldMap |
private static java.lang.String[] |
bondFields |
private static byte |
BTYPE |
private static byte |
CHRG |
private static byte |
COEF_INDICES |
private static byte[] |
connectorFieldMap |
private static java.lang.String[] |
connectorFields |
private java.util.Map<java.lang.String,java.lang.String[]> |
connectors |
private static byte |
CONTRACTIONS |
private static byte |
DIPOLE |
private static byte |
EIG_VAL |
private static byte |
EIG_VEC |
private static byte |
EIG_VEC_COMPRESSED |
private int |
fieldCount |
private int[] |
fieldTypes |
private static byte |
GTO_EXP |
private java.util.Map<java.lang.String,Bond> |
htBonds |
private static byte |
ID |
private static byte |
MO_OCC |
private static byte[] |
moFieldMap |
private static java.lang.String[] |
moFields |
private int |
nAtoms |
private int |
nGaussians |
private static byte |
NORMAL_MODE |
private int |
nSlaters |
private int |
nVibrations |
private static byte |
objCls1 |
private static byte |
objCls2 |
private static byte |
objID1 |
private static byte |
objID2 |
private static byte |
PCHRG |
private java.util.Map<java.lang.String,java.lang.Integer> |
propertyItemCounts |
private static byte |
SHELL |
private static byte |
STO_EXP |
private java.lang.String |
strAtomicNumbers |
private static byte |
SYM |
private static byte |
VIB_ENERGY |
private static byte[] |
vibFieldMap |
private static java.lang.String[] |
vibFields |
private static byte |
XYZ |
atomicNumbers, MIN_COEFslaterArray, slatersalphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shellsaddedData, 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 |
|---|
CsfReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
private void |
fillCsfArray(java.lang.String property,
java.lang.String[] tokens,
int i0,
java.lang.Object f,
boolean isInteger) |
private int |
getPropertyCount(java.lang.String what) |
private int |
parseLineParameters(java.lang.String[] fields,
byte[] fieldMap) |
private void |
processAtomObject() |
private void |
processBasisObject(java.lang.String sto_gto) |
private void |
processBondObject() |
private void |
processConnectorObject() |
private void |
processLocalTransform() |
private void |
processMolecularOrbitalObject() |
private void |
processVibrationObject() |
private void |
setBond(Bond bond,
java.lang.String[] connect) |
createSphericalSlaterByType, scaleSlateraddSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitalscanonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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, setupASCRprivate int nAtoms
private java.lang.String strAtomicNumbers
private int fieldCount
private int nVibrations
private int nGaussians
private int nSlaters
private java.util.Map<java.lang.String,Bond> htBonds
private java.util.Map<java.lang.String,java.lang.Integer> propertyItemCounts
private final int[] fieldTypes
private static final byte objCls1
private static final byte objID1
private static final byte objCls2
private static final byte objID2
private static final java.lang.String[] connectorFields
private static final byte[] connectorFieldMap
private java.util.Map<java.lang.String,java.lang.String[]> connectors
private static final byte ID
private static final byte SYM
private static final byte ANUM
private static final byte CHRG
private static final byte XYZ
private static final byte PCHRG
private static final java.lang.String[] atomFields
private static final byte[] atomFieldMap
private static final byte BTYPE
private static final java.lang.String[] bondFields
private static final byte[] bondFieldMap
private static final byte NORMAL_MODE
private static final byte VIB_ENERGY
private static final byte DIPOLE
private static final java.lang.String[] vibFields
private static final byte[] vibFieldMap
private static final byte EIG_VAL
private static final byte MO_OCC
private static final byte EIG_VEC
private static final byte EIG_VEC_COMPRESSED
private static final byte COEF_INDICES
private static final byte BFXN_ANGL
private static final byte STO_EXP
private static final byte CONTRACTIONS
private static final byte GTO_EXP
private static final byte SHELL
private static final java.lang.String[] moFields
private static final byte[] moFieldMap
protected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate void processLocalTransform()
throws java.lang.Exception
java.lang.Exceptionprivate int getPropertyCount(java.lang.String what)
private int parseLineParameters(java.lang.String[] fields,
byte[] fieldMap)
throws java.lang.Exception
java.lang.Exceptionprivate void fillCsfArray(java.lang.String property,
java.lang.String[] tokens,
int i0,
java.lang.Object f,
boolean isInteger)
throws java.lang.Exception
java.lang.Exceptionprivate void processConnectorObject()
throws java.lang.Exception
java.lang.Exceptionprivate void setBond(Bond bond, java.lang.String[] connect)
private void processAtomObject()
throws java.lang.Exception
java.lang.Exceptionprivate void processBondObject()
throws java.lang.Exception
java.lang.Exceptionprivate void processVibrationObject()
throws java.lang.Exception
java.lang.Exceptionprivate void processMolecularOrbitalObject()
throws java.lang.Exception
java.lang.Exceptionprivate void processBasisObject(java.lang.String sto_gto)
throws java.lang.Exception
java.lang.Exception