public class MOReader extends BasisFunctionReader
BasisFunctionReader.MOEnergySorter| Modifier and Type | Field and Description |
|---|---|
protected boolean |
allowNoOrbitals |
private static java.lang.String |
DC_LIST |
private static java.lang.String |
DS_LIST |
protected java.lang.String |
energyUnits |
private static java.lang.String |
FC_LIST |
private static java.lang.String |
FS_LIST |
int |
gaussianCount |
float[][] |
gaussians |
private boolean |
getNBOCharges |
private boolean |
getNBOs |
private boolean |
haveCoeffMap |
protected boolean |
haveNboCharges |
protected boolean |
haveNboOrbitals |
protected int |
HEADER_GAMESS_OCCUPANCIES |
protected int |
HEADER_GAMESS_ORIGINAL |
protected int |
HEADER_GAMESS_UK_MO |
protected int |
HEADER_NONE |
private int |
iMo0 |
private java.util.Map<java.lang.String,java.lang.Object> |
lastMoData |
protected javajs.util.Lst<java.lang.String> |
moTypes |
protected boolean |
orbitalsRead |
private static java.lang.String |
P_LIST |
int |
shellCount |
alphaBeta, 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 |
|---|
MOReader() |
| Modifier and Type | Method and Description |
|---|---|
void |
addCoef(java.util.Map<java.lang.String,java.lang.Object> mo,
float[] coefs,
java.lang.String type,
float energy,
float occ,
int moCount) |
protected void |
addMOData(int nColumns,
javajs.util.Lst<java.lang.String>[] data,
java.util.Map<java.lang.String,java.lang.Object>[] mos) |
boolean |
checkAndRemoveFilterKey(java.lang.String key)
Prior to filterMO all extraneous filter keys must be removed.
|
protected boolean |
checkNboLine() |
protected void |
getMOHeader(int headerType,
java.lang.String[] tokens,
java.util.Map<java.lang.String,java.lang.Object>[] mos,
int nThisLine) |
private void |
getNboCharges() |
protected void |
getNboTypes() |
protected void |
initializeReader() |
protected void |
readMolecularOrbitals(int headerType) |
private void |
readSecondOrderData() |
void |
setMOData(boolean clearOrbitals) |
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMOaddAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, 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, 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, setupASCRpublic int shellCount
public int gaussianCount
public float[][] gaussians
protected java.lang.String energyUnits
protected javajs.util.Lst<java.lang.String> moTypes
private boolean getNBOs
private boolean getNBOCharges
protected boolean haveNboCharges
protected boolean haveNboOrbitals
protected boolean orbitalsRead
private java.util.Map<java.lang.String,java.lang.Object> lastMoData
protected boolean allowNoOrbitals
protected final int HEADER_GAMESS_UK_MO
protected final int HEADER_GAMESS_OCCUPANCIES
protected final int HEADER_GAMESS_ORIGINAL
protected final int HEADER_NONE
private boolean haveCoeffMap
private static final java.lang.String P_LIST
private static final java.lang.String DS_LIST
private static final java.lang.String DC_LIST
private static final java.lang.String FS_LIST
private static java.lang.String FC_LIST
private int iMo0
protected void initializeReader()
throws java.lang.Exception
initializeReader in class AtomSetCollectionReaderjava.lang.Exceptionpublic boolean checkAndRemoveFilterKey(java.lang.String key)
key - protected boolean checkNboLine()
throws java.lang.Exception
java.lang.Exceptionprivate void getNboCharges()
throws java.lang.Exception
java.lang.Exceptionprotected void getNboTypes()
throws java.lang.Exception
java.lang.Exceptionprotected void readMolecularOrbitals(int headerType)
throws java.lang.Exception
java.lang.Exceptionpublic void addCoef(java.util.Map<java.lang.String,java.lang.Object> mo,
float[] coefs,
java.lang.String type,
float energy,
float occ,
int moCount)
protected void getMOHeader(int headerType,
java.lang.String[] tokens,
java.util.Map<java.lang.String,java.lang.Object>[] mos,
int nThisLine)
throws java.lang.Exception
java.lang.Exceptionprotected void addMOData(int nColumns,
javajs.util.Lst<java.lang.String>[] data,
java.util.Map<java.lang.String,java.lang.Object>[] mos)
public void setMOData(boolean clearOrbitals)
private void readSecondOrderData()
throws java.lang.Exception
java.lang.Exception