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, orbitals, shells
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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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, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, 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, setupASCR
public 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 AtomSetCollectionReader
java.lang.Exception
public boolean checkAndRemoveFilterKey(java.lang.String key)
key
- protected boolean checkNboLine() throws java.lang.Exception
java.lang.Exception
private void getNboCharges() throws java.lang.Exception
java.lang.Exception
protected void getNboTypes() throws java.lang.Exception
java.lang.Exception
protected void readMolecularOrbitals(int headerType) throws java.lang.Exception
java.lang.Exception
public 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.Exception
protected 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