public class GenNBOReader extends MOReader
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
---|---|
private boolean |
addBetaSet |
private boolean |
alphaOnly |
private boolean |
betaOnly |
private static java.lang.String |
DC_LIST |
private static java.lang.String |
DS_LIST |
private static java.lang.String |
FC_LIST |
private static java.lang.String |
FS_LIST |
private static java.lang.String |
GC_LIST |
private static java.lang.String |
GS_LIST |
private static java.lang.String |
HC_LIST |
private static java.lang.String |
HS_LIST |
private static java.lang.String |
IC_LIST |
private static java.lang.String |
IS_LIST |
private boolean |
is47File |
private boolean |
isOpenShell |
private boolean |
isOutputFile |
private int |
nAOs |
(package private) NBOParser |
nboParser |
private java.lang.String |
nboType |
private int |
nNOs |
private int |
nOrbitals0 |
private int |
nStructures |
private static java.lang.String |
P_LIST |
private static java.lang.String |
SP_LIST |
private java.lang.String |
topoType |
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, 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, 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 |
---|
GenNBOReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private boolean |
fillSlater(int[] slater,
int n,
int pt,
int ng) |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private void |
getAlphasAndExponents() |
private boolean |
getFile31() |
private void |
getFile46()
read the labels from xxxx.46
|
private java.lang.String |
getFileData(java.lang.String ext) |
private int[] |
getIntData() |
private static java.lang.String |
getLabelKey(java.lang.String labelKey) |
private static void |
getNBOOccupanciesStatic(javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals,
int nAOs,
int pt,
java.lang.String data,
int len,
int[] next) |
private javajs.util.Lst<java.lang.Object> |
getStructureList() |
private void |
getStructures(java.lang.String type) |
protected void |
initializeReader() |
private boolean |
readData31(java.lang.String line1) |
private void |
readData46()
read labels and not proper number of NOs, nNOs, for this nboType
|
private void |
readData47() |
private void |
readMOs() |
private void |
readNBO37Occupancies(int pt)
Read occupancies from .37 file.
|
static boolean |
readNBOCoefficients(java.util.Map<java.lang.String,java.lang.Object> moData,
java.lang.String nboType,
Viewer vwr)
Called by setNBOType in IsoExt when use issues NBO TYPE xxx
|
static void |
setNboLabels(java.lang.String[] tokens,
int nLabels,
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals,
int nOrbitals0,
java.lang.String moType) |
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, 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, 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 isOutputFile
private java.lang.String nboType
private int nOrbitals0
private boolean is47File
private boolean isOpenShell
private boolean alphaOnly
private boolean betaOnly
private int nAOs
private int nNOs
private java.lang.String topoType
private int nStructures
NBOParser nboParser
private boolean addBetaSet
private static java.lang.String P_LIST
private static java.lang.String SP_LIST
private static java.lang.String DS_LIST
private static java.lang.String DC_LIST
private static java.lang.String FS_LIST
private static java.lang.String FC_LIST
private static java.lang.String GS_LIST
private static java.lang.String GC_LIST
private static java.lang.String HS_LIST
private static java.lang.String HC_LIST
private static java.lang.String IS_LIST
private static java.lang.String IC_LIST
protected void initializeReader() throws java.lang.Exception
initializeReader
in class MOReader
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void getStructures(java.lang.String type) throws java.lang.Exception
java.lang.Exception
private javajs.util.Lst<java.lang.Object> getStructureList()
private java.lang.String getFileData(java.lang.String ext) throws java.lang.Exception
java.lang.Exception
private boolean getFile31() throws java.lang.Exception
java.lang.Exception
private void getFile46() throws java.lang.Exception
java.lang.Exception
private void readData47() throws java.lang.Exception
java.lang.Exception
private int[] getIntData() throws java.lang.Exception
java.lang.Exception
private boolean fillSlater(int[] slater, int n, int pt, int ng)
private void getAlphasAndExponents() throws java.lang.Exception
java.lang.Exception
private boolean readData31(java.lang.String line1) throws java.lang.Exception
java.lang.Exception
private void readData46() throws java.lang.Exception
java.lang.Exception
private static java.lang.String getLabelKey(java.lang.String labelKey)
public static boolean readNBOCoefficients(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String nboType, Viewer vwr)
moData
- nboType
- vwr
- private static void getNBOOccupanciesStatic(javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nAOs, int pt, java.lang.String data, int len, int[] next)
private void readMOs() throws java.lang.Exception
java.lang.Exception
private void readNBO37Occupancies(int pt) throws java.lang.Exception
pt
- java.lang.Exception
public static void setNboLabels(java.lang.String[] tokens, int nLabels, javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nOrbitals0, java.lang.String moType)