Package org.jmol.adapter.readers.quantum

Class GenNBOReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.MOReader

org.jmol.adapter.readers.quantum.GenNBOReader

All Implemented Interfaces:

javajs.api.GenericLineReader

public class GenNBOReader
extends MOReader

NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure

Author:

hansonr

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

BasisFunctionReader.MOEnergySorter

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	addBetaSet
private boolean	alphaOnly
private boolean	betaOnly
private static String	DC_LIST
private static String	DS_LIST
private static String	FC_LIST
private static String	FS_LIST
private static String	GC_LIST
private static String	GS_LIST
private static String	HC_LIST
private static String	HS_LIST
private static String	IC_LIST
private static String	IS_LIST
private boolean	is47File
private boolean	isOpenShell
private boolean	isOutputFile
private int	nAOs
(package private) NBOParser	nboParser
private String	nboType
private int	nNOs
private int	nOrbitals0
private int	nStructures
private static String	P_LIST
private static String	PS_LIST
private static String	SP_LIST
private static String	SPS_LIST
private String	topoType

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
GenNBOReader()

Method Summary

Modifier and Type	Method	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 String	getFileData(String ext)
private int[]	getIntData()
private static String	getLabelKey(String labelKey)
private static void	getNBOOccupanciesStatic(javajs.util.Lst<Map<String,Object>> orbitals, int nAOs, int pt, String data, int len, int[] next)
private javajs.util.Lst<Object>	getStructureList()
private void	getStructures(String type)
protected void	initializeReader()
private boolean	readData31(String line1)
private Map<String,String[]>	readData46(String labelKey)	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(Map<String,Object> moData, String nboType, Viewer vwr)	Called by setNBOType in IsoExt when use issues NBO TYPE xxx
private Map<String,String[]>	readOutputProperties(String data)
private boolean	resetDF()
private void	setLabels(Map<String,String[]> map, String key, String line)
private void	setMap(Map<String,String[]> map, String labelKey, int nNOs, boolean doAll)
static void	setNboLabels(String[] tokens, int nLabels, javajs.util.Lst<Map<String,Object>> orbitals, int nOrbitals0, String moType)

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

isOutputFile

private boolean isOutputFile

nboType

private String nboType

nOrbitals0

private int nOrbitals0

is47File

private boolean is47File

isOpenShell

private boolean isOpenShell

alphaOnly

private boolean alphaOnly

betaOnly

private boolean betaOnly

nAOs

private int nAOs

nNOs

private int nNOs

topoType

private String topoType

nStructures

private int nStructures

nboParser

NBOParser nboParser

addBetaSet

private boolean addBetaSet

P_LIST

private static String P_LIST

PS_LIST

private static String PS_LIST

SP_LIST

private static String SP_LIST

SPS_LIST

private static String SPS_LIST

DS_LIST

private static String DS_LIST

DC_LIST

private static String DC_LIST

FS_LIST

private static String FS_LIST

FC_LIST

private static String FC_LIST

GS_LIST

private static String GS_LIST

GC_LIST

private static String GC_LIST

HS_LIST

private static String HS_LIST

HC_LIST

private static String HC_LIST

IS_LIST

private static String IS_LIST

IC_LIST

private static String IC_LIST

Constructor Detail

GenNBOReader

public GenNBOReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class MOReader

Throws:

Exception

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

getStructures

private void getStructures(String type)
                    throws Exception

Throws:

Exception

getStructureList

private javajs.util.Lst<Object> getStructureList()

getFileData

private String getFileData(String ext)
                    throws Exception

Throws:

Exception

getFile31

private boolean getFile31()
                   throws Exception

Throws:

Exception

getFile46

private void getFile46()

read the labels from xxxx.46

Throws:

Exception

readOutputProperties

private Map<String,String[]> readOutputProperties(String data)

setLabels

private void setLabels(Map<String,String[]> map,
                       String key,
                       String line)

readData47

private void readData47()
                 throws Exception

Throws:

Exception

getIntData

private int[] getIntData()
                  throws Exception

Throws:

Exception

fillSlater

private boolean fillSlater(int[] slater,
                           int n,
                           int pt,
                           int ng)

resetDF

private boolean resetDF()

getAlphasAndExponents

private void getAlphasAndExponents()
                            throws Exception

Throws:

Exception

readData31

private boolean readData31(String line1)
                    throws Exception

Throws:

Exception

readData46

private Map<String,String[]> readData46(String labelKey)
                                       throws Exception

read labels and not proper number of NOs, nNOs, for this nboType

Returns:

Throws:

Exception

setMap

private void setMap(Map<String,String[]> map,
                    String labelKey,
                    int nNOs,
                    boolean doAll)

getLabelKey

private static String getLabelKey(String labelKey)

readNBOCoefficients

public static boolean readNBOCoefficients(Map<String,Object> moData,
                                          String nboType,
                                          Viewer vwr)

Called by setNBOType in IsoExt when use issues NBO TYPE xxx

Parameters:

moData -

nboType -

vwr -

Returns:

true if sucessful or false if required file is missing

getNBOOccupanciesStatic

private static void getNBOOccupanciesStatic(javajs.util.Lst<Map<String,Object>> orbitals,
                                            int nAOs,
                                            int pt,
                                            String data,
                                            int len,
                                            int[] next)

readMOs

private void readMOs()
              throws Exception

Throws:

Exception

readNBO37Occupancies

private void readNBO37Occupancies(int pt)
                           throws Exception

Read occupancies from .37 file. Called by readMOs.

Parameters:

pt -

Throws:

Exception

setNboLabels

public static void setNboLabels(String[] tokens,
                                int nLabels,
                                javajs.util.Lst<Map<String,Object>> orbitals,
                                int nOrbitals0,
                                String moType)