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, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, 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

private static void

addAuxFile(Map<String,Object> moData, String fileName, Map<String,Object> htParams)

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, addSlaterBasis, 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, checkAndRemoveFilterKey, 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, getFilterWithCase, 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 Details
- 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 Details
- GenNBOReader
  
  public GenNBOReader()
Method Details
- 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
- 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
- addAuxFile
  
  private static void addAuxFile(Map<String,Object> moData, String fileName, Map<String,Object> htParams)
- 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)

Class GenNBOReader

Nested Class Summary

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

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Details

isOutputFile

nboType

nOrbitals0

is47File

isOpenShell

alphaOnly

betaOnly

nAOs

nNOs

topoType

nStructures

nboParser

addBetaSet

P_LIST

PS_LIST

SP_LIST

SPS_LIST

DS_LIST

DC_LIST

FS_LIST

FC_LIST

GS_LIST

GC_LIST

HS_LIST

HC_LIST

IS_LIST

IC_LIST

Constructor Details

GenNBOReader

Method Details

initializeReader

finalizeSubclassReader

checkLine

getStructures

getStructureList

getFileData

getFile31

getFile46

readOutputProperties

setLabels

readData47

getIntData

fillSlater

resetDF

getAlphasAndExponents

readData31

readData46

setMap

getLabelKey

readNBOCoefficients

addAuxFile

getNBOOccupanciesStatic

readMOs

readNBO37Occupancies

setNboLabels