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 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`	`PS_LIST`
`private static java.lang.String`	`SP_LIST`
`private static java.lang.String`	`SPS_LIST`
`private java.lang.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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, paramsCentroid, paramsLattice, 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private static void`	`addAuxFile(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String fileName, java.util.Map<java.lang.String,java.lang.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 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 java.util.Map<java.lang.String,java.lang.String[]>`	`readData46(java.lang.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(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
`private java.util.Map<java.lang.String,java.lang.String[]>`	`readOutputProperties(java.lang.String data)`
`private boolean`	`resetDF()`
`private void`	`setLabels(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String key, java.lang.String line)`
`private void`	`setMap(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String labelKey, int nNOs, boolean doAll)`
`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)`

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, 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 java.lang.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 java.lang.String topoType
```

nStructures
```
private int nStructures
```

nboParser
```
NBOParser nboParser
```

addBetaSet
```
private boolean addBetaSet
```

P_LIST
```
private static java.lang.String P_LIST
```

PS_LIST

private static java.lang.String PS_LIST

SP_LIST

private static java.lang.String SP_LIST

SPS_LIST

private static java.lang.String SPS_LIST

DS_LIST

private static java.lang.String DS_LIST

DC_LIST

private static java.lang.String DC_LIST

FS_LIST

private static java.lang.String FS_LIST

FC_LIST

private static java.lang.String FC_LIST

GS_LIST

private static java.lang.String GS_LIST

GC_LIST

private static java.lang.String GC_LIST

HS_LIST

private static java.lang.String HS_LIST

HC_LIST

private static java.lang.String HC_LIST

IS_LIST

private static java.lang.String IS_LIST

IC_LIST

private static java.lang.String IC_LIST

Constructor Detail
- GenNBOReader
```
public GenNBOReader()
```

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:: initializeReader in class MOReader
Throws:: java.lang.Exception

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

getStructures

private void getStructures(java.lang.String type)
                    throws java.lang.Exception

Throws:: java.lang.Exception

getStructureList

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

getFileData

private java.lang.String getFileData(java.lang.String ext)
                              throws java.lang.Exception

Throws:: java.lang.Exception

getFile31

private boolean getFile31()
                   throws java.lang.Exception

Throws:: java.lang.Exception

getFile46
```
private void getFile46()
```
read the labels from xxxx.46

Throws:

java.lang.Exception

readOutputProperties

private java.util.Map<java.lang.String,java.lang.String[]> readOutputProperties(java.lang.String data)

setLabels

private void setLabels(java.util.Map<java.lang.String,java.lang.String[]> map,
                       java.lang.String key,
                       java.lang.String line)

readData47

private void readData47()
                 throws java.lang.Exception

Throws:: java.lang.Exception

getIntData

private int[] getIntData()
                  throws java.lang.Exception

Throws:: java.lang.Exception

fillSlater

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

resetDF
```
private boolean resetDF()
```

getAlphasAndExponents

private void getAlphasAndExponents()
                            throws java.lang.Exception

Throws:: java.lang.Exception

readData31

private boolean readData31(java.lang.String line1)
                    throws java.lang.Exception

Throws:: java.lang.Exception

readData46

private java.util.Map<java.lang.String,java.lang.String[]> readData46(java.lang.String labelKey)
                                                                     throws java.lang.Exception

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

Returns:
Throws:: java.lang.Exception

setMap

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

getLabelKey

private static java.lang.String getLabelKey(java.lang.String labelKey)

readNBOCoefficients

public 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

Parameters:: moData -; nboType -; vwr -
Returns:: true if sucessful or false if required file is missing

addAuxFile

private static void addAuxFile(java.util.Map<java.lang.String,java.lang.Object> moData,
                               java.lang.String fileName,
                               java.util.Map<java.lang.String,java.lang.Object> htParams)

getNBOOccupanciesStatic

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)

readMOs

private void readMOs()
              throws java.lang.Exception

Throws:: java.lang.Exception

readNBO37Occupancies
```
private void readNBO37Occupancies(int pt)
                           throws java.lang.Exception
```
Read occupancies from .37 file. Called by readMOs.

Parameters:

pt -

Throws:

java.lang.Exception

setNboLabels

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)

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 Detail

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 Detail

GenNBOReader

Method Detail

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