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

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 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 boolean`	`isArchive`
`private boolean`	`isOutputFile`
`private java.lang.String`	`nboType`
`private int`	`nOrbitals0`
`private static java.lang.String`	`P_LIST`
`private static java.lang.String`	`SP_LIST`

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, orbitals, shells

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

Constructors
Constructor Description

GenNBOReader()

Method Summary

All Methods Instance Methods Concrete Methods
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()`
`private java.lang.String`	`getFileData(java.lang.String ext)`
`private int[]`	`getIntData()`
`protected void`	`initializeReader()`
`private boolean`	`readData31(java.lang.String line1)`
`private void`	`readData46()`
`private void`	`readData47()`
`private void`	`readMOs()`

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, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, 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
```

isArchive
```
private boolean isArchive
```

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

SP_LIST

private static java.lang.String SP_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

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

readMOs

private void readMOs()
              throws java.lang.Exception

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

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()
                throws java.lang.Exception

Throws:: java.lang.Exception

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)

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 void readData46()
                 throws java.lang.Exception

Throws:: java.lang.Exception

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

isArchive

P_LIST

SP_LIST

DS_LIST

DC_LIST

FS_LIST

FC_LIST

Constructor Detail

GenNBOReader

Method Detail

initializeReader

finalizeSubclassReader

readMOs

checkLine

getFileData

getFile31

getFile46

readData47

getIntData

fillSlater

getAlphasAndExponents

readData31

readData46