MOReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.quantum.BasisFunctionReader
  - - org.jmol.adapter.readers.quantum.MOReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

GamessReader, GaussianReader, GenNBOReader, JaguarReader, NWChemReader, PsiReader, QchemReader
```
public class MOReader
extends BasisFunctionReader
```
General methods for reading molecular orbital data, including embedded output from the NBO program. In particular, when the AONBO keyword is included. requires the following sort of construct: public AtomSetCollection readAtomSetCollection(BufferedReader reader) { readAtomSetCollection(reader, "some type"); } protected boolean checkLine() { if (line.indexOf(...)) { doThis(); return true/false; } if (line.indexOf(...)) { doThat(); return true/false; } return checkNboLine(); }

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  BasisFunctionReader.MOEnergySorter

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`allowNoOrbitals`
`private static String`	`DC_LIST`
`private static String`	`DS_LIST`
`protected String`	`energyUnits`
`private static String`	`FC_LIST`
`private static String`	`FS_LIST`
`int`	`gaussianCount`
`float[][]`	`gaussians`
`private boolean`	`getNBOCharges`
`private boolean`	`getNBOs`
`private boolean`	`haveCoeffMap`
`protected boolean`	`haveNboCharges`
`protected boolean`	`haveNboOrbitals`
`protected int`	`HEADER_GAMESS_OCCUPANCIES`
`protected int`	`HEADER_GAMESS_ORIGINAL`
`protected int`	`HEADER_GAMESS_UK_MO`
`protected int`	`HEADER_NONE`
`private int`	`iMo0`
`private Map<String,Object>`	`lastMoData`
`protected javajs.util.Lst<String>`	`moTypes`
`protected boolean`	`orbitalsRead`
`private static String`	`P_LIST`
`int`	`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 and Description

MOReader()

Constructors
Constructor and Description
`MOReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCoef(Map<String,Object> mo, float[] coefs, String type, float energy, float occ, int moCount)`
`protected void`	`addMOData(int nColumns, javajs.util.Lst<String>[] data, Map<String,Object>[] mos)`
`boolean`	`checkAndRemoveFilterKey(String key)` Prior to filterMO all extraneous filter keys must be removed.
`protected boolean`	`checkNboLine()`
`protected void`	`getMOHeader(int headerType, String[] tokens, Map<String,Object>[] mos, int nThisLine)`
`private void`	`getNboCharges()`
`protected void`	`getNboTypes()`
`protected void`	`initializeReader()`
`protected void`	`readMolecularOrbitals(int headerType)`
`private void`	`readSecondOrderData()`
`void`	`setMOData(boolean clearOrbitals)`

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, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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

shellCount
```
public int shellCount
```

gaussianCount
```
public int gaussianCount
```

gaussians
```
public float[][] gaussians
```

energyUnits
```
protected String energyUnits
```

moTypes

protected javajs.util.Lst<String> moTypes

getNBOs
```
private boolean getNBOs
```

getNBOCharges
```
private boolean getNBOCharges
```

haveNboCharges
```
protected boolean haveNboCharges
```

haveNboOrbitals
```
protected boolean haveNboOrbitals
```

orbitalsRead
```
protected boolean orbitalsRead
```

lastMoData
```
private Map<String,Object> lastMoData
```

allowNoOrbitals
```
protected boolean allowNoOrbitals
```

HEADER_GAMESS_UK_MO
```
protected final int HEADER_GAMESS_UK_MO
```
See Also:

Constant Field Values

HEADER_GAMESS_OCCUPANCIES
```
protected final int HEADER_GAMESS_OCCUPANCIES
```
See Also:

Constant Field Values

HEADER_GAMESS_ORIGINAL
```
protected final int HEADER_GAMESS_ORIGINAL
```
See Also:

Constant Field Values

HEADER_NONE
```
protected final int HEADER_NONE
```
See Also:

Constant Field Values

haveCoeffMap
```
private boolean haveCoeffMap
```

P_LIST
```
private static final String P_LIST
```
See Also:

Constant Field Values

DS_LIST
```
private static final String DS_LIST
```
See Also:

Constant Field Values

DC_LIST
```
private static final String DC_LIST
```
See Also:

Constant Field Values

FS_LIST
```
private static final String FS_LIST
```
See Also:

Constant Field Values

FC_LIST
```
private static String FC_LIST
```

iMo0
```
private int iMo0
```

Constructor Detail
- MOReader
```
public MOReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

Exception

checkAndRemoveFilterKey
```
public boolean checkAndRemoveFilterKey(String key)
```
Prior to filterMO all extraneous filter keys must be removed.

Parameters:

key -

Returns:

true if the key existed; filter is set null if this is the only key

checkNboLine

protected boolean checkNboLine()
                        throws Exception

Returns:: true if need to read line
Throws:: Exception

getNboCharges

private void getNboCharges()
                    throws Exception

Throws:: Exception

getNboTypes

protected void getNboTypes()
                    throws Exception

Throws:: Exception

readMolecularOrbitals

protected void readMolecularOrbitals(int headerType)
                              throws Exception

Throws:: Exception

addCoef

public void addCoef(Map<String,Object> mo,
                    float[] coefs,
                    String type,
                    float energy,
                    float occ,
                    int moCount)

getMOHeader

protected void getMOHeader(int headerType,
                           String[] tokens,
                           Map<String,Object>[] mos,
                           int nThisLine)
                    throws Exception

Throws:: Exception

addMOData

protected void addMOData(int nColumns,
                         javajs.util.Lst<String>[] data,
                         Map<String,Object>[] mos)

setMOData

public void setMOData(boolean clearOrbitals)

readSecondOrderData

private void readSecondOrderData()
                          throws Exception

Throws:: Exception

Class MOReader

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.BasisFunctionReader

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

Constructor Summary

Method Summary

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

shellCount

gaussianCount

gaussians

energyUnits

moTypes

getNBOs

getNBOCharges

haveNboCharges

haveNboOrbitals

orbitalsRead

lastMoData

allowNoOrbitals

HEADER_GAMESS_UK_MO

HEADER_GAMESS_OCCUPANCIES

HEADER_GAMESS_ORIGINAL

HEADER_NONE

haveCoeffMap

P_LIST

DS_LIST

DC_LIST

FS_LIST

FC_LIST

iMo0

Constructor Detail

MOReader

Method Detail

initializeReader

checkAndRemoveFilterKey

checkNboLine

getNboCharges

getNboTypes

readMolecularOrbitals

addCoef

getMOHeader

addMOData

setMOData

readSecondOrderData