Package org.jmol.adapter.readers.quantum

Class 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	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, 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
MOReader()

Method Summary

Modifier and Type	Method	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, 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, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, 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