org.jmol.adapter.readers.quantum.MOReader

All Implemented Interfaces:: javajs.api.GenericLineReader

Direct Known Subclasses:: GaussianReader, GenNBOReader, JaguarReader, NWChemReader, OrcaReader, PsiReader, QchemReader, SlaterReader

public abstract 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 final String

DC_LIST

private static final String

DS_LIST

protected String

energyUnits

private static String

FC_LIST

protected boolean

forceMOPAC

private static final String

FS_LIST

int

gaussianCount

float[][]

gaussians

private boolean

getNBOCharges

private boolean

getNBOs

private boolean

haveCoeffMap

protected boolean

haveNboCharges

protected boolean

haveNboOrbitals

protected final int

HEADER_GAMESS_OCCUPANCIES

protected final int

HEADER_GAMESS_ORIGINAL

protected final int

HEADER_GAMESS_UK_MO

protected final int

HEADER_NONE

private int

iMo0

protected Map<String,Object>

lastMoData

protected javajs.util.Lst<String>

moTypes

protected boolean

orbitalsRead

private static final String

P_LIST

int

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

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)

protected void

addSlaterBasis()

See MopacSlaterReader

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, checkAndRemoveFilterKey, 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, 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
- 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
  
  protected Map<String,Object> lastMoData
- allowNoOrbitals
  
  protected boolean allowNoOrbitals
- forceMOPAC
  
  protected boolean forceMOPAC
- 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 Details
- MOReader
  
  public MOReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- 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
- addSlaterBasis
  
  protected void addSlaterBasis()
  
  See MopacSlaterReader
- 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 Details

shellCount

gaussianCount

gaussians

energyUnits

moTypes

getNBOs

getNBOCharges

haveNboCharges

haveNboOrbitals

orbitalsRead

lastMoData

allowNoOrbitals

forceMOPAC

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 Details

MOReader

Method Details

initializeReader

checkNboLine

getNboCharges

getNboTypes

readMolecularOrbitals

addSlaterBasis

addCoef

getMOHeader

addMOData

setMOData

readSecondOrderData