org.jmol.adapter.readers.xml.XmlMOReader

All Implemented Interfaces:: javajs.api.GenericLineReader

Direct Known Subclasses:: XmlMolproReader

public abstract class XmlMOReader extends XmlCmlReader

An abstract class accessing MOReader -- currently just for XmlMolproReader only. Several assumptions here.

Author:: hansonr Bob Hanson hansonr@stolaf.edu

Field Summary

Fields

Modifier and Type

Field

Description

private String[]

basisAtoms

private javajs.util.Lst<float[]>

basisData

private String

basisId

private String[]

basisIds

private String

calcType

private int

coefCount

protected String

dclist

protected String

dslist

protected String

fclist

protected String

fslist

private int

gaussianCount

private int

groupCount

private Map<String,int[]>

htSlaterIDs

protected boolean

iHaveCoefMaps

private int

iModelMO

private boolean

isSpherical

private javajs.util.Lst<javajs.util.Lst<float[]>>

lstGaussians

private int

maxContraction

private int

maxL

private int

minL

private int

moCount

private MOReader

moReader

private float

orbEnergy

private float

orbOcc

private boolean

skipMOs

private int

slaterCount

Fields inherited from class org.jmol.adapter.readers.xml.XmlCmlReader
ASSOCIATION, CML, CRYSTAL, CRYSTAL_SCALAR, CRYSTAL_SYMMETRY, CRYSTAL_SYMMETRY_TRANSFORM3, htModelAtomMap, LATTICE_VECTOR, MODULE, MOLECULE, MOLECULE_ATOM, MOLECULE_ATOM_ARRAY, MOLECULE_ATOM_BUILTIN, MOLECULE_ATOM_SCALAR, MOLECULE_BOND, MOLECULE_BOND_ARRAY, MOLECULE_BOND_BUILTIN, MOLECULE_BOND_STEREO, MOLECULE_FORMULA, moleculeID, processing, START, state, SYMMETRY, tokens

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent

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

XmlMOReader()
Method Summary

Modifier and Type

Method

Description

private void

buildSlaters()

private String[]

getXlink(String href, String key, boolean addMoleculeID)

protected boolean

processEndMO(String localName)

protected boolean

processStartMO(String localName)

protected void

processXml(XmlReader parent, Object saxReader)

the current state

Methods inherited from class org.jmol.adapter.readers.xml.XmlCmlReader
applySymmetryAndSetTrajectory, breakOutAtomTokens, breakOutBondTokens, checkAtomArrayLength, checkBondArrayLength, endDocument, processEnd2, processEndElement, processStart2, processStartElement

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
createDomNodeJS, finalizeSubclassReader, initializeReader, processDOM, processXml2, setKeepChars

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, 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
- moReader
  
  private MOReader moReader
- skipMOs
  
  private boolean skipMOs
- htSlaterIDs
  
  private Map<String,int[]> htSlaterIDs
- basisData
  
  private javajs.util.Lst<float[]> basisData
- basisId
  
  private String basisId
- isSpherical
  
  private boolean isSpherical
- minL
  
  private int minL
- maxL
  
  private int maxL
- basisIds
  
  private String[] basisIds
- basisAtoms
  
  private String[] basisAtoms
- orbOcc
  
  private float orbOcc
- orbEnergy
  
  private float orbEnergy
- gaussianCount
  
  private int gaussianCount
- slaterCount
  
  private int slaterCount
- coefCount
  
  private int coefCount
- groupCount
  
  private int groupCount
- lstGaussians
  
  private javajs.util.Lst<javajs.util.Lst<float[]>> lstGaussians
- moCount
  
  private int moCount
- calcType
  
  private String calcType
- iModelMO
  
  private int iModelMO
- dclist
  
  protected String dclist
- dslist
  
  protected String dslist
- fclist
  
  protected String fclist
- fslist
  
  protected String fslist
- iHaveCoefMaps
  
  protected boolean iHaveCoefMaps
- maxContraction
  
  private int maxContraction
Constructor Details
- XmlMOReader
  
  public XmlMOReader()
Method Details
- processXml
  
  protected void processXml(XmlReader parent, Object saxReader) throws Exception
  
  Description copied from class: XmlCmlReader
  
  the current state
  
  Overrides:
  
  processXml in class XmlCmlReader
  
  Throws:
  
  Exception
- processStartMO
  
  protected boolean processStartMO(String localName)
- processEndMO
  
  protected boolean processEndMO(String localName)
- buildSlaters
  
  private void buildSlaters()
- getXlink
  
  private String[] getXlink(String href, String key, boolean addMoleculeID)

Class XmlMOReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.xml.XmlCmlReader

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.xml.XmlCmlReader

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

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

Methods inherited from class java.lang.Object

Field Details

moReader

skipMOs

htSlaterIDs

basisData

basisId

isSpherical

minL

maxL

basisIds

basisAtoms

orbOcc

orbEnergy

gaussianCount

slaterCount

coefCount

groupCount

lstGaussians

moCount

calcType

iModelMO

dclist

dslist

fclist

fslist

iHaveCoefMaps

maxContraction

Constructor Details

XmlMOReader

Method Details

processXml

processStartMO

processEndMO

buildSlaters

getXlink