Package org.jmol.adapter.readers.xml

Class XmlMOReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

org.jmol.adapter.readers.xml.XmlCmlReader

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, 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
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, initCML, initializeReader, processDOM, processXml2, setKeepChars

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

addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, 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, 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, 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

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 Detail

XmlMOReader

public XmlMOReader()

Method Detail

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)