Package org.jmol.adapter.readers.xml
Class XmlMOReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xml.XmlReader
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- org.jmol.adapter.readers.xml.XmlCmlReader
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- org.jmol.adapter.readers.xml.XmlMOReader
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- 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
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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
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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
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Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent
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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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description XmlMOReader()
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Method Summary
All Methods Instance Methods Concrete Methods 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
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Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
createDomNodeJS, initCML, initializeReader, processDOM, processXml2, setKeepChars
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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
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Field Detail
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moReader
private MOReader moReader
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skipMOs
private boolean skipMOs
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basisData
private javajs.util.Lst<float[]> basisData
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basisId
private String basisId
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isSpherical
private boolean isSpherical
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minL
private int minL
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maxL
private int maxL
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basisIds
private String[] basisIds
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basisAtoms
private String[] basisAtoms
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orbOcc
private float orbOcc
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orbEnergy
private float orbEnergy
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gaussianCount
private int gaussianCount
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slaterCount
private int slaterCount
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coefCount
private int coefCount
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groupCount
private int groupCount
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lstGaussians
private javajs.util.Lst<javajs.util.Lst<float[]>> lstGaussians
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moCount
private int moCount
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calcType
private String calcType
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iModelMO
private int iModelMO
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dclist
protected String dclist
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dslist
protected String dslist
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fclist
protected String fclist
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fslist
protected String fslist
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iHaveCoefMaps
protected boolean iHaveCoefMaps
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maxContraction
private int maxContraction
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Method Detail
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processXml
protected void processXml(XmlReader parent, Object saxReader) throws Exception
Description copied from class:XmlCmlReader
the current state- Overrides:
processXml
in classXmlCmlReader
- Throws:
Exception
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processStartMO
protected boolean processStartMO(String localName)
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processEndMO
protected boolean processEndMO(String localName)
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buildSlaters
private void buildSlaters()
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