public abstract class XmlMOReader extends XmlCmlReader
Modifier and Type | Field and 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 |
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_FORMULA, moleculeID, processing, START, state, SYMMETRY, tokens
atom, atts, chars, keepChars, parent
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
XmlMOReader() |
Modifier and Type | Method and 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
|
applySymmetryAndSetTrajectory, breakOutAtomTokens, breakOutBondTokens, checkAtomArrayLength, checkBondArrayLength, endDocument, processEnd2, processEndElement, processStart2, processStartElement
createDomNodeJS, initCML, initializeReader, processDOM, processXml2, setKeepChars
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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
private MOReader moReader
private boolean skipMOs
private javajs.util.Lst<float[]> basisData
private String basisId
private boolean isSpherical
private int minL
private int maxL
private String[] basisIds
private String[] basisAtoms
private float orbOcc
private float orbEnergy
private int gaussianCount
private int slaterCount
private int coefCount
private int groupCount
private javajs.util.Lst<javajs.util.Lst<float[]>> lstGaussians
private int moCount
private String calcType
private int iModelMO
protected String dclist
protected String dslist
protected String fclist
protected String fslist
protected boolean iHaveCoefMaps
private int maxContraction
protected void processXml(XmlReader parent, Object saxReader) throws Exception
XmlCmlReader
processXml
in class XmlCmlReader
Exception
protected boolean processStartMO(String localName)
protected boolean processEndMO(String localName)
private void buildSlaters()