XmlMolproReader
public abstract class XmlMOReader extends XmlCmlReader
Modifier and Type | Field | Description |
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private java.lang.String[] |
basisAtoms |
|
private javajs.util.Lst<float[]> |
basisData |
|
private java.lang.String |
basisId |
|
private java.lang.String[] |
basisIds |
|
private java.lang.String |
calcType |
|
private int |
coefCount |
|
protected java.lang.String |
dclist |
|
protected java.lang.String |
dslist |
|
protected java.lang.String |
fclist |
|
protected java.lang.String |
fslist |
|
private int |
gaussianCount |
|
private int |
groupCount |
|
private java.util.Map<java.lang.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 |
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
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
Constructor | Description |
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XmlMOReader() |
Modifier and Type | Method | Description |
---|---|---|
private void |
buildSlaters() |
|
private java.lang.String[] |
getXlink(java.lang.String href,
java.lang.String key,
boolean addMoleculeID) |
|
protected boolean |
processEndMO(java.lang.String localName) |
|
protected boolean |
processStartMO(java.lang.String localName) |
|
protected void |
processXml(XmlReader parent,
java.lang.Object saxReader) |
the current state
|
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
applySymmetryAndSetTrajectory, breakOutAtomTokens, breakOutBondTokens, checkAtomArrayLength, checkBondArrayLength, endDocument, processEnd2, processEndElement, processStart2, processStartElement
createDomNodeJS, initCML, initializeReader, processDOM, processXml2, setKeepChars
private MOReader moReader
private boolean skipMOs
private java.util.Map<java.lang.String,int[]> htSlaterIDs
private javajs.util.Lst<float[]> basisData
private java.lang.String basisId
private boolean isSpherical
private int minL
private int maxL
private java.lang.String[] basisIds
private java.lang.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 java.lang.String calcType
private int iModelMO
protected java.lang.String dclist
protected java.lang.String dslist
protected java.lang.String fclist
protected java.lang.String fslist
protected boolean iHaveCoefMaps
private int maxContraction
protected void processXml(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
XmlCmlReader
processXml
in class XmlCmlReader
java.lang.Exception
protected boolean processStartMO(java.lang.String localName)
protected boolean processEndMO(java.lang.String localName)
private void buildSlaters()
private java.lang.String[] getXlink(java.lang.String href, java.lang.String key, boolean addMoleculeID)