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:
GenericLineReader
- Direct Known Subclasses:
XmlMolproReader
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
FieldsModifier and TypeFieldDescriptionprotected Stringprotected Stringprotected Stringprotected Stringprotected booleanFields inherited from class 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, tokensFields inherited from class 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, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected booleanprocessEndMO(String localName) protected booleanprocessStartMO(String localName) protected voidprocessXml(XmlReader parent, Object saxReader) the current stateMethods inherited from class XmlCmlReader
applySymmetryAndSetTrajectory, endDocument, processEnd2, processStart2, processStartElementMethods inherited from class XmlReader
finalizeSubclassReader, initializeReader, previewXML, processDOM, processXml2, setKeepCharsMethods inherited from class AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, 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, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR, warnSkippingOperation
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Field Details
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dclist
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dslist
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fclist
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fslist
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iHaveCoefMaps
protected boolean iHaveCoefMaps
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Constructor Details
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XmlMOReader
public XmlMOReader()
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Method Details
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processXml
Description copied from class:XmlCmlReaderthe current state- Overrides:
processXmlin classXmlCmlReader- Parameters:
parent-saxReader-- Throws:
Exception
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processStartMO
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processEndMO
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