Package org.jmol.adapter.readers.xml
Class XmlChemDrawReader
- 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.XmlChemDrawReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class XmlChemDrawReader extends XmlReader
An chem3d c3xml reader
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Field Summary
Fields Modifier and Type Field Description private javajs.util.Lst<java.lang.Object[]>
bonds
private boolean
is3D
private float
maxX
private float
maxY
private float
maxZ
private float
minX
private float
minY
private float
minZ
(package private) boolean
optimize2D
private Atom
warningAtom
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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, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, 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, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, 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
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Constructor Summary
Constructors Constructor Description XmlChemDrawReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
center()
protected void
finalizeSubclassReader()
optional reader-specific method run first.private void
fixConnections()
(package private) void
processEndElement(java.lang.String localName)
void
processStartElement(java.lang.String localName, java.lang.String nodeName)
protected void
processXml(XmlReader parent, java.lang.Object saxReader)
private void
setAtom(java.lang.String key)
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Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, 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, 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, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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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optimize2D
boolean optimize2D
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minX
private float minX
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minY
private float minY
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minZ
private float minZ
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maxZ
private float maxZ
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maxY
private float maxY
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maxX
private float maxX
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is3D
private boolean is3D
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bonds
private javajs.util.Lst<java.lang.Object[]> bonds
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warningAtom
private Atom warningAtom
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Method Detail
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processXml
protected void processXml(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
- Overrides:
processXml
in classXmlReader
- Throws:
java.lang.Exception
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processStartElement
public void processStartElement(java.lang.String localName, java.lang.String nodeName)
- Overrides:
processStartElement
in classXmlReader
nodeName
- TODO
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setAtom
private void setAtom(java.lang.String key)
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processEndElement
void processEndElement(java.lang.String localName)
- Overrides:
processEndElement
in classXmlReader
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classXmlReader
- Throws:
java.lang.Exception
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fixConnections
private void fixConnections()
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center
private void center()
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