Package org.jmol.adapter.readers.xml
Class XmlArgusReader
- 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.XmlArgusReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class XmlArgusReader extends XmlReader
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
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Field Summary
Fields Modifier and Type Field Description private static int
ATOM
private java.lang.String
atomName1
private java.lang.String
atomName2
private static int
BOND
private int
bondOrder
private int
elementContext
private static java.lang.String[]
keepCharsList
private static int
MOLECULE
private int
ptTrans
private float[]
trans
private static int
TRANSFORMMAT
private static int
UNSET
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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 XmlArgusReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private int
parseBondToken(java.lang.String str)
(package private) void
processEndElement(java.lang.String localName)
void
processStartElement(java.lang.String localName, java.lang.String nodeName)
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Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, finalizeSubclassReader, initCML, initializeReader, processDOM, processXml, 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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keepCharsList
private static java.lang.String[] keepCharsList
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atomName1
private java.lang.String atomName1
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atomName2
private java.lang.String atomName2
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bondOrder
private int bondOrder
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elementContext
private int elementContext
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UNSET
private static final int UNSET
- See Also:
- Constant Field Values
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MOLECULE
private static final int MOLECULE
- See Also:
- Constant Field Values
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ATOM
private static final int ATOM
- See Also:
- Constant Field Values
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BOND
private static final int BOND
- See Also:
- Constant Field Values
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TRANSFORMMAT
private static final int TRANSFORMMAT
- See Also:
- Constant Field Values
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trans
private float[] trans
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ptTrans
private int ptTrans
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Method Detail
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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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parseBondToken
private int parseBondToken(java.lang.String str)
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processEndElement
void processEndElement(java.lang.String localName)
- Overrides:
processEndElement
in classXmlReader
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