public class XmlArgusReader extends XmlReader
Modifier and Type | Field and 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 |
atom, atts, chars, domAttributes, keepChars, parent
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
XmlArgusReader() |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String[] |
getDOMAttributes() |
private int |
parseBondToken(java.lang.String str) |
(package private) void |
processEndElement(java.lang.String localName) |
void |
processStartElement(java.lang.String localName) |
applySymmetryAndSetTrajectory, initializeReader, processDOM, processXml, PX, setKeepChars
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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 static java.lang.String[] keepCharsList
private java.lang.String atomName1
private java.lang.String atomName2
private int bondOrder
private int elementContext
private static final int UNSET
private static final int MOLECULE
private static final int ATOM
private static final int BOND
private static final int TRANSFORMMAT
private float[] trans
private int ptTrans
protected java.lang.String[] getDOMAttributes()
getDOMAttributes
in class XmlReader
public void processStartElement(java.lang.String localName)
processStartElement
in class XmlReader
private int parseBondToken(java.lang.String str)
void processEndElement(java.lang.String localName)
processEndElement
in class XmlReader