javajs.api.GenericLineReader
public class XmlArgusReader extends XmlReader
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 |
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
Constructor | Description |
---|---|
XmlArgusReader() |
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) |
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, createDomNodeJS, endDocument, initCML, initializeReader, processDOM, processXml, processXml2, setKeepChars
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
public void processStartElement(java.lang.String localName, java.lang.String nodeName)
processStartElement
in class XmlReader
nodeName
- TODOprivate int parseBondToken(java.lang.String str)
void processEndElement(java.lang.String localName)
processEndElement
in class XmlReader