public class XmlReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
protected Atom |
atom |
private java.lang.Object[] |
attArgs |
private java.lang.Object[] |
attribs |
java.util.Map<java.lang.String,java.lang.String> |
atts |
protected java.lang.String |
chars |
protected java.lang.String[] |
domAttributes |
private java.lang.Object[] |
domObj |
protected boolean |
keepChars |
private java.lang.Object[] |
nullObj |
protected XmlReader |
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 |
---|
XmlReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
protected java.lang.String[] |
getDOMAttributes() |
private void |
getDOMAttributesA(java.lang.Object[] attributes) |
void |
initializeReader() |
private java.lang.Object |
jsObjectCall(java.lang.Object[] jsObject,
java.lang.String method,
java.lang.Object[] args) |
private java.lang.Object |
jsObjectGetMember(java.lang.Object[] jsObject,
java.lang.String name) |
private java.lang.String |
parseXML() |
protected void |
processDOM(java.lang.Object DOMNode) |
(package private) void |
processEndElement(java.lang.String localName) |
protected void |
processStartElement(java.lang.String localName) |
protected void |
processXml(XmlReader parent,
java.lang.Object saxReader) |
protected void |
PX(XmlReader parent,
java.lang.Object saxReader) |
private java.lang.String |
selectReaderAndGo(java.lang.Object saxReader) |
protected void |
setKeepChars(boolean TF) |
private void |
setMyError(java.lang.String err) |
private void |
walkDOMTree() |
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
protected Atom atom
protected java.lang.String[] domAttributes
protected XmlReader parent
public java.util.Map<java.lang.String,java.lang.String> atts
protected boolean keepChars
protected java.lang.String chars
private java.lang.Object[] domObj
private java.lang.Object[] attribs
private java.lang.Object[] attArgs
private java.lang.Object[] nullObj
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
private void setMyError(java.lang.String err)
private java.lang.String parseXML()
private java.lang.String selectReaderAndGo(java.lang.Object saxReader)
protected void processXml(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
parent
- saxReader
- java.lang.Exception
protected void PX(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
java.lang.Exception
public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
protected void processDOM(java.lang.Object DOMNode)
processDOM
in class AtomSetCollectionReader
protected java.lang.String[] getDOMAttributes()
protected void processStartElement(java.lang.String localName)
localName
- protected void setKeepChars(boolean TF)
void processEndElement(java.lang.String localName)
localName
- private void walkDOMTree()
private void getDOMAttributesA(java.lang.Object[] attributes)
private java.lang.Object jsObjectCall(java.lang.Object[] jsObject, java.lang.String method, java.lang.Object[] args)
private java.lang.Object jsObjectGetMember(java.lang.Object[] jsObject, java.lang.String name)