public class XmlReader extends AtomSetCollectionReader
| Modifier and Type | Class and Description |
|---|---|
private class |
XmlReader.NVPair |
| 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 Bond |
bond |
protected javajs.util.SB |
chars |
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, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
XmlReader() |
| Modifier and Type | Method and Description |
|---|---|
void |
applySymmetryAndSetTrajectory() |
(package private) java.lang.Object |
createDomNodeJS(java.lang.String id,
java.lang.Object data)
totally untested, probably useless
|
void |
endDocument() |
private java.lang.String |
fixLocal(java.lang.String name) |
private void |
getDOMAttributesA(java.lang.Object[] attributes) |
protected void |
initCML() |
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,
java.lang.String nodeName) |
protected void |
processXml(XmlReader parent,
java.lang.Object saxReader) |
protected void |
processXml2(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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, 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, 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, setupASCRprotected Atom atom
protected Bond bond
protected XmlReader parent
public java.util.Map<java.lang.String,java.lang.String> atts
protected boolean keepChars
protected javajs.util.SB 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 AtomSetCollectionReaderjava.lang.Exceptionprotected void initCML()
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.Exceptionprotected void processXml2(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
java.lang.Exceptionjava.lang.Object createDomNodeJS(java.lang.String id,
java.lang.Object data)
id - data - public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory in class AtomSetCollectionReaderprotected void processDOM(java.lang.Object DOMNode)
processDOM in class AtomSetCollectionReaderprotected void processStartElement(java.lang.String localName,
java.lang.String nodeName)
localName - nodeName - TODOprotected void setKeepChars(boolean TF)
void processEndElement(java.lang.String localName)
localName - private void walkDOMTree()
private java.lang.String fixLocal(java.lang.String name)
private void getDOMAttributesA(java.lang.Object[] attributes)
private java.lang.Object jsObjectCall(java.lang.Object[] jsObject,
java.lang.String method,
java.lang.Object[] args)
jsObject - method - args - private java.lang.Object jsObjectGetMember(java.lang.Object[] jsObject,
java.lang.String name)
public void endDocument()