public class XmlReader extends AtomSetCollectionReader
Modifier and Type | Class and Description |
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private class |
XmlReader.NVPair |
Modifier and Type | Field and Description |
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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 |
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XmlReader() |
Modifier and Type | Method and Description |
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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, setupASCR
protected 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 AtomSetCollectionReader
java.lang.Exception
protected 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.Exception
protected void processXml2(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
java.lang.Exception
java.lang.Object createDomNodeJS(java.lang.String id, java.lang.Object data)
id
- data
- public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
protected void processDOM(java.lang.Object DOMNode)
processDOM
in class AtomSetCollectionReader
protected 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()