public class XmlCmlReader extends XmlReader
Modifier and Type | Field and Description |
---|---|
private int |
aaLen |
protected static int |
ASSOCIATION
state constants
|
private Atom[] |
atomArray |
private java.util.Properties |
atomIdNames |
private int |
atomIndex0 |
private Bond[] |
bondArray |
private int |
bondCount |
private java.lang.String |
cellParameterType |
private boolean |
checkedSerial |
protected static int |
CML
state constants
|
protected static int |
CRYSTAL
state constants
|
protected static int |
CRYSTAL_SCALAR
state constants
|
protected static int |
CRYSTAL_SYMMETRY
state constants
|
protected static int |
CRYSTAL_SYMMETRY_TRANSFORM3
state constants
|
private javajs.util.BS |
deleteAtoms |
private boolean |
embeddedCrystal |
private boolean |
haveMolecule |
protected java.util.Map<java.lang.String,java.lang.Object> |
htModelAtomMap |
private boolean |
isSerial |
private javajs.util.Lst<java.lang.String[]> |
joinList |
protected static int |
LATTICE_VECTOR
state constants
|
private int |
latticeVectorPtr |
private java.lang.String |
localSpaceGroupName |
private java.util.Map<Atom,java.lang.String> |
mapRtoA |
protected static int |
MODULE
state constants
|
private int |
moduleNestingLevel |
protected static int |
MOLECULE
state constants
|
protected static int |
MOLECULE_ATOM
state constants
|
protected static int |
MOLECULE_ATOM_ARRAY
state constants
|
protected static int |
MOLECULE_ATOM_BUILTIN
state constants
|
protected static int |
MOLECULE_ATOM_SCALAR
state constants
|
protected static int |
MOLECULE_BOND
state constants
|
protected static int |
MOLECULE_BOND_ARRAY
state constants
|
protected static int |
MOLECULE_BOND_BUILTIN
state constants
|
protected static int |
MOLECULE_BOND_STEREO
state constants
|
protected static int |
MOLECULE_FORMULA
state constants
|
protected java.lang.String |
moleculeID |
private int |
moleculeNesting |
private boolean |
optimize2d |
protected boolean |
processing |
private java.lang.String |
scalarDictRef |
private java.lang.String |
scalarDictValue |
private java.lang.String |
scalarTitle |
protected static int |
START
state constants
|
protected int |
state |
protected static int |
SYMMETRY
state constants
|
private int |
tokenCount |
protected java.lang.String[] |
tokens |
private static java.lang.String[] |
unitCellParamTags |
atom, atts, bond, chars, keepChars, 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 |
---|
XmlCmlReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addAtom(Atom atom) |
private void |
addBond(Bond bond) |
private void |
addNewBond(java.lang.String a1,
java.lang.String a2,
int order) |
void |
applySymmetryAndSetTrajectory() |
(package private) void |
breakOutAtomTokens(java.lang.String str) |
(package private) void |
breakOutBondTokens(java.lang.String str) |
private void |
breakOutTokens(java.lang.String str) |
(package private) void |
checkAtomArrayLength(int newAtomCount) |
(package private) void |
checkBondArrayLength(int newBondCount) |
private boolean |
checkBondToR(java.lang.String a1name,
java.lang.String a2name)
Checks to see if we have a bond to R and, if so, adds this R atom
as a key to its attached atom
|
private void |
checkUnitCellItem(java.lang.String[] tags,
java.lang.String value) |
private void |
createNewAtomSet() |
void |
endDocument() |
private java.lang.String |
fixSerialName(java.lang.String a) |
private int |
getAtomIndex(java.lang.String label) |
private void |
getDictRefValue() |
private int |
parseBondToken(java.lang.String str) |
void |
processEnd2(java.lang.String name) |
(package private) void |
processEndElement(java.lang.String name) |
protected void |
processStart2(java.lang.String name) |
void |
processStartElement(java.lang.String name,
java.lang.String nodeName) |
protected void |
processXml(XmlReader parent,
java.lang.Object saxReader)
the current state
|
private void |
setAtomNames() |
createDomNodeJS, initCML, initializeReader, processDOM, processXml2, setKeepChars
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
private java.lang.String scalarDictRef
private java.lang.String scalarDictValue
private java.lang.String scalarTitle
private java.lang.String cellParameterType
private boolean checkedSerial
private boolean isSerial
private int moleculeNesting
private int latticeVectorPtr
private boolean embeddedCrystal
private java.util.Properties atomIdNames
protected java.lang.String[] tokens
private int aaLen
private Atom[] atomArray
private int bondCount
private Bond[] bondArray
private int tokenCount
private int moduleNestingLevel
private boolean haveMolecule
private java.lang.String localSpaceGroupName
protected boolean processing
protected int state
private int atomIndex0
private javajs.util.Lst<java.lang.String[]> joinList
private java.util.Map<Atom,java.lang.String> mapRtoA
private javajs.util.BS deleteAtoms
protected java.lang.String moleculeID
protected java.util.Map<java.lang.String,java.lang.Object> htModelAtomMap
private boolean optimize2d
protected static final int START
protected static final int CML
protected static final int CRYSTAL
protected static final int CRYSTAL_SCALAR
protected static final int CRYSTAL_SYMMETRY
protected static final int CRYSTAL_SYMMETRY_TRANSFORM3
protected static final int MOLECULE
protected static final int MOLECULE_ATOM_ARRAY
protected static final int MOLECULE_ATOM
protected static final int MOLECULE_ATOM_SCALAR
protected static final int MOLECULE_BOND_ARRAY
protected static final int MOLECULE_BOND
protected static final int MOLECULE_BOND_STEREO
protected static final int MOLECULE_FORMULA
protected static final int MOLECULE_ATOM_BUILTIN
protected static final int MOLECULE_BOND_BUILTIN
protected static final int MODULE
protected static final int SYMMETRY
protected static final int LATTICE_VECTOR
protected static final int ASSOCIATION
private static final java.lang.String[] unitCellParamTags
protected void processXml(XmlReader parent, java.lang.Object saxReader) throws java.lang.Exception
processXml
in class XmlReader
java.lang.Exception
public void processStartElement(java.lang.String name, java.lang.String nodeName)
processStartElement
in class XmlReader
nodeName
- TODOprotected void processStart2(java.lang.String name)
private int getAtomIndex(java.lang.String label)
void processEndElement(java.lang.String name)
processEndElement
in class XmlReader
public void processEnd2(java.lang.String name)
private void addBond(Bond bond)
private boolean checkBondToR(java.lang.String a1name, java.lang.String a2name)
a1name
- a2name
- private void setAtomNames()
private void addNewBond(java.lang.String a1, java.lang.String a2, int order)
private java.lang.String fixSerialName(java.lang.String a)
private void getDictRefValue()
private void checkUnitCellItem(java.lang.String[] tags, java.lang.String value)
private void addAtom(Atom atom)
private int parseBondToken(java.lang.String str)
private void breakOutTokens(java.lang.String str)
void breakOutAtomTokens(java.lang.String str)
void checkAtomArrayLength(int newAtomCount)
void breakOutBondTokens(java.lang.String str)
void checkBondArrayLength(int newBondCount)
private void createNewAtomSet()
public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class XmlReader
public void endDocument()
endDocument
in class XmlReader