public class PDBConvention extends CMLCoreModule
This is a lousy implementation, though. Problems that will arise:
<list sequence="">
is foundWhat is does:
atomAromaticities, atomCounter, atomCustomProperty, atomDictRefs, atomEnumeration, atomicNumbers, atomParities, bondARef1, bondARef2, bondAromaticity, bondCounter, bondCustomProperty, bondDictRefs, bondElid, bondid, bondStereo, BUILTIN, crystalScalar, curRef, currentAtom, currentBond, currentChars, currentChemFile, currentChemModel, currentChemSequence, CurrentElement, currentMolecule, currentMoleculeSet, currentMonomer, currentReaction, currentReactionSet, currentStrand, DICTREF, elementTitle, elid, elsym, eltitles, exactMasses, formalCharges, formula, formulaCounter, hCounts, inchi, isotope, logger, moleculeCustomProperty, occupancies, order, parityARef1, parityARef2, parityARef3, parityARef4, parityAtomsGiven, parityGiven, partialCharges, spinMultiplicities, stereoGiven, SYSTEMID, unitcellparams, x2, x3, xfract, y2, y3, yfract, z3, zfract
Constructor and Description |
---|
PDBConvention(IChemFile chemFile) |
PDBConvention(ICMLModule conv) |
Modifier and Type | Method and Description |
---|---|
void |
characterData(org.openscience.cdk.io.cml.CMLStack xpath,
char[] ch,
int start,
int length) |
void |
endDocument() |
void |
endElement(org.openscience.cdk.io.cml.CMLStack xpath,
String uri,
String local,
String raw) |
void |
newSequence() |
void |
startElement(org.openscience.cdk.io.cml.CMLStack xpath,
String uri,
String local,
String raw,
Attributes atts) |
protected void |
storeAtomData() |
protected void |
storeData() |
addArrayElementsTo, inherit, newAtomData, newBondData, newCrystalData, newFormulaData, newMolecule, newMoleculeData, notify, returnChemFile, startDocument, storeBondData
public PDBConvention(IChemFile chemFile)
public PDBConvention(ICMLModule conv)
public void endDocument()
endDocument
in interface ICMLModule
endDocument
in class CMLCoreModule
public void startElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw, Attributes atts)
startElement
in interface ICMLModule
startElement
in class CMLCoreModule
public void newSequence()
public void endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String local, String raw)
endElement
in interface ICMLModule
endElement
in class CMLCoreModule
public void characterData(org.openscience.cdk.io.cml.CMLStack xpath, char[] ch, int start, int length)
characterData
in interface ICMLModule
characterData
in class CMLCoreModule
protected void storeData()
storeData
in class CMLCoreModule
protected void storeAtomData()
storeAtomData
in class CMLCoreModule
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