public class MDMoleculeConvention extends CMLCoreModule
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 |
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MDMoleculeConvention(IChemFile chemFile) |
MDMoleculeConvention(ICMLModule conv) |
Modifier and Type | Method and Description |
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void |
endElement(org.openscience.cdk.io.cml.CMLStack xpath,
String uri,
String name,
String raw)
Finish up parsing of elements in mdmolecule.
|
void |
startElement(org.openscience.cdk.io.cml.CMLStack xpath,
String uri,
String local,
String raw,
Attributes atts)
Add parsing of elements in mdmolecule:
mdmolecule
chargeGroup
id
cgNumber
atomArray
switchingAtom
residue
id
title
resNumber
atomArray
|
addArrayElementsTo, characterData, endDocument, inherit, newAtomData, newBondData, newCrystalData, newFormulaData, newMolecule, newMoleculeData, notify, returnChemFile, startDocument, storeAtomData, storeBondData, storeData
public MDMoleculeConvention(IChemFile chemFile)
public MDMoleculeConvention(ICMLModule conv)
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 endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String name, String raw)
endElement
in interface ICMLModule
endElement
in class CMLCoreModule
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