Package org.openscience.cdk.io.cml
Class MDMoleculeConvention
- java.lang.Object
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- org.openscience.cdk.io.cml.CMLCoreModule
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- org.openscience.cdk.io.cml.MDMoleculeConvention
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- All Implemented Interfaces:
ICMLModule
public class MDMoleculeConvention extends CMLCoreModule
Implements a Convention for parsing an MDMolecule from CML.- Author:
- Ola Spjuth <ola.spjuth@farmbio.uu.se>
- Source code:
- main
- Belongs to CDK module:
- libiomd
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Field Summary
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Fields inherited from class org.openscience.cdk.io.cml.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
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Constructor Summary
Constructors Constructor Description MDMoleculeConvention(IChemFile chemFile)
MDMoleculeConvention(ICMLModule conv)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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-
Methods inherited from class org.openscience.cdk.io.cml.CMLCoreModule
addArrayElementsTo, characterData, endDocument, inherit, newAtomData, newBondData, newCrystalData, newFormulaData, newMolecule, newMoleculeData, notify, returnChemFile, startDocument, storeAtomData, storeBondData, storeData
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Constructor Detail
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MDMoleculeConvention
public MDMoleculeConvention(IChemFile chemFile)
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MDMoleculeConvention
public MDMoleculeConvention(ICMLModule conv)
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Method Detail
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startElement
public 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- Specified by:
startElement
in interfaceICMLModule
- Overrides:
startElement
in classCMLCoreModule
- To do:
- The JavaDoc of this class needs to be converted into HTML
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endElement
public void endElement(org.openscience.cdk.io.cml.CMLStack xpath, String uri, String name, String raw)
Finish up parsing of elements in mdmolecule.- Specified by:
endElement
in interfaceICMLModule
- Overrides:
endElement
in classCMLCoreModule
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