Package org.openscience.cdk.io.cml

Class MDMoleculeConvention

java.lang.Object

org.openscience.cdk.io.cml.CMLCoreModule

org.openscience.cdk.io.cml.MDMoleculeConvention

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

Field Summary

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

Constructor Summary

Constructors

Constructor	Description
MDMoleculeConvention(IChemFile chemFile)
MDMoleculeConvention(ICMLModule conv)

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MDMoleculeConvention

public MDMoleculeConvention(IChemFile chemFile)

MDMoleculeConvention

public MDMoleculeConvention(ICMLModule conv)

Method Detail

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 interface ICMLModule

Overrides:

startElement in class CMLCoreModule

To do:

The JavaDoc of this class needs to be converted into HTML

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 interface ICMLModule

Overrides:

endElement in class CMLCoreModule