Class CMLCoreModule

All Implemented Interfaces:
Direct Known Subclasses:
CDKConvention, CMLReactionModule, JMOLANIMATIONConvention, MDLMolConvention, MDMoleculeConvention, PDBConvention, PMPConvention, QSARConvention

public class CMLCoreModule extends Object implements ICMLModule
Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4]).

Please file a bug report if this parser fails to parse a certain element or attribute value in a valid CML document.

Egon Willighagen <>
Source code:
Belongs to CDK module:
  • Field Details

    • logger

      protected ILoggingTool logger

      protected final String SYSTEMID
      See Also:
    • currentChemFile

      protected IChemFile currentChemFile
    • currentMolecule

      protected IAtomContainer currentMolecule
    • currentMoleculeSet

      protected IAtomContainerSet currentMoleculeSet
    • currentChemModel

      protected IChemModel currentChemModel
    • currentChemSequence

      protected IChemSequence currentChemSequence
    • currentReactionSet

      protected IReactionSet currentReactionSet
    • currentReaction

      protected IReaction currentReaction
    • currentAtom

      protected IAtom currentAtom
    • currentBond

      protected IBond currentBond
    • currentStrand

      protected IStrand currentStrand
    • currentMonomer

      protected IMonomer currentMonomer
    • atomEnumeration

      protected Map<String,IAtom> atomEnumeration
    • moleculeCustomProperty

      protected List<String> moleculeCustomProperty
    • formulaCounter

      protected int formulaCounter
    • atomCounter

      protected int atomCounter
    • elsym

      protected List<String> elsym
    • eltitles

      protected List<String> eltitles
    • elid

      protected List<String> elid
    • formula

      protected List<String> formula
    • formalCharges

      protected List<String> formalCharges
    • partialCharges

      protected List<String> partialCharges
    • isotope

      protected List<String> isotope
    • atomicNumbers

      protected List<String> atomicNumbers
    • exactMasses

      protected List<String> exactMasses
    • x3

      protected List<String> x3
    • y3

      protected List<String> y3
    • z3

      protected List<String> z3
    • x2

      protected List<String> x2
    • y2

      protected List<String> y2
    • xfract

      protected List<String> xfract
    • yfract

      protected List<String> yfract
    • zfract

      protected List<String> zfract
    • hCounts

      protected List<String> hCounts
    • atomParities

      protected List<String> atomParities
    • parityARef1

      protected List<String> parityARef1
    • parityARef2

      protected List<String> parityARef2
    • parityARef3

      protected List<String> parityARef3
    • parityARef4

      protected List<String> parityARef4
    • atomDictRefs

      protected List<String> atomDictRefs
    • atomAromaticities

      protected List<String> atomAromaticities
    • spinMultiplicities

      protected List<String> spinMultiplicities
    • occupancies

      protected List<String> occupancies
    • atomCustomProperty

      protected Map<Integer,List<String>> atomCustomProperty
    • parityAtomsGiven

      protected boolean parityAtomsGiven
    • parityGiven

      protected boolean parityGiven
    • bondCounter

      protected int bondCounter
    • bondid

      protected List<String> bondid
    • bondARef1

      protected List<String> bondARef1
    • bondARef2

      protected List<String> bondARef2
    • order

      protected List<String> order
    • bondStereo

      protected List<String> bondStereo
    • bondDictRefs

      protected List<String> bondDictRefs
    • bondElid

      protected List<String> bondElid
    • bondAromaticity

      protected List<Boolean> bondAromaticity
    • bondCustomProperty

      protected Map<String,Map<String,String>> bondCustomProperty
    • stereoGiven

      protected boolean stereoGiven
    • inchi

      protected String inchi
    • curRef

      protected int curRef
    • CurrentElement

      protected int CurrentElement

      protected String BUILTIN

      protected String DICTREF
    • elementTitle

      protected String elementTitle
    • currentChars

      protected String currentChars
    • unitcellparams

      protected double[] unitcellparams
    • crystalScalar

      protected int crystalScalar
  • Constructor Details

    • CMLCoreModule

      public CMLCoreModule(IChemFile chemFile)
    • CMLCoreModule

      public CMLCoreModule(ICMLModule conv)
  • Method Details

    • inherit

      public void inherit(ICMLModule convention)
      Specified by:
      inherit in interface ICMLModule
    • returnChemFile

      public IChemFile returnChemFile()
      Specified by:
      returnChemFile in interface ICMLModule
    • newMolecule

      protected void newMolecule()
      Clean all data about parsed data.
    • newMoleculeData

      protected void newMoleculeData()
      Clean all data about the molecule itself.
    • newFormulaData

      protected void newFormulaData()
      Clean all data about read formulas.
    • newAtomData

      protected void newAtomData()
      Clean all data about read atoms.
    • newBondData

      protected void newBondData()
      Clean all data about read bonds.
    • newCrystalData

      protected void newCrystalData()
      Clean all data about read bonds.
    • startDocument

      public void startDocument()
      Specified by:
      startDocument in interface ICMLModule
    • endDocument

      public void endDocument()
      Specified by:
      endDocument in interface ICMLModule
    • startElement

      public void startElement( xpath, String uri, String local, String raw, Attributes atts)
      Specified by:
      startElement in interface ICMLModule
    • endElement

      public void endElement( xpath, String uri, String name, String raw)
      Specified by:
      endElement in interface ICMLModule
    • characterData

      public void characterData( xpath, char[] ch, int start, int length)
      Specified by:
      characterData in interface ICMLModule
    • notify

      protected void notify(String message, String systemId, int line, int column)
    • storeData

      protected void storeData()
    • storeAtomData

      protected void storeAtomData()
    • storeBondData

      protected void storeBondData()
    • addArrayElementsTo

      protected int addArrayElementsTo(List<String> toAddto, String array)