test_class.file: storage/libiocml/src/test/java/org/openscience/cdk/libio/cml/ConvertorTest.java
test_class.identifier: ConvertorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testCdkBondToCMLBond_Wedge() throws IOException {
  
          IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
          IBond bond = builder.newInstance(IBond.class);
          bond.setOrder(IBond.Order.SINGLE);
          bond.setStereo(IBond.Stereo.UP);
  
          Convertor convertor = new Convertor(true, null);
          CMLBond cmlBond = convertor.cdkBondToCMLBond(bond);
  
          ByteArrayOutputStream out = new ByteArrayOutputStream();
  
          Serializer serializer = new Serializer(out, "UTF-8");
  
          serializer.write(new Document(cmlBond));
  
          out.close();
  
          String expected = "<bondStereo dictRef=\"cml:W\">W</bondStereo>";
          String actual = new String(out.toByteArray());
  
          Assert.assertTrue(actual.contains(expected));
  
      }
test_case.class_method_signature: ConvertorTest.testCdkBondToCMLBond_Wedge()
test_case.full_signature: @Test public void testCdkBondToCMLBond_Wedge()
test_case.identifier: testCdkBondToCMLBond_Wedge
test_case.invocations: getInstance newInstance setOrder setStereo cdkBondToCMLBond write close toByteArray assertTrue contains
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCdkBondToCMLBond_Wedge()
focal_class.declarator: NS_CML           = "http://www.xml-cml.org/schema"
focal_class.modifier: public final static
focal_class.original_string: public final static String          NS_CML           = "http://www.xml-cml.org/schema";
focal_class.type: String
focal_class.var_name: NS_CML
focal_class.declarator: logger           = LoggingToolFactory.createLoggingTool(Convertor.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool         logger           = LoggingToolFactory.createLoggingTool(Convertor.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: CUSTOMIZERS_LIST = "libio-cml-customizers.set"
focal_class.modifier: private final static
focal_class.original_string: private final static String         CUSTOMIZERS_LIST = "libio-cml-customizers.set";
focal_class.type: String
focal_class.var_name: CUSTOMIZERS_LIST
focal_class.declarator: customizers      = null
focal_class.modifier: private
focal_class.original_string: private Map<String, ICMLCustomizer> customizers      = null;
focal_class.type: Map<String, ICMLCustomizer>
focal_class.var_name: customizers
focal_class.declarator: useCMLIDs
focal_class.modifier: private
focal_class.original_string: private boolean                     useCMLIDs;
focal_class.type: boolean
focal_class.var_name: useCMLIDs
focal_class.declarator: prefix
focal_class.modifier: private
focal_class.original_string: private String                      prefix;
focal_class.type: String
focal_class.var_name: prefix
focal_class.file: storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java
focal_class.identifier: Convertor
focal_class.class_method_signature: Convertor.Convertor(boolean useCMLIDs, String prefix)
focal_class.full_signature: public  Convertor(boolean useCMLIDs, String prefix)
focal_class.identifier: Convertor
focal_class.modifiers: public
focal_class.parameters: (boolean useCMLIDs, String prefix)
focal_class.signature:  Convertor(boolean useCMLIDs, String prefix)
focal_class.class_method_signature: Convertor.registerCustomizer(ICMLCustomizer customizer)
focal_class.full_signature: public void registerCustomizer(ICMLCustomizer customizer)
focal_class.identifier: registerCustomizer
focal_class.modifiers: public
focal_class.parameters: (ICMLCustomizer customizer)
focal_class.return: void
focal_class.signature: void registerCustomizer(ICMLCustomizer customizer)
focal_class.class_method_signature: Convertor.setupCustomizers()
focal_class.full_signature: private void setupCustomizers()
focal_class.identifier: setupCustomizers
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setupCustomizers()
focal_class.class_method_signature: Convertor.cdkChemFileToCMLList(IChemFile file)
focal_class.full_signature: public CMLCml cdkChemFileToCMLList(IChemFile file)
focal_class.identifier: cdkChemFileToCMLList
focal_class.modifiers: public
focal_class.parameters: (IChemFile file)
focal_class.return: CMLCml
focal_class.signature: CMLCml cdkChemFileToCMLList(IChemFile file)
focal_class.class_method_signature: Convertor.cdkChemFileToCMLList(IChemFile file, boolean setIDs)
focal_class.full_signature: private CMLCml cdkChemFileToCMLList(IChemFile file, boolean setIDs)
focal_class.identifier: cdkChemFileToCMLList
focal_class.modifiers: private
focal_class.parameters: (IChemFile file, boolean setIDs)
focal_class.return: CMLCml
focal_class.signature: CMLCml cdkChemFileToCMLList(IChemFile file, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkChemSequenceToCMLList(IChemSequence sequence)
focal_class.full_signature: public CMLList cdkChemSequenceToCMLList(IChemSequence sequence)
focal_class.identifier: cdkChemSequenceToCMLList
focal_class.modifiers: public
focal_class.parameters: (IChemSequence sequence)
focal_class.return: CMLList
focal_class.signature: CMLList cdkChemSequenceToCMLList(IChemSequence sequence)
focal_class.class_method_signature: Convertor.cdkChemSequenceToCMLList(IChemSequence sequence, boolean setIDs)
focal_class.full_signature: private CMLList cdkChemSequenceToCMLList(IChemSequence sequence, boolean setIDs)
focal_class.identifier: cdkChemSequenceToCMLList
focal_class.modifiers: private
focal_class.parameters: (IChemSequence sequence, boolean setIDs)
focal_class.return: CMLList
focal_class.signature: CMLList cdkChemSequenceToCMLList(IChemSequence sequence, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkChemModelToCMLList(IChemModel model)
focal_class.full_signature: public CMLList cdkChemModelToCMLList(IChemModel model)
focal_class.identifier: cdkChemModelToCMLList
focal_class.modifiers: public
focal_class.parameters: (IChemModel model)
focal_class.return: CMLList
focal_class.signature: CMLList cdkChemModelToCMLList(IChemModel model)
focal_class.class_method_signature: Convertor.cdkChemModelToCMLList(IChemModel model, boolean setIDs)
focal_class.full_signature: private CMLList cdkChemModelToCMLList(IChemModel model, boolean setIDs)
focal_class.identifier: cdkChemModelToCMLList
focal_class.modifiers: private
focal_class.parameters: (IChemModel model, boolean setIDs)
focal_class.return: CMLList
focal_class.signature: CMLList cdkChemModelToCMLList(IChemModel model, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)
focal_class.full_signature: public CMLCml cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)
focal_class.identifier: cdkReactionSchemeToCMLReactionSchemeAndMoleculeList
focal_class.modifiers: public
focal_class.parameters: (IReactionScheme cdkScheme)
focal_class.return: CMLCml
focal_class.signature: CMLCml cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme)
focal_class.class_method_signature: Convertor.cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)
focal_class.full_signature: public CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)
focal_class.identifier: cdkReactionSchemeToCMLReactionScheme
focal_class.modifiers: public
focal_class.parameters: (IReactionScheme cdkScheme)
focal_class.return: CMLReactionScheme
focal_class.signature: CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme)
focal_class.class_method_signature: Convertor.cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme, boolean setIDs)
focal_class.full_signature: private CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme, boolean setIDs)
focal_class.identifier: cdkReactionSchemeToCMLReactionScheme
focal_class.modifiers: private
focal_class.parameters: (IReactionScheme cdkScheme, boolean setIDs)
focal_class.return: CMLReactionScheme
focal_class.signature: CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkReactionToCMLReactionStep(IReaction reaction)
focal_class.full_signature: public CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction)
focal_class.identifier: cdkReactionToCMLReactionStep
focal_class.modifiers: public
focal_class.parameters: (IReaction reaction)
focal_class.return: CMLReactionStep
focal_class.signature: CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction)
focal_class.class_method_signature: Convertor.cdkReactionToCMLReactionStep(IReaction reaction, boolean setIDs)
focal_class.full_signature: private CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction, boolean setIDs)
focal_class.identifier: cdkReactionToCMLReactionStep
focal_class.modifiers: private
focal_class.parameters: (IReaction reaction, boolean setIDs)
focal_class.return: CMLReactionStep
focal_class.signature: CMLReactionStep cdkReactionToCMLReactionStep(IReaction reaction, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkReactionSetToCMLReactionList(IReactionSet reactionSet)
focal_class.full_signature: public CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet)
focal_class.identifier: cdkReactionSetToCMLReactionList
focal_class.modifiers: public
focal_class.parameters: (IReactionSet reactionSet)
focal_class.return: CMLReactionList
focal_class.signature: CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet)
focal_class.class_method_signature: Convertor.cdkReactionSetToCMLReactionList(IReactionSet reactionSet, boolean setIDs)
focal_class.full_signature: private CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet, boolean setIDs)
focal_class.identifier: cdkReactionSetToCMLReactionList
focal_class.modifiers: private
focal_class.parameters: (IReactionSet reactionSet, boolean setIDs)
focal_class.return: CMLReactionList
focal_class.signature: CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)
focal_class.full_signature: public CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)
focal_class.identifier: cdkAtomContainerSetToCMLList
focal_class.modifiers: public
focal_class.parameters: (IAtomContainerSet moleculeSet)
focal_class.return: CMLMoleculeList
focal_class.signature: CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)
focal_class.class_method_signature: Convertor.cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet, boolean setIDs)
focal_class.full_signature: private CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet, boolean setIDs)
focal_class.identifier: cdkAtomContainerSetToCMLList
focal_class.modifiers: private
focal_class.parameters: (IAtomContainerSet moleculeSet, boolean setIDs)
focal_class.return: CMLMoleculeList
focal_class.signature: CMLMoleculeList cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkReactionToCMLReaction(IReaction reaction)
focal_class.full_signature: public CMLReaction cdkReactionToCMLReaction(IReaction reaction)
focal_class.identifier: cdkReactionToCMLReaction
focal_class.modifiers: public
focal_class.parameters: (IReaction reaction)
focal_class.return: CMLReaction
focal_class.signature: CMLReaction cdkReactionToCMLReaction(IReaction reaction)
focal_class.class_method_signature: Convertor.cdkReactionToCMLReaction(IReaction reaction, boolean setIDs)
focal_class.full_signature: private CMLReaction cdkReactionToCMLReaction(IReaction reaction, boolean setIDs)
focal_class.identifier: cdkReactionToCMLReaction
focal_class.modifiers: private
focal_class.parameters: (IReaction reaction, boolean setIDs)
focal_class.return: CMLReaction
focal_class.signature: CMLReaction cdkReactionToCMLReaction(IReaction reaction, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkCrystalToCMLMolecule(ICrystal crystal)
focal_class.full_signature: public CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal)
focal_class.identifier: cdkCrystalToCMLMolecule
focal_class.modifiers: public
focal_class.parameters: (ICrystal crystal)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal)
focal_class.class_method_signature: Convertor.cdkCrystalToCMLMolecule(ICrystal crystal, boolean setIDs)
focal_class.full_signature: private CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal, boolean setIDs)
focal_class.identifier: cdkCrystalToCMLMolecule
focal_class.modifiers: private
focal_class.parameters: (ICrystal crystal, boolean setIDs)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
focal_class.full_signature: public CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
focal_class.identifier: cdkPDBPolymerToCMLMolecule
focal_class.modifiers: public
focal_class.parameters: (IPDBPolymer pdbPolymer)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
focal_class.class_method_signature: Convertor.cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer, boolean setIDs)
focal_class.full_signature: private CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer, boolean setIDs)
focal_class.identifier: cdkPDBPolymerToCMLMolecule
focal_class.modifiers: private
focal_class.parameters: (IPDBPolymer pdbPolymer, boolean setIDs)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkMonomerToCMLMolecule(IMonomer monomer)
focal_class.full_signature: public CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer)
focal_class.identifier: cdkMonomerToCMLMolecule
focal_class.modifiers: public
focal_class.parameters: (IMonomer monomer)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer)
focal_class.class_method_signature: Convertor.cdkMonomerToCMLMolecule(IMonomer monomer, boolean setIDs)
focal_class.full_signature: private CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer, boolean setIDs)
focal_class.identifier: cdkMonomerToCMLMolecule
focal_class.modifiers: private
focal_class.parameters: (IMonomer monomer, boolean setIDs)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkMonomerToCMLMolecule(IMonomer monomer, boolean setIDs)
focal_class.class_method_signature: Convertor.cdkAtomContainerToCMLMolecule(IAtomContainer structure)
focal_class.full_signature: public CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure)
focal_class.identifier: cdkAtomContainerToCMLMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer structure)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure)
focal_class.class_method_signature: Convertor.cdkAtomContainerToCMLMolecule(IAtomContainer structure, boolean setIDs, boolean isRef)
focal_class.full_signature: private CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure, boolean setIDs, boolean isRef)
focal_class.identifier: cdkAtomContainerToCMLMolecule
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer structure, boolean setIDs, boolean isRef)
focal_class.return: CMLMolecule
focal_class.signature: CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure, boolean setIDs, boolean isRef)
focal_class.class_method_signature: Convertor.addDictRef(IChemObject object, CMLElement cmlElement)
focal_class.full_signature: private boolean addDictRef(IChemObject object, CMLElement cmlElement)
focal_class.identifier: addDictRef
focal_class.modifiers: private
focal_class.parameters: (IChemObject object, CMLElement cmlElement)
focal_class.return: boolean
focal_class.signature: boolean addDictRef(IChemObject object, CMLElement cmlElement)
focal_class.class_method_signature: Convertor.addAtomID(IAtom cdkAtom, CMLAtom cmlAtom)
focal_class.full_signature: private boolean addAtomID(IAtom cdkAtom, CMLAtom cmlAtom)
focal_class.identifier: addAtomID
focal_class.modifiers: private
focal_class.parameters: (IAtom cdkAtom, CMLAtom cmlAtom)
focal_class.return: boolean
focal_class.signature: boolean addAtomID(IAtom cdkAtom, CMLAtom cmlAtom)
focal_class.class_method_signature: Convertor.cdkAtomToCMLAtom(IAtom cdkAtom)
focal_class.full_signature: public CMLAtom cdkAtomToCMLAtom(IAtom cdkAtom)
focal_class.identifier: cdkAtomToCMLAtom
focal_class.modifiers: public
focal_class.parameters: (IAtom cdkAtom)
focal_class.return: CMLAtom
focal_class.signature: CMLAtom cdkAtomToCMLAtom(IAtom cdkAtom)
focal_class.class_method_signature: Convertor.cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
focal_class.full_signature: public CMLAtom cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
focal_class.identifier: cdkAtomToCMLAtom
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container, IAtom cdkAtom)
focal_class.return: CMLAtom
focal_class.signature: CMLAtom cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
focal_class.class_method_signature: Convertor.cdkBondToCMLBond(IBond cdkBond)
focal_class.full_signature: public CMLBond cdkBondToCMLBond(IBond cdkBond)
focal_class.identifier: cdkBondToCMLBond
focal_class.modifiers: public
focal_class.parameters: (IBond cdkBond)
focal_class.return: CMLBond
focal_class.signature: CMLBond cdkBondToCMLBond(IBond cdkBond)
focal_class.class_method_signature: Convertor.writeProperties(IChemObject object, CMLElement cmlElement)
focal_class.full_signature: private void writeProperties(IChemObject object, CMLElement cmlElement)
focal_class.identifier: writeProperties
focal_class.modifiers: private
focal_class.parameters: (IChemObject object, CMLElement cmlElement)
focal_class.return: void
focal_class.signature: void writeProperties(IChemObject object, CMLElement cmlElement)
focal_class.class_method_signature: Convertor.mapFractionalCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.full_signature: private void mapFractionalCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.identifier: mapFractionalCoordsToCML
focal_class.modifiers: private
focal_class.parameters: (CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.return: void
focal_class.signature: void mapFractionalCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.class_method_signature: Convertor.map3DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.full_signature: private void map3DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.identifier: map3DCoordsToCML
focal_class.modifiers: private
focal_class.parameters: (CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.return: void
focal_class.signature: void map3DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.class_method_signature: Convertor.map2DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.full_signature: private void map2DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.identifier: map2DCoordsToCML
focal_class.modifiers: private
focal_class.parameters: (CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.return: void
focal_class.signature: void map2DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom)
focal_class.class_method_signature: Convertor.checkPrefix(CMLElement element)
focal_class.full_signature: private void checkPrefix(CMLElement element)
focal_class.identifier: checkPrefix
focal_class.modifiers: private
focal_class.parameters: (CMLElement element)
focal_class.return: void
focal_class.signature: void checkPrefix(CMLElement element)
focal_method.body: public CMLBond cdkBondToCMLBond(IBond cdkBond) {
          CMLBond cmlBond = new CMLBond();
          this.checkPrefix(cmlBond);
          if (cdkBond.getID() == null || cdkBond.getID().length() == 0) {
              cmlBond.setId("b" + cdkBond.hashCode());
          } else {
              cmlBond.setId(cdkBond.getID());
          }
  
          String[] atomRefArray = new String[cdkBond.getAtomCount()];
          for (int i = 0; i < cdkBond.getAtomCount(); i++) {
              String atomID = cdkBond.getAtom(i).getID();
              if (atomID == null || atomID.length() == 0) {
                  atomRefArray[i] = "a" + Integer.valueOf(cdkBond.getAtom(i).hashCode()).toString();
              } else {
                  atomRefArray[i] = atomID;
              }
          }
          if (atomRefArray.length == 2) {
              cmlBond.setAtomRefs2(atomRefArray);
          } else {
              cmlBond.setAtomRefs(atomRefArray);
          }
  
          IBond.Order border = cdkBond.getOrder();
          if (border == Order.SINGLE) {
              cmlBond.setOrder("S");
          } else if (border == Order.DOUBLE) {
              cmlBond.setOrder("D");
          } else if (border == Order.TRIPLE) {
              cmlBond.setOrder("T");
          } else {
              CMLScalar scalar = new CMLScalar();
              this.checkPrefix(scalar);
              //            scalar.setDataType("xsd:float");
              scalar.setDictRef("cdk:bondOrder");
              scalar.setTitle("order");
              scalar.setValue(cdkBond.getOrder().numeric());
              cmlBond.appendChild(scalar);
          }
          if (cdkBond.getFlag(CDKConstants.ISAROMATIC)) {
              CMLBondType bType = new CMLBondType();
              bType.setDictRef("cdk:aromaticBond");
              cmlBond.appendChild(bType);
          }
  
          if (cdkBond.getStereo() == IBond.Stereo.UP || cdkBond.getStereo() == IBond.Stereo.DOWN) {
              CMLBondStereo bondStereo = new CMLBondStereo();
              this.checkPrefix(bondStereo);
              if (cdkBond.getStereo() == IBond.Stereo.UP) {
                  bondStereo.setDictRef("cml:W");
                  bondStereo.setXMLContent("W");
              } else {
                  bondStereo.setDictRef("cml:H");
                  bondStereo.setXMLContent("H");
              }
              cmlBond.appendChild(bondStereo);
          }
          if (cdkBond.getProperties().size() > 0) writeProperties(cdkBond, cmlBond);
  
          Iterator<String> elements = customizers.keySet().iterator();
          while (elements.hasNext()) {
              ICMLCustomizer customizer = customizers.get(elements.next());
              try {
                  customizer.customize(cdkBond, cmlBond);
              } catch (Exception exception) {
                  logger.error("Error while customizing CML output with customizer: ", customizer.getClass().getName());
                  logger.debug(exception);
              }
          }
  
          return cmlBond;
      }
focal_method.class_method_signature: Convertor.cdkBondToCMLBond(IBond cdkBond)
focal_method.full_signature: public CMLBond cdkBondToCMLBond(IBond cdkBond)
focal_method.identifier: cdkBondToCMLBond
focal_method.invocations: checkPrefix getID length getID setId hashCode setId getID getAtomCount getAtomCount getID getAtom length toString valueOf hashCode getAtom setAtomRefs2 setAtomRefs getOrder setOrder setOrder setOrder checkPrefix setDictRef setTitle setValue numeric getOrder appendChild getFlag setDictRef appendChild getStereo getStereo checkPrefix getStereo setDictRef setXMLContent setDictRef setXMLContent appendChild size getProperties writeProperties iterator keySet hasNext get next customize error getName getClass debug
focal_method.modifiers: public
focal_method.parameters: (IBond cdkBond)
focal_method.return: CMLBond
focal_method.signature: CMLBond cdkBondToCMLBond(IBond cdkBond)