test_class.declarator: standAlone = false
test_class.modifier: public
test_class.original_string: public boolean                           standAlone = false;
test_class.type: boolean
test_class.var_name: standAlone
test_class.declarator: logger     = LoggingToolFactory
                                                                  .createLoggingTool(TemplateHandlerTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool              logger     = LoggingToolFactory
                                                                  .createLoggingTool(TemplateHandlerTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.declarator: sp         = null
test_class.modifier: private static
test_class.original_string: private static SmilesParser              sp         = null;
test_class.type: SmilesParser
test_class.var_name: sp
test_class.declarator: sdg        = null
test_class.modifier: private static
test_class.original_string: private static StructureDiagramGenerator sdg        = null;
test_class.type: StructureDiagramGenerator
test_class.var_name: sdg
test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/TemplateHandlerTest.java
test_class.identifier: TemplateHandlerTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test public void convert() throws IOException {
          TemplateHandler templateHandler = new TemplateHandler(SilentChemObjectBuilder.getInstance());
          ByteArrayOutputStream bout = new ByteArrayOutputStream();
          templateHandler.toIdentityTemplateLibrary().store(bout);
          assertThat(new String(bout.toByteArray()), is("C1C2CC3CC1CC(C2)C3 |(-1.07,-1.59,;.38,-1.21,;1.82,-1.59,;1.07,-.29,;-.38,-.67,;-1.82,-.29,;-1.82,1.21,;-.37,1.59,;.38,.29,;1.07,1.21,)|\n"
                                                        + "C12C3C4C1C5C2C3C45 |(.62,-.99,;-.88,-1.12,;-1.23,.43,;.26,.57,;.88,1.12,;1.23,-.43,;-.26,-.57,;-.62,.98,)|\n"
                                                        + "C1C2CC3C4CC5CC(C14)C(C2)C3C5 |(-1.82,2.15,;-.37,2.53,;1.07,2.15,;1.07,.65,;-.38,.27,;-.38,-1.23,;.37,-2.53,;-1.07,-2.15,;-1.07,-.65,;-1.82,.65,;.38,-.27,;.38,1.23,;1.82,-.65,;1.82,-2.15,)|\n"
                                                        + "C1CCC2C(C1)CCC3C4CCCC4CCC23 |(-6.51,.72,;-6.51,-.78,;-5.22,-1.53,;-3.92,-.78,;-3.92,.72,;-5.22,1.47,;-2.62,1.47,;-1.32,.72,;-1.32,-.78,;-.02,-1.53,;1.41,-1.07,;2.29,-2.28,;1.41,-3.49,;-.02,-3.03,;-1.32,-3.78,;-2.62,-3.03,;-2.62,-1.53,)|\n"
                                                        + "C1CCCCCCCCCCCCC1 |(-.04,1.51,;1.26,.76,;1.26,-.74,;2.56,-1.49,;2.56,-2.99,;1.29,-3.72,;1.31,-5.29,;-.09,-5.89,;-1.34,-5.24,;-1.34,-3.74,;-2.63,-2.99,;-2.63,-1.49,;-1.34,-.74,;-1.34,.76,)|\n"));
      }
test_case.class_method_signature: TemplateHandlerTest.convert()
test_case.full_signature: @Test public void convert()
test_case.identifier: convert
test_case.invocations: getInstance store toIdentityTemplateLibrary assertThat toByteArray is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void convert()
focal_class.declarator: LOGGER       = LoggingToolFactory.createLoggingTool(TemplateHandler.class)
focal_class.modifier: private final static
focal_class.original_string: private final static ILoggingTool         LOGGER       = LoggingToolFactory.createLoggingTool(TemplateHandler.class);
focal_class.type: ILoggingTool
focal_class.var_name: LOGGER
focal_class.declarator: templates    = new ArrayList<>()
focal_class.modifier: private final
focal_class.original_string: private final        List<IAtomContainer> templates    = new ArrayList<>();
focal_class.type: List<IAtomContainer>
focal_class.var_name: templates
focal_class.declarator: anonPatterns = new ArrayList<>()
focal_class.modifier: private final
focal_class.original_string: private final        List<Pattern>        anonPatterns = new ArrayList<>();
focal_class.type: List<Pattern>
focal_class.var_name: anonPatterns
focal_class.declarator: elemPatterns = new ArrayList<>()
focal_class.modifier: private final
focal_class.original_string: private final        List<Pattern>        elemPatterns = new ArrayList<>();
focal_class.type: List<Pattern>
focal_class.var_name: elemPatterns
focal_class.declarator: elemAtomMatcher = new AtomMatcher() {
          @Override
          public boolean matches(IAtom a, IAtom b) {
              return a.getAtomicNumber().equals(b.getAtomicNumber());
          }
      }
focal_class.modifier: private final
focal_class.original_string: private final AtomMatcher elemAtomMatcher = new AtomMatcher() {
          @Override
          public boolean matches(IAtom a, IAtom b) {
              return a.getAtomicNumber().equals(b.getAtomicNumber());
          }
      };
focal_class.type: AtomMatcher
focal_class.var_name: elemAtomMatcher
focal_class.declarator: anonAtomMatcher = new AtomMatcher() {
          @Override
          public boolean matches(IAtom a, IAtom b) {
              return true;
          }
      }
focal_class.modifier: private final
focal_class.original_string: private final AtomMatcher anonAtomMatcher = new AtomMatcher() {
          @Override
          public boolean matches(IAtom a, IAtom b) {
              return true;
          }
      };
focal_class.type: AtomMatcher
focal_class.var_name: anonAtomMatcher
focal_class.declarator: anonBondMatcher = new BondMatcher() {
          @Override
          public boolean matches(IBond a, IBond b) {
              return true;
          }
      }
focal_class.modifier: private final
focal_class.original_string: private final BondMatcher anonBondMatcher = new BondMatcher() {
          @Override
          public boolean matches(IBond a, IBond b) {
              return true;
          }
      };
focal_class.type: BondMatcher
focal_class.var_name: anonBondMatcher
focal_class.file: tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java
focal_class.identifier: TemplateHandler
focal_class.class_method_signature: TemplateHandler.TemplateHandler(IChemObjectBuilder builder)
focal_class.full_signature: public  TemplateHandler(IChemObjectBuilder builder)
focal_class.identifier: TemplateHandler
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.signature:  TemplateHandler(IChemObjectBuilder builder)
focal_class.class_method_signature: TemplateHandler.TemplateHandler()
focal_class.full_signature: public  TemplateHandler()
focal_class.identifier: TemplateHandler
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  TemplateHandler()
focal_class.class_method_signature: TemplateHandler.loadTemplates(IChemObjectBuilder builder)
focal_class.full_signature: public void loadTemplates(IChemObjectBuilder builder)
focal_class.identifier: loadTemplates
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void loadTemplates(IChemObjectBuilder builder)
focal_class.class_method_signature: TemplateHandler.addMolecule(IAtomContainer molecule)
focal_class.full_signature: public void addMolecule(IAtomContainer molecule)
focal_class.identifier: addMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: void
focal_class.signature: void addMolecule(IAtomContainer molecule)
focal_class.class_method_signature: TemplateHandler.removeMolecule(IAtomContainer molecule)
focal_class.full_signature: public IAtomContainer removeMolecule(IAtomContainer molecule)
focal_class.identifier: removeMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer removeMolecule(IAtomContainer molecule)
focal_class.class_method_signature: TemplateHandler.mapTemplateExact(IAtomContainer molecule)
focal_class.full_signature: public boolean mapTemplateExact(IAtomContainer molecule)
focal_class.identifier: mapTemplateExact
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: boolean
focal_class.signature: boolean mapTemplateExact(IAtomContainer molecule)
focal_class.class_method_signature: TemplateHandler.mapTemplates(IAtomContainer molecule)
focal_class.full_signature: public boolean mapTemplates(IAtomContainer molecule)
focal_class.identifier: mapTemplates
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: boolean
focal_class.signature: boolean mapTemplates(IAtomContainer molecule)
focal_class.class_method_signature: TemplateHandler.getTemplateCount()
focal_class.full_signature: public int getTemplateCount()
focal_class.identifier: getTemplateCount
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getTemplateCount()
focal_class.class_method_signature: TemplateHandler.getTemplateAt(int position)
focal_class.full_signature: public IAtomContainer getTemplateAt(int position)
focal_class.identifier: getTemplateAt
focal_class.modifiers: public
focal_class.parameters: (int position)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getTemplateAt(int position)
focal_class.class_method_signature: TemplateHandler.getMappedSubstructures(IAtomContainer molecule)
focal_class.full_signature: public IAtomContainerSet getMappedSubstructures(IAtomContainer molecule)
focal_class.identifier: getMappedSubstructures
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtomContainerSet
focal_class.signature: IAtomContainerSet getMappedSubstructures(IAtomContainer molecule)
focal_class.class_method_signature: TemplateHandler.createSingleton(IAtomContainer template)
focal_class.full_signature: public static TemplateHandler createSingleton(IAtomContainer template)
focal_class.identifier: createSingleton
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer template)
focal_class.return: TemplateHandler
focal_class.signature: TemplateHandler createSingleton(IAtomContainer template)
focal_class.class_method_signature: TemplateHandler.createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols)
focal_class.full_signature: public static TemplateHandler createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols)
focal_class.identifier: createFromSubstructure
focal_class.modifiers: public static
focal_class.parameters: (Pattern ptrn, Iterable<IAtomContainer> mols)
focal_class.return: TemplateHandler
focal_class.signature: TemplateHandler createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols)
focal_class.class_method_signature: TemplateHandler.createFromSubstructure(Pattern ptrn, IAtomContainer mol)
focal_class.full_signature: public static TemplateHandler createFromSubstructure(Pattern ptrn, IAtomContainer mol)
focal_class.identifier: createFromSubstructure
focal_class.modifiers: public static
focal_class.parameters: (Pattern ptrn, IAtomContainer mol)
focal_class.return: TemplateHandler
focal_class.signature: TemplateHandler createFromSubstructure(Pattern ptrn, IAtomContainer mol)
focal_class.class_method_signature: TemplateHandler.toIdentityTemplateLibrary()
focal_class.full_signature:  IdentityTemplateLibrary toIdentityTemplateLibrary()
focal_class.identifier: toIdentityTemplateLibrary
focal_class.parameters: ()
focal_class.return: IdentityTemplateLibrary
focal_class.signature: IdentityTemplateLibrary toIdentityTemplateLibrary()
focal_method.body: IdentityTemplateLibrary toIdentityTemplateLibrary() {
          IdentityTemplateLibrary lib = IdentityTemplateLibrary.empty();
          for (IAtomContainer mol : templates) {
              lib.add(AtomContainerManipulator.anonymise(mol));
          }
          return lib;
      }
focal_method.class_method_signature: TemplateHandler.toIdentityTemplateLibrary()
focal_method.full_signature:  IdentityTemplateLibrary toIdentityTemplateLibrary()
focal_method.identifier: toIdentityTemplateLibrary
focal_method.invocations: empty add anonymise
focal_method.parameters: ()
focal_method.return: IdentityTemplateLibrary
focal_method.signature: IdentityTemplateLibrary toIdentityTemplateLibrary()