test_class.file: tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java
test_class.identifier: TemplateHandler3DTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testAnonFingerprints() throws Exception {
          BitSet[] expected = new BitSet[]{
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
              parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}")};
  
          String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          List<IBitFingerprint> data = new TemplateExtractor().makeFingerprintsFromSdf(true, true,
                                                                                       new HashMap<String, Integer>(), new BufferedReader(new InputStreamReader(ins)), 10);
          QueryChemObject obj = new QueryChemObject(DefaultChemObjectBuilder.getInstance());
          obj.getBuilder();
          for (int i = 0; i < data.size(); i++) {
              IBitFingerprint bs = data.get(i);
              Assert.assertEquals(expected[i], bs.asBitSet());
          }
      }
test_case.class_method_signature: TemplateHandler3DTest.testAnonFingerprints()
test_case.full_signature: @Test public void testAnonFingerprints()
test_case.identifier: testAnonFingerprints
test_case.invocations: parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet parseBitSet getResourceAsStream getClassLoader getClass makeFingerprintsFromSdf getInstance getBuilder size get assertEquals asBitSet
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAnonFingerprints()
focal_class.declarator: builder       = SilentChemObjectBuilder.getInstance()
focal_class.modifier: private static final
focal_class.original_string: private static final IChemObjectBuilder builder       = SilentChemObjectBuilder.getInstance();
focal_class.type: IChemObjectBuilder
focal_class.var_name: builder
focal_class.declarator: TEMPLATE_PATH = "data/ringTemplateStructures.sdf.gz"
focal_class.modifier: public static final
focal_class.original_string: public static final  String             TEMPLATE_PATH = "data/ringTemplateStructures.sdf.gz";
focal_class.type: String
focal_class.var_name: TEMPLATE_PATH
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: queries   = new ArrayList<>()
focal_class.modifier: private final
focal_class.original_string: private final List<IQueryAtomContainer> queries   = new ArrayList<>();
focal_class.type: List<IQueryAtomContainer>
focal_class.var_name: queries
focal_class.declarator: patterns  = new ArrayList<>()
focal_class.modifier: private final
focal_class.original_string: private final List<Pattern>             patterns  = new ArrayList<>();
focal_class.type: List<Pattern>
focal_class.var_name: patterns
focal_class.declarator: self = null
focal_class.modifier: private static
focal_class.original_string: private static TemplateHandler3D self = null;
focal_class.type: TemplateHandler3D
focal_class.var_name: self
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(TemplateHandler3D.class)
focal_class.modifier: private final
focal_class.original_string: private final ILoggingTool logger = LoggingToolFactory.createLoggingTool(TemplateHandler3D.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: universalIsomorphismTester = new UniversalIsomorphismTester()
focal_class.modifier: private
focal_class.original_string: private UniversalIsomorphismTester universalIsomorphismTester = new UniversalIsomorphismTester();
focal_class.type: UniversalIsomorphismTester
focal_class.var_name: universalIsomorphismTester
focal_class.file: tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
focal_class.identifier: TemplateHandler3D
focal_class.class_method_signature: TemplateHandler3D.TemplateHandler3D()
focal_class.full_signature: private  TemplateHandler3D()
focal_class.identifier: TemplateHandler3D
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.signature:  TemplateHandler3D()
focal_class.class_method_signature: TemplateHandler3D.getInstance()
focal_class.full_signature: public static TemplateHandler3D getInstance()
focal_class.identifier: getInstance
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: TemplateHandler3D
focal_class.signature: TemplateHandler3D getInstance()
focal_class.class_method_signature: TemplateHandler3D.addTemplateMol(IAtomContainer mol)
focal_class.full_signature: private void addTemplateMol(IAtomContainer mol)
focal_class.identifier: addTemplateMol
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void addTemplateMol(IAtomContainer mol)
focal_class.class_method_signature: TemplateHandler3D.loadTemplates()
focal_class.full_signature: private void loadTemplates()
focal_class.identifier: loadTemplates
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void loadTemplates()
focal_class.class_method_signature: TemplateHandler3D.getBitSetFromFile(StringTokenizer st)
focal_class.full_signature: public static BitSet getBitSetFromFile(StringTokenizer st)
focal_class.identifier: getBitSetFromFile
focal_class.modifiers: public static
focal_class.parameters: (StringTokenizer st)
focal_class.return: BitSet
focal_class.signature: BitSet getBitSetFromFile(StringTokenizer st)
focal_class.class_method_signature: TemplateHandler3D.getLargestRingSet(List<IRingSet> ringSystems)
focal_class.full_signature: public IRingSet getLargestRingSet(List<IRingSet> ringSystems)
focal_class.identifier: getLargestRingSet
focal_class.modifiers: public
focal_class.parameters: (List<IRingSet> ringSystems)
focal_class.return: IRingSet
focal_class.signature: IRingSet getLargestRingSet(List<IRingSet> ringSystems)
focal_class.class_method_signature: TemplateHandler3D.getAllInOneContainer(IRingSet ringSet)
focal_class.full_signature: private IAtomContainer getAllInOneContainer(IRingSet ringSet)
focal_class.identifier: getAllInOneContainer
focal_class.modifiers: private
focal_class.parameters: (IRingSet ringSet)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAllInOneContainer(IRingSet ringSet)
focal_class.class_method_signature: TemplateHandler3D.mapTemplates(IAtomContainer ringSystems,
                               double numberOfRingAtoms)
focal_class.full_signature: @Deprecated public void mapTemplates(IAtomContainer ringSystems,
                               double numberOfRingAtoms)
focal_class.identifier: mapTemplates
focal_class.modifiers: @Deprecated public
focal_class.parameters: (IAtomContainer ringSystems,
                               double numberOfRingAtoms)
focal_class.return: void
focal_class.signature: void mapTemplates(IAtomContainer ringSystems,
                               double numberOfRingAtoms)
focal_class.class_method_signature: TemplateHandler3D.isExactMatch(IAtomContainer query,
                                   Map<IChemObject, IChemObject> mapping)
focal_class.full_signature: private boolean isExactMatch(IAtomContainer query,
                                   Map<IChemObject, IChemObject> mapping)
focal_class.identifier: isExactMatch
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer query,
                                   Map<IChemObject, IChemObject> mapping)
focal_class.return: boolean
focal_class.signature: boolean isExactMatch(IAtomContainer query,
                                   Map<IChemObject, IChemObject> mapping)
focal_class.class_method_signature: TemplateHandler3D.mapTemplates(IAtomContainer mol, int numberOfRingAtoms)
focal_class.full_signature: public void mapTemplates(IAtomContainer mol, int numberOfRingAtoms)
focal_class.identifier: mapTemplates
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer mol, int numberOfRingAtoms)
focal_class.return: void
focal_class.signature: void mapTemplates(IAtomContainer mol, int numberOfRingAtoms)
focal_class.class_method_signature: TemplateHandler3D.assignCoords(IAtomContainer template,
                                Map<IChemObject, IChemObject> map)
focal_class.full_signature: private void assignCoords(IAtomContainer template,
                                Map<IChemObject, IChemObject> map)
focal_class.identifier: assignCoords
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer template,
                                Map<IChemObject, IChemObject> map)
focal_class.return: void
focal_class.signature: void assignCoords(IAtomContainer template,
                                Map<IChemObject, IChemObject> map)
focal_class.class_method_signature: TemplateHandler3D.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: TemplateHandler3D.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_method.body: public static TemplateHandler3D getInstance() throws CDKException {
          if (self == null) {
              self = new TemplateHandler3D();
          }
          return self;
      }
focal_method.class_method_signature: TemplateHandler3D.getInstance()
focal_method.full_signature: public static TemplateHandler3D getInstance()
focal_method.identifier: getInstance
focal_method.modifiers: public static
focal_method.parameters: ()
focal_method.return: TemplateHandler3D
focal_method.signature: TemplateHandler3D getInstance()