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 testFingerprints() throws Exception {
          BitSet[] expected = new BitSet[]{
              parseBitSet("{3, 5, 8, 18, 29, 33, 39, 65, 71, 90, 105, 125, 140, 170, 182, 192, 199, 203, 209, 213, 226, 271, 272, 287, 301, 304, 319, 368, 386, 423, 433, 540, 590, 605, 618, 620, 629, 641, 649, 672, 681, 690, 694, 696, 697, 716, 726, 745, 748, 751, 760, 765, 775, 777, 780, 792, 799, 805, 810, 825, 829, 836, 844, 850, 876, 880, 882, 888, 899, 914, 924, 929, 932, 935, 967, 971, 1004, 1013, 1015, 1023}"),
              parseBitSet("{3, 8, 18, 29, 33, 65, 90, 101, 109, 117, 125, 127, 140, 170, 190, 192, 209, 213, 218, 226, 271, 272, 286, 287, 301, 304, 319, 386, 423, 433, 566, 590, 605, 618, 629, 641, 646, 649, 672, 690, 694, 696, 716, 726, 745, 748, 765, 775, 777, 780, 783, 792, 805, 810, 825, 829, 836, 844, 850, 876, 882, 899, 914, 924, 932, 934, 956, 967, 971, 994, 1004, 1013, 1015, 1023}"),
              parseBitSet("{3, 18, 26, 32, 33, 43, 140, 155, 188, 189, 226, 238, 262, 267, 287, 315, 319, 326, 375, 450, 577, 629, 644, 690, 719, 732, 745, 746, 751, 775, 847, 850, 881, 959, 971, 995, 1015, 1019}"),
              parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
              parseBitSet("{3, 13, 18, 22, 26, 29, 33, 43, 71, 85, 90, 101, 103, 109, 117, 118, 125, 127, 140, 145, 153, 155, 182, 188, 189, 190, 199, 218, 225, 226, 238, 269, 272, 286, 287, 301, 304, 315, 319, 326, 370, 375, 386, 408, 423, 433, 450, 493, 502, 556, 566, 577, 590, 598, 605, 617, 618, 629, 644, 649, 672, 679, 690, 691, 694, 696, 716, 719, 727, 732, 745, 748, 751, 760, 762, 765, 775, 777, 783, 805, 806, 810, 821, 829, 844, 847, 850, 876, 888, 899, 914, 923, 924, 926, 927, 929, 934, 956, 959, 966, 971, 990, 995, 1006, 1013, 1015, 1019}"),
              parseBitSet("{3, 18, 29, 33, 53, 65, 90, 105, 125, 192, 203, 269, 271, 272, 293, 301, 319, 345, 364, 376, 386, 433, 540, 569, 590, 605, 618, 641, 649, 672, 675, 681, 696, 745, 748, 765, 780, 790, 798, 799, 801, 805, 825, 829, 836, 837, 844, 853, 876, 882, 891, 899, 914, 924, 932, 967, 996, 1004, 1013}"),
              parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
              parseBitSet("{3, 18, 33, 192, 319, 745, 780, 882}"),
              parseBitSet("{3, 18, 26, 32, 33, 43, 140, 155, 188, 189, 226, 238, 262, 267, 287, 315, 319, 326, 375, 450, 577, 629, 644, 690, 719, 732, 745, 746, 751, 775, 847, 850, 881, 959, 971, 995, 1015, 1019}"),
              parseBitSet("{3, 18, 29, 33, 90, 105, 125, 272, 280, 301, 433, 521, 590, 618, 651, 672, 696, 698, 745, 760, 829, 844, 876, 890, 899, 924, 1013}")};
  
          String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          List<IBitFingerprint> data = new TemplateExtractor().makeFingerprintsFromSdf(true, false,
                  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.testFingerprints()
test_case.full_signature: @Test public void testFingerprints()
test_case.identifier: testFingerprints
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 testFingerprints()
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()