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(OverlapResolverTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger     = LoggingToolFactory.createLoggingTool(OverlapResolverTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.declarator: sdg        = null
test_class.original_string: StructureDiagramGenerator   sdg        = null;
test_class.type: StructureDiagramGenerator
test_class.var_name: sdg
test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/OverlapResolverTest.java
test_class.identifier: OverlapResolverTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testResolveOverlap2() throws Exception {
          logger.debug("Test case with neither bond nor atom overlap");
          String filename = "data/cml/overlaptest2.cml";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          CMLReader reader = new CMLReader(ins);
          IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
          IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
          //MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
          double score = new OverlapResolver().getOverlapScore(atomContainer, new Vector(), new Vector());
          Assert.assertEquals(0.0, score, 0.0001);
          logger.debug("End of test case with neither bond nor atom overlap");
  
      }
test_case.class_method_signature: OverlapResolverTest.testResolveOverlap2()
test_case.full_signature: @Test public void testResolveOverlap2()
test_case.identifier: testResolveOverlap2
test_case.invocations: debug getResourceAsStream getClassLoader getClass read get getAllAtomContainers getOverlapScore assertEquals debug
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testResolveOverlap2()
focal_class.declarator: logger   = LoggingToolFactory.createLoggingTool(OverlapResolver.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger   = LoggingToolFactory.createLoggingTool(OverlapResolver.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: maxSteps = 10000
focal_class.original_string: int                         maxSteps = 10000;
focal_class.type: int
focal_class.var_name: maxSteps
focal_class.file: tool/sdg/src/main/java/org/openscience/cdk/layout/OverlapResolver.java
focal_class.identifier: OverlapResolver
focal_class.class_method_signature: OverlapResolver.OverlapResolver()
focal_class.full_signature: public  OverlapResolver()
focal_class.identifier: OverlapResolver
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  OverlapResolver()
focal_class.class_method_signature: OverlapResolver.resolveOverlap(IAtomContainer ac, IRingSet sssr)
focal_class.full_signature: public double resolveOverlap(IAtomContainer ac, IRingSet sssr)
focal_class.identifier: resolveOverlap
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, IRingSet sssr)
focal_class.return: double
focal_class.signature: double resolveOverlap(IAtomContainer ac, IRingSet sssr)
focal_class.class_method_signature: OverlapResolver.displace(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.full_signature: public double displace(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.identifier: displace
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.return: double
focal_class.signature: double displace(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.class_method_signature: OverlapResolver.getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.full_signature: public double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.identifier: getOverlapScore
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.return: double
focal_class.signature: double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_class.class_method_signature: OverlapResolver.getAtomOverlapScore(IAtomContainer ac, Vector overlappingAtoms)
focal_class.full_signature: public double getAtomOverlapScore(IAtomContainer ac, Vector overlappingAtoms)
focal_class.identifier: getAtomOverlapScore
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, Vector overlappingAtoms)
focal_class.return: double
focal_class.signature: double getAtomOverlapScore(IAtomContainer ac, Vector overlappingAtoms)
focal_class.class_method_signature: OverlapResolver.getBondOverlapScore(IAtomContainer ac, Vector overlappingBonds)
focal_class.full_signature: public double getBondOverlapScore(IAtomContainer ac, Vector overlappingBonds)
focal_class.identifier: getBondOverlapScore
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, Vector overlappingBonds)
focal_class.return: double
focal_class.signature: double getBondOverlapScore(IAtomContainer ac, Vector overlappingBonds)
focal_class.class_method_signature: OverlapResolver.areIntersected(IBond bond1, IBond bond2)
focal_class.full_signature: public boolean areIntersected(IBond bond1, IBond bond2)
focal_class.identifier: areIntersected
focal_class.modifiers: public
focal_class.parameters: (IBond bond1, IBond bond2)
focal_class.return: boolean
focal_class.signature: boolean areIntersected(IBond bond1, IBond bond2)
focal_method.body: public double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds) {
          double overlapScore = 0;
          overlapScore = getAtomOverlapScore(ac, overlappingAtoms);
          //overlapScore += getBondOverlapScore(ac, overlappingBonds);
          return overlapScore;
      }
focal_method.class_method_signature: OverlapResolver.getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_method.full_signature: public double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_method.identifier: getOverlapScore
focal_method.invocations: getAtomOverlapScore
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)
focal_method.return: double
focal_method.signature: double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds)