test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingTest.java
test_class.identifier: SingleMappingTest
test_case.body: @Test
      public void testGetOverLaps() throws CDKException {
          IAtom atomSource = new Atom("R");
          IAtom atomTarget = new Atom("R");
          IAtomContainer source = new AtomContainer();
          source.addAtom(atomSource);
          IAtomContainer target = new AtomContainer();
          target.addAtom(atomTarget);
          boolean removeHydrogen = false;
          SingleMapping instance = new SingleMapping();
          assertNotNull(instance.getOverLaps(source, target, removeHydrogen));
      }
test_case.class_method_signature: SingleMappingTest.testGetOverLaps()
test_case.full_signature: @Test public void testGetOverLaps()
test_case.identifier: testGetOverLaps
test_case.invocations: addAtom addAtom assertNotNull getOverLaps
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetOverLaps()
focal_class.declarator: source             = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer          source             = null;
focal_class.type: IAtomContainer
focal_class.var_name: source
focal_class.declarator: target             = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer          target             = null;
focal_class.type: IAtomContainer
focal_class.var_name: target
focal_class.declarator: mappings           = null
focal_class.modifier: private
focal_class.original_string: private List<Map<IAtom, IAtom>> mappings           = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: mappings
focal_class.declarator: connectedBondOrder = null
focal_class.modifier: private
focal_class.original_string: private Map<Integer, Double>    connectedBondOrder = null;
focal_class.type: Map<Integer, Double>
focal_class.var_name: connectedBondOrder
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java
focal_class.identifier: SingleMapping
focal_class.class_method_signature: SingleMapping.SingleMapping()
focal_class.full_signature: public  SingleMapping()
focal_class.identifier: SingleMapping
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  SingleMapping()
focal_class.class_method_signature: SingleMapping.getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_class.full_signature: protected List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_class.identifier: getOverLaps
focal_class.modifiers: protected
focal_class.parameters: (IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_class.return: List<Map<IAtom, IAtom>>
focal_class.signature: List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_class.class_method_signature: SingleMapping.getOverLaps(IQueryAtomContainer source, IAtomContainer target,
              boolean removeHydrogen)
focal_class.full_signature: protected List<Map<IAtom, IAtom>> getOverLaps(IQueryAtomContainer source, IAtomContainer target,
              boolean removeHydrogen)
focal_class.identifier: getOverLaps
focal_class.modifiers: protected
focal_class.parameters: (IQueryAtomContainer source, IAtomContainer target,
              boolean removeHydrogen)
focal_class.return: List<Map<IAtom, IAtom>>
focal_class.signature: List<Map<IAtom, IAtom>> getOverLaps(IQueryAtomContainer source, IAtomContainer target,
              boolean removeHydrogen)
focal_class.class_method_signature: SingleMapping.setSourceSingleAtomMap(IQueryAtomContainer source, boolean removeHydrogen)
focal_class.full_signature: private void setSourceSingleAtomMap(IQueryAtomContainer source, boolean removeHydrogen)
focal_class.identifier: setSourceSingleAtomMap
focal_class.modifiers: private
focal_class.parameters: (IQueryAtomContainer source, boolean removeHydrogen)
focal_class.return: void
focal_class.signature: void setSourceSingleAtomMap(IQueryAtomContainer source, boolean removeHydrogen)
focal_class.class_method_signature: SingleMapping.setSourceSingleAtomMap(boolean removeHydrogen)
focal_class.full_signature: private void setSourceSingleAtomMap(boolean removeHydrogen)
focal_class.identifier: setSourceSingleAtomMap
focal_class.modifiers: private
focal_class.parameters: (boolean removeHydrogen)
focal_class.return: void
focal_class.signature: void setSourceSingleAtomMap(boolean removeHydrogen)
focal_class.class_method_signature: SingleMapping.setTargetSingleAtomMap(boolean removeHydrogen)
focal_class.full_signature: private void setTargetSingleAtomMap(boolean removeHydrogen)
focal_class.identifier: setTargetSingleAtomMap
focal_class.modifiers: private
focal_class.parameters: (boolean removeHydrogen)
focal_class.return: void
focal_class.signature: void setTargetSingleAtomMap(boolean removeHydrogen)
focal_class.class_method_signature: SingleMapping.postFilter()
focal_class.full_signature: private void postFilter()
focal_class.identifier: postFilter
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void postFilter()
focal_class.class_method_signature: SingleMapping.sortByValue(Map<K, V> map)
focal_class.full_signature: private Map<K, V> sortByValue(Map<K, V> map)
focal_class.identifier: sortByValue
focal_class.modifiers: private
focal_class.parameters: (Map<K, V> map)
focal_class.return: Map<K, V>
focal_class.signature: Map<K, V> sortByValue(Map<K, V> map)
focal_method.body: protected List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
              throws CDKException {
  
          mappings = new ArrayList<Map<IAtom, IAtom>>();
          connectedBondOrder = new TreeMap<Integer, Double>();
          this.source = source;
          this.target = target;
  
          if (source.getAtomCount() == 1 || (source.getAtomCount() > 0 && source.getBondCount() == 0)) {
              setSourceSingleAtomMap(removeHydrogen);
          }
          if (target.getAtomCount() == 1 || (target.getAtomCount() > 0 && target.getBondCount() == 0)) {
              setTargetSingleAtomMap(removeHydrogen);
          }
  
          postFilter();
          return mappings;
      }
focal_method.class_method_signature: SingleMapping.getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_method.full_signature: protected List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_method.identifier: getOverLaps
focal_method.invocations: getAtomCount getAtomCount getBondCount setSourceSingleAtomMap getAtomCount getAtomCount getBondCount setTargetSingleAtomMap postFilter
focal_method.modifiers: protected
focal_method.parameters: (IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
focal_method.return: List<Map<IAtom, IAtom>>
focal_method.signature: List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)