test_class.file: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptorTest.java
test_class.identifier: AtomHybridizationDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testBug1701073() throws Exception {
  
          String[] smiles = new String[]{"C1CCCC=2[C]1(C(=O)NN2)C", "C1CCCC=2[C]1(C(=O)NN2)O",
                  "C[Si](C)(C)[CH](Br)CC(F)(Br)F", "c1(ccc(cc1)O)C#N", "CCN(CC)C#CC#CC(=O)OC",
                  "C(#CN1CCCCC1)[Sn](C)(C)C", "c1([As+](c2ccccc2)(c2ccccc2)C)ccccc1.[I-]",
                  "c1(noc(n1)CCC(=O)N(CC)CC)c1ccc(cc1)C", "c1c(c(ccc1)O)/C=N/CCCC", "c1(ccc(cc1)C#Cc1ccc(cc1)C#C)OC"};
  
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol;
          Iterator<IAtom> atoms;
  
          for (String smile : smiles) {
              mol = sp.parseSmiles(smile);
              addImplicitHydrogens(mol);
              AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
              atoms = mol.atoms().iterator();
              while (atoms.hasNext()) {
                  IAtom atom = atoms.next();
                  ((IntegerResult) descriptor.calculate(atom, mol).getValue()).intValue();
              }
          }
  
      }
test_case.class_method_signature: AtomHybridizationDescriptorTest.testBug1701073()
test_case.full_signature: @Test public void testBug1701073()
test_case.identifier: testBug1701073
test_case.invocations: getInstance parseSmiles addImplicitHydrogens convertImplicitToExplicitHydrogens iterator atoms hasNext next intValue getValue calculate
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testBug1701073()
focal_class.declarator: atman   = null
focal_class.original_string: AtomTypeManipulator atman   = null;
focal_class.type: AtomTypeManipulator
focal_class.var_name: atman
focal_class.declarator: atom    = null
focal_class.original_string: IAtom               atom    = null;
focal_class.type: IAtom
focal_class.var_name: atom
focal_class.declarator: matched = null
focal_class.original_string: IAtomType           matched = null;
focal_class.type: IAtomType
focal_class.var_name: matched
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java
focal_class.identifier: AtomHybridizationDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: AtomHybridizationDescriptor.getSpecification()
focal_class.full_signature: @Override public DescriptorSpecification getSpecification()
focal_class.identifier: getSpecification
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: DescriptorSpecification
focal_class.signature: DescriptorSpecification getSpecification()
focal_class.class_method_signature: AtomHybridizationDescriptor.setParameters(Object[] params)
focal_class.full_signature: @Override public void setParameters(Object[] params)
focal_class.identifier: setParameters
focal_class.modifiers: @Override public
focal_class.parameters: (Object[] params)
focal_class.return: void
focal_class.signature: void setParameters(Object[] params)
focal_class.class_method_signature: AtomHybridizationDescriptor.getParameters()
focal_class.full_signature: @Override public Object[] getParameters()
focal_class.identifier: getParameters
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Object[]
focal_class.signature: Object[] getParameters()
focal_class.class_method_signature: AtomHybridizationDescriptor.getDescriptorNames()
focal_class.full_signature: @Override public String[] getDescriptorNames()
focal_class.identifier: getDescriptorNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getDescriptorNames()
focal_class.class_method_signature: AtomHybridizationDescriptor.getDummyDescriptorValue(Exception e)
focal_class.full_signature: private DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.identifier: getDummyDescriptorValue
focal_class.modifiers: private
focal_class.parameters: (Exception e)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.class_method_signature: AtomHybridizationDescriptor.calculate(IAtom atom, IAtomContainer container)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom, IAtomContainer container)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_class.class_method_signature: AtomHybridizationDescriptor.getParameterNames()
focal_class.full_signature: @Override public String[] getParameterNames()
focal_class.identifier: getParameterNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getParameterNames()
focal_class.class_method_signature: AtomHybridizationDescriptor.getParameterType(String name)
focal_class.full_signature: @Override public Object getParameterType(String name)
focal_class.identifier: getParameterType
focal_class.modifiers: @Override public
focal_class.parameters: (String name)
focal_class.return: Object
focal_class.signature: Object getParameterType(String name)
focal_class.superclass: extends AbstractAtomicDescriptor
focal_method.body: @Override
      public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
          try {
              matched = CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom);
          } catch (CDKException e) {
              return getDummyDescriptorValue(e);
          }
          if (matched == null) {
              int atnum = container.indexOf(atom);
              return getDummyDescriptorValue(new CDKException("The matched atom type was null (atom number " + atnum
                      + ") " + atom.getSymbol()));
          }
          Hybridization atomHybridization = matched.getHybridization();
          IntegerResult result = new IntegerResult(atomHybridization == null ? 0 : atomHybridization.ordinal());
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), result,
                  getDescriptorNames());
      }
focal_method.class_method_signature: AtomHybridizationDescriptor.calculate(IAtom atom, IAtomContainer container)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_method.identifier: calculate
focal_method.invocations: findMatchingAtomType getInstance getBuilder getDummyDescriptorValue indexOf getDummyDescriptorValue getSymbol getHybridization ordinal getSpecification getParameterNames getParameters getDescriptorNames
focal_method.modifiers: @Override public
focal_method.parameters: (IAtom atom, IAtomContainer container)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtom atom, IAtomContainer container)