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 testAtomHybridizationDescriptorTest() throws ClassNotFoundException, CDKException, java.lang.Exception {
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("C#CC=CC"); //
          addExplicitHydrogens(mol);
          IAtomType.Hybridization[] expectedStates = new IAtomType.Hybridization[]{IAtomType.Hybridization.SP1,
                  IAtomType.Hybridization.SP1, IAtomType.Hybridization.SP2, IAtomType.Hybridization.SP2,
                  IAtomType.Hybridization.SP3};
          for (int i = 0; i < expectedStates.length; i++) {
              Assert.assertEquals(expectedStates[i].ordinal(), ((IntegerResult) descriptor.calculate(mol.getAtom(i), mol)
                      .getValue()).intValue());
          }
      }
test_case.class_method_signature: AtomHybridizationDescriptorTest.testAtomHybridizationDescriptorTest()
test_case.full_signature: @Test public void testAtomHybridizationDescriptorTest()
test_case.identifier: testAtomHybridizationDescriptorTest
test_case.invocations: getInstance parseSmiles addExplicitHydrogens assertEquals ordinal intValue getValue calculate getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAtomHybridizationDescriptorTest()
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)