test_class.file: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
test_class.identifier: AtomHybridizationVSEPRDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testAtomHybridizationVSEPRDescriptorTest_5() throws ClassNotFoundException, CDKException,
              java.lang.Exception {
          AtomHybridizationVSEPRDescriptor descriptor = new AtomHybridizationVSEPRDescriptor();
  
          //XeF4
          IAtomContainer molecule = new AtomContainer();
          Atom Xe1 = new Atom("Xe");
          Atom F2 = new Atom("F");
          Atom F3 = new Atom("F");
          Atom F4 = new Atom("F");
          Atom F5 = new Atom("F");
          molecule.addAtom(Xe1);
          molecule.addAtom(F2);
          molecule.addAtom(F3);
          molecule.addAtom(F4);
          molecule.addAtom(F5);
          Bond b1 = new Bond(Xe1, F2, IBond.Order.SINGLE);
          Bond b2 = new Bond(Xe1, F3, IBond.Order.SINGLE);
          Bond b3 = new Bond(Xe1, F4, IBond.Order.SINGLE);
          Bond b4 = new Bond(Xe1, F5, IBond.Order.SINGLE);
          molecule.addBond(b1);
          molecule.addBond(b2);
          molecule.addBond(b3);
          molecule.addBond(b4);
  
          assertAtomTypesPerceived(molecule);
          Assert.assertEquals(IAtomType.Hybridization.SP3D2.ordinal(),
                  ((IntegerResult) descriptor.calculate(molecule.getAtom(0), molecule).getValue()).intValue());
  
      }
test_case.class_method_signature: AtomHybridizationVSEPRDescriptorTest.testAtomHybridizationVSEPRDescriptorTest_5()
test_case.full_signature: @Test public void testAtomHybridizationVSEPRDescriptorTest_5()
test_case.identifier: testAtomHybridizationVSEPRDescriptorTest_5
test_case.invocations: addAtom addAtom addAtom addAtom addAtom addBond addBond addBond addBond assertAtomTypesPerceived assertEquals ordinal intValue getValue calculate getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAtomHybridizationVSEPRDescriptorTest_5()
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
focal_class.identifier: AtomHybridizationVSEPRDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: AtomHybridizationVSEPRDescriptor.AtomHybridizationVSEPRDescriptor()
focal_class.full_signature: public  AtomHybridizationVSEPRDescriptor()
focal_class.identifier: AtomHybridizationVSEPRDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  AtomHybridizationVSEPRDescriptor()
focal_class.class_method_signature: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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: AtomHybridizationVSEPRDescriptor.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) {
          IAtomType atomType;
          try {
              atomType = CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom);
          } catch (CDKException e) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
                      (int) Double.NaN), // does that work??
                      getDescriptorNames(), new CDKException("Atom type was null"));
          }
          if (atomType == null) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
                      (int) Double.NaN), // does that work??
                      getDescriptorNames(), new CDKException("Atom type was null"));
  
          }
  
          if (atomType.getHybridization() == null) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
                      (int) Double.NaN), // does that work??
                      getDescriptorNames(), new CDKException("Hybridization was null"));
          }
          int hybridizationCDK = atomType.getHybridization().ordinal();
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
                  hybridizationCDK), getDescriptorNames());
      }
focal_method.class_method_signature: AtomHybridizationVSEPRDescriptor.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 getSpecification getParameterNames getParameters getDescriptorNames getSpecification getParameterNames getParameters getDescriptorNames getHybridization getSpecification getParameterNames getParameters getDescriptorNames ordinal getHybridization 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)