test_class.declarator: sp      = new SmilesParser(DefaultChemObjectBuilder.getInstance())
test_class.modifier: private
test_class.original_string: private SmilesParser            sp      = new SmilesParser(DefaultChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: sp
test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private
test_class.original_string: private IChemObjectBuilder      builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.declarator: lpcheck = new LonePairElectronChecker()
test_class.modifier: private
test_class.original_string: private LonePairElectronChecker lpcheck = new LonePairElectronChecker();
test_class.type: LonePairElectronChecker
test_class.var_name: lpcheck
test_class.file: legacy/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java
test_class.identifier: IPMolecularLearningDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test
      @Category(SlowTest.class)
      public void testIPDescriptor0() throws Exception {
  
          IAtomContainer mol = builder.newInstance(IAtomContainer.class);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addBond(0, 1, Order.SINGLE);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addBond(1, 2, Order.SINGLE);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addBond(1, 3, Order.SINGLE);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addBond(3, 4, Order.SINGLE);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));
          mol.addBond(3, 5, Order.SINGLE);
  
          addExplicitHydrogens(mol);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
          lpcheck.saturate(mol);
  
          IPMolecularLearningDescriptor descriptor = new IPMolecularLearningDescriptor();
          double result = ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue();
          double resultAccordingNIST = 0.0;
  
          Assert.assertEquals(resultAccordingNIST, result, 0.0001);
      }
test_case.class_method_signature: IPMolecularLearningDescriptorTest.testIPDescriptor0()
test_case.full_signature: @Test @Category(SlowTest.class) public void testIPDescriptor0()
test_case.identifier: testIPDescriptor0
test_case.invocations: newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate doubleValue getValue calculate assertEquals
test_case.modifiers: @Test @Category(SlowTest.class) public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testIPDescriptor0()
focal_class.declarator: addlp = true
focal_class.modifier: private
focal_class.original_string: private boolean               addlp = true;
focal_class.type: boolean
focal_class.var_name: addlp
focal_class.declarator: names = {"MolIP"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] names = {"MolIP"};
focal_class.type: String[]
focal_class.var_name: names
focal_class.file: legacy/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptor.java
focal_class.identifier: IPMolecularLearningDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: IPMolecularLearningDescriptor.IPMolecularLearningDescriptor()
focal_class.full_signature: public  IPMolecularLearningDescriptor()
focal_class.identifier: IPMolecularLearningDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  IPMolecularLearningDescriptor()
focal_class.class_method_signature: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtomContainer atomContainer)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtomContainer atomContainer)
focal_class.class_method_signature: IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
focal_class.full_signature: public DescriptorValue calculatePlus(IAtomContainer container)
focal_class.identifier: calculatePlus
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculatePlus(IAtomContainer container)
focal_class.class_method_signature: IPMolecularLearningDescriptor.arrangingEnergy(ArrayList<Double> array)
focal_class.full_signature: private DoubleArrayResult arrangingEnergy(ArrayList<Double> array)
focal_class.identifier: arrangingEnergy
focal_class.modifiers: private
focal_class.parameters: (ArrayList<Double> array)
focal_class.return: DoubleArrayResult
focal_class.signature: DoubleArrayResult arrangingEnergy(ArrayList<Double> array)
focal_class.class_method_signature: IPMolecularLearningDescriptor.getDescriptorResultType()
focal_class.full_signature: @Override public IDescriptorResult getDescriptorResultType()
focal_class.identifier: getDescriptorResultType
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IDescriptorResult
focal_class.signature: IDescriptorResult getDescriptorResultType()
focal_class.class_method_signature: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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 AbstractMolecularDescriptor
focal_method.body: @Override
      public DescriptorValue calculate(IAtomContainer atomContainer) {
          IAtomContainer local;
          if (addlp) {
              try {
                  local = (IAtomContainer) atomContainer.clone();
                  LonePairElectronChecker lpcheck = new LonePairElectronChecker();
                  lpcheck.saturate(local);
              } catch (CloneNotSupportedException e) {
                  return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                          Double.NaN), getDescriptorNames(), e);
              } catch (CDKException e) {
                  return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                          Double.NaN), getDescriptorNames(), e);
              }
  
          } else
              local = atomContainer;
  
          DoubleResult value;
          try {
              value = new DoubleResult(((DoubleArrayResult) calculatePlus(local).getValue()).get(0));
          } catch (CDKException e) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                      Double.NaN), getDescriptorNames(), e);
          }
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), value,
                  getDescriptorNames());
      }
focal_method.class_method_signature: IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtomContainer atomContainer)
focal_method.identifier: calculate
focal_method.invocations: clone saturate getSpecification getParameterNames getParameters getDescriptorNames getSpecification getParameterNames getParameters getDescriptorNames get getValue calculatePlus getSpecification getParameterNames getParameters getDescriptorNames getSpecification getParameterNames getParameters getDescriptorNames
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainer atomContainer)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtomContainer atomContainer)