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 testBug_2787332_triclosan() throws Exception {
          IAtomContainer mol = builder.newInstance(IAtomContainer.class);
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//0
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//1
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//2
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//3
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//4
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//5
          mol.addAtom(builder.newInstance(IAtom.class, "O"));//6
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//7
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//8
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//9
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//10
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//11
          mol.addAtom(builder.newInstance(IAtom.class, "C"));//12
          mol.addAtom(builder.newInstance(IAtom.class, "Cl"));//13
          mol.addAtom(builder.newInstance(IAtom.class, "Cl"));//14
          mol.addAtom(builder.newInstance(IAtom.class, "O"));//15
          mol.addAtom(builder.newInstance(IAtom.class, "Cl"));//16
  
          mol.addBond(0, 1, Order.SINGLE);
          mol.addBond(1, 2, Order.DOUBLE);
          mol.addBond(2, 3, Order.SINGLE);
          mol.addBond(3, 4, Order.DOUBLE);
          mol.addBond(4, 5, Order.SINGLE);
          mol.addBond(5, 0, Order.DOUBLE);
          mol.addBond(5, 6, Order.SINGLE);
          mol.addBond(6, 7, Order.SINGLE);
          mol.addBond(7, 8, Order.DOUBLE);
          mol.addBond(8, 9, Order.SINGLE);
          mol.addBond(9, 10, Order.DOUBLE);
          mol.addBond(10, 11, Order.SINGLE);
          mol.addBond(11, 12, Order.DOUBLE);
          mol.addBond(12, 7, Order.SINGLE);
          mol.addBond(0, 13, Order.SINGLE);
          mol.addBond(2, 14, Order.SINGLE);
          mol.addBond(10, 16, Order.SINGLE);
          mol.addBond(12, 15, Order.SINGLE);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
          CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol.getBuilder());
          adder.addImplicitHydrogens(mol);
          AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
  
          IPMolecularLearningDescriptor descriptor = new IPMolecularLearningDescriptor();
          DoubleArrayResult dar = ((DoubleArrayResult) ((IPMolecularLearningDescriptor) descriptor).calculatePlus(mol)
                  .getValue());
  
          Assert.assertEquals(6, dar.length());
      }
test_case.class_method_signature: IPMolecularLearningDescriptorTest.testBug_2787332_triclosan()
test_case.full_signature: @Test @Category(SlowTest.class) public void testBug_2787332_triclosan()
test_case.identifier: testBug_2787332_triclosan
test_case.invocations: newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond percieveAtomTypesAndConfigureAtoms getInstance getBuilder addImplicitHydrogens convertImplicitToExplicitHydrogens getValue calculatePlus assertEquals length
test_case.modifiers: @Test @Category(SlowTest.class) public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testBug_2787332_triclosan()
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: public DescriptorValue calculatePlus(IAtomContainer container) throws CDKException {
  
          ArrayList<Double> dar = new ArrayList<Double>();
          for (Iterator<IAtom> itA = container.atoms().iterator(); itA.hasNext();) {
              IAtom atom = itA.next();
              double value = IonizationPotentialTool.predictIP(container, atom);
              if (value != 0) dar.add(value);
          }
          for (Iterator<IBond> itB = container.bonds().iterator(); itB.hasNext();) {
              IBond bond = itB.next();
              if (bond.getOrder() == IBond.Order.DOUBLE & bond.getBegin().getSymbol().equals("C")
                      & bond.getEnd().getSymbol().equals("C")) {
                  double value = IonizationPotentialTool.predictIP(container, bond);
                  if (value != 0) dar.add(value);
  
              }
          }
  
          DoubleArrayResult results = arrangingEnergy(dar);
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), results,
                  getDescriptorNames(), null);
  
      }
focal_method.class_method_signature: IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
focal_method.full_signature: public DescriptorValue calculatePlus(IAtomContainer container)
focal_method.identifier: calculatePlus
focal_method.invocations: iterator atoms hasNext next predictIP add iterator bonds hasNext next getOrder equals getSymbol getBegin equals getSymbol getEnd predictIP add arrangingEnergy getSpecification getParameterNames getParameters getDescriptorNames
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer container)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculatePlus(IAtomContainer container)