test_class.file: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptorTest.java
test_class.identifier: IsProtonInAromaticSystemDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testIsProtonInAromaticSystemDescriptor() throws ClassNotFoundException, CDKException,
              java.lang.Exception {
          IAtomicDescriptor descriptor = new IsProtonInAromaticSystemDescriptor();
          Object[] params = {new Boolean(true)};
          descriptor.setParameters(params);
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("Oc1cc(OC)c(cc1Br)Br");
          addExplicitHydrogens(mol);
          assertThat(mol.getAtom(11).getSymbol(), is("H"));
          assertThat(mol.getAtom(12).getSymbol(), is("H"));
          assertThat(mol.getAtom(13).getSymbol(), is("H"));
          assertThat(mol.getAtom(14).getSymbol(), is("H"));
          assertThat(mol.getAtom(15).getSymbol(), is("H"));
          assertThat(mol.getAtom(16).getSymbol(), is("H"));
          Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(11), mol).getValue()).intValue());
          Assert.assertEquals(1, ((IntegerResult) descriptor.calculate(mol.getAtom(12), mol).getValue()).intValue());
          Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(13), mol).getValue()).intValue());
          Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(14), mol).getValue()).intValue());
          Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(15), mol).getValue()).intValue());
          Assert.assertEquals(1, ((IntegerResult) descriptor.calculate(mol.getAtom(16), mol).getValue()).intValue());
      }
test_case.class_method_signature: IsProtonInAromaticSystemDescriptorTest.testIsProtonInAromaticSystemDescriptor()
test_case.full_signature: @Test public void testIsProtonInAromaticSystemDescriptor()
test_case.identifier: testIsProtonInAromaticSystemDescriptor
test_case.invocations: setParameters getInstance parseSmiles addExplicitHydrogens assertThat getSymbol getAtom is assertThat getSymbol getAtom is assertThat getSymbol getAtom is assertThat getSymbol getAtom is assertThat getSymbol getAtom is assertThat getSymbol getAtom is assertEquals intValue getValue calculate getAtom assertEquals intValue getValue calculate getAtom assertEquals intValue getValue calculate getAtom assertEquals intValue getValue calculate getAtom assertEquals intValue getValue calculate getAtom assertEquals intValue getValue calculate getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testIsProtonInAromaticSystemDescriptor()
focal_class.declarator: NAMES            = {"protonInArmaticSystem"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] NAMES            = {"protonInArmaticSystem"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: checkAromaticity = false
focal_class.modifier: private
focal_class.original_string: private boolean               checkAromaticity = false;
focal_class.type: boolean
focal_class.var_name: checkAromaticity
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
focal_class.identifier: IsProtonInAromaticSystemDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: IsProtonInAromaticSystemDescriptor.IsProtonInAromaticSystemDescriptor()
focal_class.full_signature: public  IsProtonInAromaticSystemDescriptor()
focal_class.identifier: IsProtonInAromaticSystemDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  IsProtonInAromaticSystemDescriptor()
focal_class.class_method_signature: IsProtonInAromaticSystemDescriptor.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: IsProtonInAromaticSystemDescriptor.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: IsProtonInAromaticSystemDescriptor.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: IsProtonInAromaticSystemDescriptor.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: IsProtonInAromaticSystemDescriptor.calculate(IAtom atom, IAtomContainer atomContainer)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom, IAtomContainer atomContainer)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer)
focal_class.class_method_signature: IsProtonInAromaticSystemDescriptor.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: IsProtonInAromaticSystemDescriptor.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: public IsProtonInAromaticSystemDescriptor() {}
focal_method.class_method_signature: IsProtonInAromaticSystemDescriptor.IsProtonInAromaticSystemDescriptor()
focal_method.full_signature: public  IsProtonInAromaticSystemDescriptor()
focal_method.identifier: IsProtonInAromaticSystemDescriptor
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  IsProtonInAromaticSystemDescriptor()