test_class.file: descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java
test_class.identifier: BasicGroupCountDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test(expected = IllegalStateException.class)
      public void uninitalisedError() {
          new BasicGroupCountDescriptor().calculate(new AtomContainer());
      }
test_case.class_method_signature: BasicGroupCountDescriptorTest.uninitalisedError()
test_case.full_signature: @Test(expected = IllegalStateException.class) public void uninitalisedError()
test_case.identifier: uninitalisedError
test_case.invocations: calculate
test_case.modifiers: @Test(expected = IllegalStateException.class) public
test_case.parameters: ()
test_case.return: void
test_case.signature: void uninitalisedError()
focal_class.declarator: SMARTS_STRINGS = {"[$([NH2]-[CX4])]", "[$([NH](-[CX4])-[CX4])]",
              "[$(N(-[CX4])(-[CX4])-[CX4])]", "[$([*;+;!$(*~[*;-])])]", "[$(N=C-N)]", "[$(N-C=N)]"}
focal_class.modifier: private final static
focal_class.original_string: private final static String[] SMARTS_STRINGS = {"[$([NH2]-[CX4])]", "[$([NH](-[CX4])-[CX4])]",
              "[$(N(-[CX4])(-[CX4])-[CX4])]", "[$([*;+;!$(*~[*;-])])]", "[$(N=C-N)]", "[$(N-C=N)]"};
focal_class.type: String[]
focal_class.var_name: SMARTS_STRINGS
focal_class.declarator: NAMES          = {"nBase"}
focal_class.modifier: private final static
focal_class.original_string: private final static String[] NAMES          = {"nBase"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: tools            = new ArrayList<SmartsPattern>()
focal_class.modifier: private
focal_class.original_string: private List<SmartsPattern> tools            = new ArrayList<SmartsPattern>();
focal_class.type: List<SmartsPattern>
focal_class.var_name: tools
focal_class.file: descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java
focal_class.identifier: BasicGroupCountDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: BasicGroupCountDescriptor.BasicGroupCountDescriptor()
focal_class.full_signature: public  BasicGroupCountDescriptor()
focal_class.identifier: BasicGroupCountDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  BasicGroupCountDescriptor()
focal_class.class_method_signature: BasicGroupCountDescriptor.initialise(IChemObjectBuilder builder)
focal_class.full_signature: @Override public void initialise(IChemObjectBuilder builder)
focal_class.identifier: initialise
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void initialise(IChemObjectBuilder builder)
focal_class.class_method_signature: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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: BasicGroupCountDescriptor.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.class_method_signature: BasicGroupCountDescriptor.getDummyDescriptorValue(Exception exception)
focal_class.full_signature: private DescriptorValue getDummyDescriptorValue(Exception exception)
focal_class.identifier: getDummyDescriptorValue
focal_class.modifiers: private
focal_class.parameters: (Exception exception)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue getDummyDescriptorValue(Exception exception)
focal_class.superclass: extends AbstractMolecularDescriptor
focal_method.body: @Override
      public DescriptorValue calculate(IAtomContainer atomContainer) {
  
          if (tools.isEmpty()) {
              throw new IllegalStateException("descriptor is not initalised, invoke 'initalise' first");
          }
  
          atomContainer = clone(atomContainer);
          for (IAtom atom : atomContainer.atoms()) {
              if (atom.getImplicitHydrogenCount() == null)
                  atom.setImplicitHydrogenCount(0);
          }
  
          int count = 0;
          for (SmartsPattern ptrn : tools) {
              count += ptrn.matchAll(atomContainer).count();
          }
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
                  count), getDescriptorNames());
      }
focal_method.class_method_signature: BasicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtomContainer atomContainer)
focal_method.identifier: calculate
focal_method.invocations: isEmpty clone atoms getImplicitHydrogenCount setImplicitHydrogenCount count matchAll 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)