test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: public static
test_class.original_string: public static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.file: tool/group/src/test/java/org/openscience/cdk/group/AtomRefinableTest.java
test_class.identifier: AtomRefinableTest
test_case.body: @Test
      public void getVertexCount() {
          IAtomContainer ac = makeAtomContainer("CCCC");
          AtomRefinable refinable = new AtomRefinable(ac);
          assertEquals(ac.getAtomCount(), refinable.getVertexCount());
      }
test_case.class_method_signature: AtomRefinableTest.getVertexCount()
test_case.full_signature: @Test public void getVertexCount()
test_case.identifier: getVertexCount
test_case.invocations: makeAtomContainer assertEquals getAtomCount getVertexCount
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void getVertexCount()
focal_class.declarator: atomContainer
focal_class.modifier: private final
focal_class.original_string: private final IAtomContainer atomContainer;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.declarator: connectionTable
focal_class.modifier: private
focal_class.original_string: private int[][] connectionTable;
focal_class.type: int[][]
focal_class.var_name: connectionTable
focal_class.declarator: bondOrders
focal_class.modifier: private
focal_class.original_string: private int[][] bondOrders;
focal_class.type: int[][]
focal_class.var_name: bondOrders
focal_class.declarator: ignoreElements
focal_class.modifier: private
focal_class.original_string: private boolean ignoreElements;
focal_class.type: boolean
focal_class.var_name: ignoreElements
focal_class.declarator: ignoreBondOrders
focal_class.modifier: private
focal_class.original_string: private boolean ignoreBondOrders;
focal_class.type: boolean
focal_class.var_name: ignoreBondOrders
focal_class.declarator: maxBondOrder
focal_class.modifier: private
focal_class.original_string: private int maxBondOrder;
focal_class.type: int
focal_class.var_name: maxBondOrder
focal_class.file: tool/group/src/main/java/org/openscience/cdk/group/AtomRefinable.java
focal_class.identifier: AtomRefinable
focal_class.interfaces: implements Refinable
focal_class.class_method_signature: AtomRefinable.AtomRefinable(IAtomContainer atomContainer)
focal_class.full_signature: public  AtomRefinable(IAtomContainer atomContainer)
focal_class.identifier: AtomRefinable
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.signature:  AtomRefinable(IAtomContainer atomContainer)
focal_class.class_method_signature: AtomRefinable.AtomRefinable(IAtomContainer atomContainer, boolean ignoreElements, boolean ignoreBondOrders)
focal_class.full_signature: public  AtomRefinable(IAtomContainer atomContainer, boolean ignoreElements, boolean ignoreBondOrders)
focal_class.identifier: AtomRefinable
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, boolean ignoreElements, boolean ignoreBondOrders)
focal_class.signature:  AtomRefinable(IAtomContainer atomContainer, boolean ignoreElements, boolean ignoreBondOrders)
focal_class.class_method_signature: AtomRefinable.neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.full_signature: @Override public Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.identifier: neighboursInBlock
focal_class.modifiers: @Override public
focal_class.parameters: (Set<Integer> block, int vertexIndex)
focal_class.return: Invariant
focal_class.signature: Invariant neighboursInBlock(Set<Integer> block, int vertexIndex)
focal_class.class_method_signature: AtomRefinable.getSimpleInvariant(Set<Integer> block, int vertexIndex)
focal_class.full_signature: private Invariant getSimpleInvariant(Set<Integer> block, int vertexIndex)
focal_class.identifier: getSimpleInvariant
focal_class.modifiers: private
focal_class.parameters: (Set<Integer> block, int vertexIndex)
focal_class.return: Invariant
focal_class.signature: Invariant getSimpleInvariant(Set<Integer> block, int vertexIndex)
focal_class.class_method_signature: AtomRefinable.getMultipleInvariant(Set<Integer> block, int vertexIndex)
focal_class.full_signature: private Invariant getMultipleInvariant(Set<Integer> block, int vertexIndex)
focal_class.identifier: getMultipleInvariant
focal_class.modifiers: private
focal_class.parameters: (Set<Integer> block, int vertexIndex)
focal_class.return: Invariant
focal_class.signature: Invariant getMultipleInvariant(Set<Integer> block, int vertexIndex)
focal_class.class_method_signature: AtomRefinable.getVertexCount()
focal_class.full_signature: @Override public int getVertexCount()
focal_class.identifier: getVertexCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getVertexCount()
focal_class.class_method_signature: AtomRefinable.getConnectivity(int vertexI, int vertexJ)
focal_class.full_signature: @Override public int getConnectivity(int vertexI, int vertexJ)
focal_class.identifier: getConnectivity
focal_class.modifiers: @Override public
focal_class.parameters: (int vertexI, int vertexJ)
focal_class.return: int
focal_class.signature: int getConnectivity(int vertexI, int vertexJ)
focal_class.class_method_signature: AtomRefinable.getConnectedIndices(int vertexIndex)
focal_class.full_signature: private int[] getConnectedIndices(int vertexIndex)
focal_class.identifier: getConnectedIndices
focal_class.modifiers: private
focal_class.parameters: (int vertexIndex)
focal_class.return: int[]
focal_class.signature: int[] getConnectedIndices(int vertexIndex)
focal_class.class_method_signature: AtomRefinable.getInitialPartition()
focal_class.full_signature: @Override public Partition getInitialPartition()
focal_class.identifier: getInitialPartition
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Partition
focal_class.signature: Partition getInitialPartition()
focal_class.class_method_signature: AtomRefinable.setupConnectionTable(IAtomContainer atomContainer)
focal_class.full_signature: private void setupConnectionTable(IAtomContainer atomContainer)
focal_class.identifier: setupConnectionTable
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void setupConnectionTable(IAtomContainer atomContainer)
focal_method.body: @Override
      public int getVertexCount() {
          return atomContainer.getAtomCount();
      }
focal_method.class_method_signature: AtomRefinable.getVertexCount()
focal_method.full_signature: @Override public int getVertexCount()
focal_method.identifier: getVertexCount
focal_method.invocations: getAtomCount
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: int
focal_method.signature: int getVertexCount()