test_class.declarator: parser
test_class.modifier: private
test_class.original_string: private SmilesParser       parser;
test_class.type: SmilesParser
test_class.var_name: parser
test_class.declarator: builder
test_class.modifier: private
test_class.original_string: private IChemObjectBuilder builder;
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.declarator: mol
test_class.modifier: private
test_class.original_string: private IAtomContainer     mol;
test_class.type: IAtomContainer
test_class.var_name: mol
test_class.declarator: molSig
test_class.modifier: private
test_class.original_string: private MoleculeSignature  molSig;
test_class.type: MoleculeSignature
test_class.var_name: molSig
test_class.file: descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeSignatureTest.java
test_class.identifier: MoleculeSignatureTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void napthaleneWithDoubleBondsAndHydrogenHeightTest() {
          IAtomContainer napthalene = builder.newInstance(IAtomContainer.class);
          for (int i = 0; i < 10; i++) {
              napthalene.addAtom(builder.newInstance(IAtom.class, "C"));
          }
          napthalene.addBond(0, 1, IBond.Order.SINGLE);
          napthalene.addBond(0, 5, IBond.Order.DOUBLE);
          napthalene.addBond(1, 2, IBond.Order.DOUBLE);
          napthalene.addBond(1, 6, IBond.Order.SINGLE);
          napthalene.addBond(2, 3, IBond.Order.SINGLE);
          napthalene.addBond(2, 9, IBond.Order.SINGLE);
          napthalene.addBond(3, 4, IBond.Order.DOUBLE);
          napthalene.addBond(4, 5, IBond.Order.SINGLE);
          napthalene.addBond(6, 7, IBond.Order.DOUBLE);
          napthalene.addBond(7, 8, IBond.Order.SINGLE);
          napthalene.addBond(8, 9, IBond.Order.DOUBLE);
  
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(0, 10, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(3, 11, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(4, 12, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(5, 13, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(6, 14, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(7, 15, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(8, 16, IBond.Order.SINGLE);
          napthalene.addAtom(builder.newInstance(IAtom.class, "H"));
          napthalene.addBond(9, 17, IBond.Order.SINGLE);
  
          int height = 2;
          SignatureQuotientGraph mqg = new SignatureQuotientGraph(napthalene, height);
          Assert.assertEquals(4, mqg.getVertexCount());
          Assert.assertEquals(6, mqg.getEdgeCount());
          Assert.assertEquals(2, mqg.numberOfLoopEdges());
      }
test_case.class_method_signature: MoleculeSignatureTest.napthaleneWithDoubleBondsAndHydrogenHeightTest()
test_case.full_signature: @Test public void napthaleneWithDoubleBondsAndHydrogenHeightTest()
test_case.identifier: napthaleneWithDoubleBondsAndHydrogenHeightTest
test_case.invocations: newInstance addAtom newInstance addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond assertEquals getVertexCount assertEquals getEdgeCount assertEquals numberOfLoopEdges
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void napthaleneWithDoubleBondsAndHydrogenHeightTest()
focal_class.declarator: molecule
focal_class.modifier: private
focal_class.original_string: private IAtomContainer molecule;
focal_class.type: IAtomContainer
focal_class.var_name: molecule
focal_class.file: descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java
focal_class.identifier: MoleculeSignature
focal_class.class_method_signature: MoleculeSignature.MoleculeSignature(IAtomContainer molecule)
focal_class.full_signature: public  MoleculeSignature(IAtomContainer molecule)
focal_class.identifier: MoleculeSignature
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.signature:  MoleculeSignature(IAtomContainer molecule)
focal_class.class_method_signature: MoleculeSignature.MoleculeSignature(IAtomContainer molecule, int height)
focal_class.full_signature: public  MoleculeSignature(IAtomContainer molecule, int height)
focal_class.identifier: MoleculeSignature
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, int height)
focal_class.signature:  MoleculeSignature(IAtomContainer molecule, int height)
focal_class.class_method_signature: MoleculeSignature.getVertexCount()
focal_class.full_signature: @Override /** {@inheritDoc} */ protected int getVertexCount()
focal_class.identifier: getVertexCount
focal_class.modifiers: @Override /** {@inheritDoc} */ protected
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getVertexCount()
focal_class.class_method_signature: MoleculeSignature.signatureStringForVertex(int vertexIndex)
focal_class.full_signature: @Override /** {@inheritDoc} */ public String signatureStringForVertex(int vertexIndex)
focal_class.identifier: signatureStringForVertex
focal_class.modifiers: @Override /** {@inheritDoc} */ public
focal_class.parameters: (int vertexIndex)
focal_class.return: String
focal_class.signature: String signatureStringForVertex(int vertexIndex)
focal_class.class_method_signature: MoleculeSignature.signatureStringForVertex(int vertexIndex, int height)
focal_class.full_signature: @Override /** {@inheritDoc} */ public String signatureStringForVertex(int vertexIndex, int height)
focal_class.identifier: signatureStringForVertex
focal_class.modifiers: @Override /** {@inheritDoc} */ public
focal_class.parameters: (int vertexIndex, int height)
focal_class.return: String
focal_class.signature: String signatureStringForVertex(int vertexIndex, int height)
focal_class.class_method_signature: MoleculeSignature.signatureForVertex(int vertexIndex)
focal_class.full_signature: @Override /** {@inheritDoc} */ public AbstractVertexSignature signatureForVertex(int vertexIndex)
focal_class.identifier: signatureForVertex
focal_class.modifiers: @Override /** {@inheritDoc} */ public
focal_class.parameters: (int vertexIndex)
focal_class.return: AbstractVertexSignature
focal_class.signature: AbstractVertexSignature signatureForVertex(int vertexIndex)
focal_class.class_method_signature: MoleculeSignature.calculateOrbits()
focal_class.full_signature: public List<Orbit> calculateOrbits()
focal_class.identifier: calculateOrbits
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Orbit>
focal_class.signature: List<Orbit> calculateOrbits()
focal_class.class_method_signature: MoleculeSignature.fromSignatureString(String signatureString, IChemObjectBuilder coBuilder)
focal_class.full_signature: public static IAtomContainer fromSignatureString(String signatureString, IChemObjectBuilder coBuilder)
focal_class.identifier: fromSignatureString
focal_class.modifiers: public static
focal_class.parameters: (String signatureString, IChemObjectBuilder coBuilder)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer fromSignatureString(String signatureString, IChemObjectBuilder coBuilder)
focal_class.class_method_signature: MoleculeSignature.toCanonicalSignatureString(int height)
focal_class.full_signature: public String toCanonicalSignatureString(int height)
focal_class.identifier: toCanonicalSignatureString
focal_class.modifiers: public
focal_class.parameters: (int height)
focal_class.return: String
focal_class.signature: String toCanonicalSignatureString(int height)
focal_class.superclass: extends AbstractGraphSignature
focal_method.body: @Override
      /** {@inheritDoc} */
      protected int getVertexCount() {
          return this.molecule.getAtomCount();
      }
focal_method.class_method_signature: MoleculeSignature.getVertexCount()
focal_method.full_signature: @Override /** {@inheritDoc} */ protected int getVertexCount()
focal_method.identifier: getVertexCount
focal_method.invocations: getAtomCount
focal_method.modifiers: @Override /** {@inheritDoc} */ protected
focal_method.parameters: ()
focal_method.return: int
focal_method.signature: int getVertexCount()