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 methyleneCyclopropeneTest() {
          IAtomContainer mol = builder.newInstance(IAtomContainer.class);
          AbstractSignatureTest.addCarbons(mol, 4);
          AbstractSignatureTest.addHydrogens(mol, 1, 2);
          AbstractSignatureTest.addHydrogens(mol, 2, 1);
          AbstractSignatureTest.addHydrogens(mol, 3, 1);
          mol.addBond(0, 1, IBond.Order.DOUBLE);
          mol.addBond(0, 2, IBond.Order.SINGLE);
          mol.addBond(0, 3, IBond.Order.SINGLE);
          mol.addBond(2, 3, IBond.Order.DOUBLE);
          MoleculeSignature molSig = new MoleculeSignature(mol);
  
          String sigFor2Height1 = molSig.signatureStringForVertex(2, 1);
          String sigFor3Height1 = molSig.signatureStringForVertex(3, 1);
          Assert.assertTrue("Height 1 signatures for atoms 2 and 3" + " should be the same",
                  sigFor2Height1.equals(sigFor3Height1));
  
          String sigFor2Height2 = molSig.signatureStringForVertex(2, 1);
          String sigFor3Height2 = molSig.signatureStringForVertex(3, 1);
          Assert.assertTrue("Height 2 signatures for atoms 2 and 3" + " should be the same",
                  sigFor2Height2.equals(sigFor3Height2));
      }
test_case.class_method_signature: MoleculeSignatureTest.methyleneCyclopropeneTest()
test_case.full_signature: @Test public void methyleneCyclopropeneTest()
test_case.identifier: methyleneCyclopropeneTest
test_case.invocations: newInstance addCarbons addHydrogens addHydrogens addHydrogens addBond addBond addBond addBond signatureStringForVertex signatureStringForVertex assertTrue equals signatureStringForVertex signatureStringForVertex assertTrue equals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void methyleneCyclopropeneTest()
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} */
      public String signatureStringForVertex(int vertexIndex) {
          AtomSignature atomSignature;
          int height = super.getHeight();
          if (height == -1) {
              atomSignature = new AtomSignature(vertexIndex, this.molecule);
          } else {
              atomSignature = new AtomSignature(vertexIndex, height, this.molecule);
          }
          return atomSignature.toCanonicalString();
      }
focal_method.class_method_signature: MoleculeSignature.signatureStringForVertex(int vertexIndex)
focal_method.full_signature: @Override /** {@inheritDoc} */ public String signatureStringForVertex(int vertexIndex)
focal_method.identifier: signatureStringForVertex
focal_method.invocations: getHeight toCanonicalString
focal_method.modifiers: @Override /** {@inheritDoc} */ public
focal_method.parameters: (int vertexIndex)
focal_method.return: String
focal_method.signature: String signatureStringForVertex(int vertexIndex)