test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private final
test_class.original_string: private final IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.declarator: g2c     = new BeamToCDK(builder)
test_class.modifier: private final
test_class.original_string: private final BeamToCDK          g2c     = new BeamToCDK(builder);
test_class.type: BeamToCDK
test_class.var_name: g2c
test_class.file: storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java
test_class.identifier: BeamToCDKTest
test_case.body: @Test
      public void methaneAtom() {
          IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).build(), 4);
          assertThat(a.getSymbol(), is("C"));
          assertThat(a.getImplicitHydrogenCount(), is(4));
      }
test_case.class_method_signature: BeamToCDKTest.methaneAtom()
test_case.full_signature: @Test public void methaneAtom()
test_case.identifier: methaneAtom
test_case.invocations: toCDKAtom build hydrogens aliphatic assertThat getSymbol is assertThat getImplicitHydrogenCount is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void methaneAtom()
focal_class.declarator: builder
focal_class.modifier: private final
focal_class.original_string: private final IChemObjectBuilder builder;
focal_class.type: IChemObjectBuilder
focal_class.var_name: builder
focal_class.declarator: templateAtom
focal_class.modifier: private final
focal_class.original_string: private final IAtom              templateAtom;
focal_class.type: IAtom
focal_class.var_name: templateAtom
focal_class.declarator: templateBond
focal_class.modifier: private final
focal_class.original_string: private final IBond              templateBond;
focal_class.type: IBond
focal_class.var_name: templateBond
focal_class.declarator: emptyContainer
focal_class.modifier: private final
focal_class.original_string: private final IAtomContainer     emptyContainer;
focal_class.type: IAtomContainer
focal_class.var_name: emptyContainer
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
focal_class.identifier: BeamToCDK
focal_class.class_method_signature: BeamToCDK.BeamToCDK(IChemObjectBuilder builder)
focal_class.full_signature:   BeamToCDK(IChemObjectBuilder builder)
focal_class.identifier: BeamToCDK
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.signature:  BeamToCDK(IChemObjectBuilder builder)
focal_class.class_method_signature: BeamToCDK.toAtomContainer(Graph g, boolean kekule)
focal_class.full_signature:  IAtomContainer toAtomContainer(Graph g, boolean kekule)
focal_class.identifier: toAtomContainer
focal_class.parameters: (Graph g, boolean kekule)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer toAtomContainer(Graph g, boolean kekule)
focal_class.class_method_signature: BeamToCDK.findCumulatedEdge(Graph g, int v, Edge e)
focal_class.full_signature: private Edge findCumulatedEdge(Graph g, int v, Edge e)
focal_class.identifier: findCumulatedEdge
focal_class.modifiers: private
focal_class.parameters: (Graph g, int v, Edge e)
focal_class.return: Edge
focal_class.signature: Edge findCumulatedEdge(Graph g, int v, Edge e)
focal_class.class_method_signature: BeamToCDK.addDoubleBondStereochemistry(Graph g, IAtomContainer ac)
focal_class.full_signature: private void addDoubleBondStereochemistry(Graph g, IAtomContainer ac)
focal_class.identifier: addDoubleBondStereochemistry
focal_class.modifiers: private
focal_class.parameters: (Graph g, IAtomContainer ac)
focal_class.return: void
focal_class.signature: void addDoubleBondStereochemistry(Graph g, IAtomContainer ac)
focal_class.class_method_signature: BeamToCDK.findDirectionalEdge(Graph g, int u)
focal_class.full_signature: private Edge findDirectionalEdge(Graph g, int u)
focal_class.identifier: findDirectionalEdge
focal_class.modifiers: private
focal_class.parameters: (Graph g, int u)
focal_class.return: Edge
focal_class.signature: Edge findDirectionalEdge(Graph g, int u)
focal_class.class_method_signature: BeamToCDK.newTetrahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.full_signature: private IStereoElement newTetrahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.identifier: newTetrahedral
focal_class.modifiers: private
focal_class.parameters: (int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.return: IStereoElement
focal_class.signature: IStereoElement newTetrahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.class_method_signature: BeamToCDK.newSquarePlanar(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.full_signature: private IStereoElement newSquarePlanar(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.identifier: newSquarePlanar
focal_class.modifiers: private
focal_class.parameters: (int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.return: IStereoElement
focal_class.signature: IStereoElement newSquarePlanar(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.class_method_signature: BeamToCDK.newTrigonalBipyramidal(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.full_signature: private IStereoElement newTrigonalBipyramidal(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.identifier: newTrigonalBipyramidal
focal_class.modifiers: private
focal_class.parameters: (int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.return: IStereoElement
focal_class.signature: IStereoElement newTrigonalBipyramidal(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.class_method_signature: BeamToCDK.newOctahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.full_signature: private IStereoElement newOctahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.identifier: newOctahedral
focal_class.modifiers: private
focal_class.parameters: (int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.return: IStereoElement
focal_class.signature: IStereoElement newOctahedral(int u, int[] vs, IAtom[] atoms, Configuration c)
focal_class.class_method_signature: BeamToCDK.getOtherDb(Graph g, int u, int v)
focal_class.full_signature: private int getOtherDb(Graph g, int u, int v)
focal_class.identifier: getOtherDb
focal_class.modifiers: private
focal_class.parameters: (Graph g, int u, int v)
focal_class.return: int
focal_class.signature: int getOtherDb(Graph g, int u, int v)
focal_class.class_method_signature: BeamToCDK.findExtendedTetrahedralEnds(Graph g, int focus)
focal_class.full_signature: private int[] findExtendedTetrahedralEnds(Graph g, int focus)
focal_class.identifier: findExtendedTetrahedralEnds
focal_class.modifiers: private
focal_class.parameters: (Graph g, int focus)
focal_class.return: int[]
focal_class.signature: int[] findExtendedTetrahedralEnds(Graph g, int focus)
focal_class.class_method_signature: BeamToCDK.newExtendedTetrahedral(int u, Graph g, IAtom[] atoms)
focal_class.full_signature: private IStereoElement newExtendedTetrahedral(int u, Graph g, IAtom[] atoms)
focal_class.identifier: newExtendedTetrahedral
focal_class.modifiers: private
focal_class.parameters: (int u, Graph g, IAtom[] atoms)
focal_class.return: IStereoElement
focal_class.signature: IStereoElement newExtendedTetrahedral(int u, Graph g, IAtom[] atoms)
focal_class.class_method_signature: BeamToCDK.insert(int v, int[] vs)
focal_class.full_signature: private static int[] insert(int v, int[] vs)
focal_class.identifier: insert
focal_class.modifiers: private static
focal_class.parameters: (int v, int[] vs)
focal_class.return: int[]
focal_class.signature: int[] insert(int v, int[] vs)
focal_class.class_method_signature: BeamToCDK.toCDKAtom(Atom beamAtom, int hCount)
focal_class.full_signature:  IAtom toCDKAtom(Atom beamAtom, int hCount)
focal_class.identifier: toCDKAtom
focal_class.parameters: (Atom beamAtom, int hCount)
focal_class.return: IAtom
focal_class.signature: IAtom toCDKAtom(Atom beamAtom, int hCount)
focal_class.class_method_signature: BeamToCDK.newCDKAtom(Atom atom)
focal_class.full_signature:  IAtom newCDKAtom(Atom atom)
focal_class.identifier: newCDKAtom
focal_class.parameters: (Atom atom)
focal_class.return: IAtom
focal_class.signature: IAtom newCDKAtom(Atom atom)
focal_class.class_method_signature: BeamToCDK.emptyContainer()
focal_class.full_signature: private IAtomContainer emptyContainer()
focal_class.identifier: emptyContainer
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer emptyContainer()
focal_class.class_method_signature: BeamToCDK.createAtom(Element element)
focal_class.full_signature: private IAtom createAtom(Element element)
focal_class.identifier: createAtom
focal_class.modifiers: private
focal_class.parameters: (Element element)
focal_class.return: IAtom
focal_class.signature: IAtom createAtom(Element element)
focal_method.body: IAtom toCDKAtom(Atom beamAtom, int hCount) {
  
          IAtom cdkAtom = newCDKAtom(beamAtom);
  
          cdkAtom.setImplicitHydrogenCount(hCount);
          cdkAtom.setFormalCharge(beamAtom.charge());
  
          if (beamAtom.isotope() >= 0) cdkAtom.setMassNumber(beamAtom.isotope());
  
          if (beamAtom.aromatic()) cdkAtom.setIsAromatic(true);
  
          if (beamAtom.atomClass() > 0) cdkAtom.setProperty(ATOM_ATOM_MAPPING, beamAtom.atomClass());
  
          return cdkAtom;
      }
focal_method.class_method_signature: BeamToCDK.toCDKAtom(Atom beamAtom, int hCount)
focal_method.full_signature:  IAtom toCDKAtom(Atom beamAtom, int hCount)
focal_method.identifier: toCDKAtom
focal_method.invocations: newCDKAtom setImplicitHydrogenCount setFormalCharge charge isotope setMassNumber isotope aromatic setIsAromatic atomClass setProperty atomClass
focal_method.parameters: (Atom beamAtom, int hCount)
focal_method.return: IAtom
focal_method.signature: IAtom toCDKAtom(Atom beamAtom, int hCount)