test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/CorrectGeometricConfigurationTest.java
test_class.identifier: CorrectGeometricConfigurationTest
test_case.body: @Test
      public void cis() {
          IAtomContainer m = new AtomContainer(5, 4, 0, 0);
          m.addAtom(atom("C", 3, -0.74d, 5.00d));
          m.addAtom(atom("C", 1, -1.49d, 3.70d));
          m.addAtom(atom("C", 1, -0.74d, 2.40d));
          m.addAtom(atom("C", 2, -1.49d, 1.10d));
          m.addAtom(atom("C", 3, -0.74d, -0.20d));
          m.addBond(0, 1, IBond.Order.SINGLE);
          m.addBond(1, 2, IBond.Order.DOUBLE);
          m.addBond(2, 3, IBond.Order.SINGLE);
          m.addBond(3, 4, IBond.Order.SINGLE);
          m.addStereoElement(new DoubleBondStereochemistry(m.getBond(1), new IBond[]{m.getBond(0), m.getBond(2)},
                  TOGETHER));
          CorrectGeometricConfiguration.correct(m);
          assertPoint(m.getAtom(0), -0.74, 5.0, 0.1);
          assertPoint(m.getAtom(1), -1.49, 3.7, 0.1);
          assertPoint(m.getAtom(2), -0.74, 2.4, 0.1);
          assertPoint(m.getAtom(3), 0.76, 2.4, 0.1);
          assertPoint(m.getAtom(4), 1.51, 1.10, 0.1);
      }
test_case.class_method_signature: CorrectGeometricConfigurationTest.cis()
test_case.full_signature: @Test public void cis()
test_case.identifier: cis
test_case.invocations: addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addBond addBond addBond addBond addStereoElement getBond getBond getBond correct assertPoint getAtom assertPoint getAtom assertPoint getAtom assertPoint getAtom assertPoint getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void cis()
focal_class.declarator: container
focal_class.modifier: private final
focal_class.original_string: private final IAtomContainer      container;
focal_class.type: IAtomContainer
focal_class.var_name: container
focal_class.declarator: graph
focal_class.modifier: private final
focal_class.original_string: private final int[][]             graph;
focal_class.type: int[][]
focal_class.var_name: graph
focal_class.declarator: atomToIndex
focal_class.modifier: private final
focal_class.original_string: private final Map<IAtom, Integer> atomToIndex;
focal_class.type: Map<IAtom, Integer>
focal_class.var_name: atomToIndex
focal_class.declarator: ringSearch
focal_class.modifier: private final
focal_class.original_string: private final RingSearch          ringSearch;
focal_class.type: RingSearch
focal_class.var_name: ringSearch
focal_class.declarator: visited
focal_class.modifier: private final
focal_class.original_string: private final boolean[]           visited;
focal_class.type: boolean[]
focal_class.var_name: visited
focal_class.file: tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java
focal_class.identifier: CorrectGeometricConfiguration
focal_class.class_method_signature: CorrectGeometricConfiguration.correct(IAtomContainer container)
focal_class.full_signature: public static IAtomContainer correct(IAtomContainer container)
focal_class.identifier: correct
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer correct(IAtomContainer container)
focal_class.class_method_signature: CorrectGeometricConfiguration.CorrectGeometricConfiguration(IAtomContainer container)
focal_class.full_signature:   CorrectGeometricConfiguration(IAtomContainer container)
focal_class.identifier: CorrectGeometricConfiguration
focal_class.parameters: (IAtomContainer container)
focal_class.signature:  CorrectGeometricConfiguration(IAtomContainer container)
focal_class.class_method_signature: CorrectGeometricConfiguration.CorrectGeometricConfiguration(IAtomContainer container, int[][] graph)
focal_class.full_signature:   CorrectGeometricConfiguration(IAtomContainer container, int[][] graph)
focal_class.identifier: CorrectGeometricConfiguration
focal_class.parameters: (IAtomContainer container, int[][] graph)
focal_class.signature:  CorrectGeometricConfiguration(IAtomContainer container, int[][] graph)
focal_class.class_method_signature: CorrectGeometricConfiguration.adjust(IDoubleBondStereochemistry dbs)
focal_class.full_signature: private void adjust(IDoubleBondStereochemistry dbs)
focal_class.identifier: adjust
focal_class.modifiers: private
focal_class.parameters: (IDoubleBondStereochemistry dbs)
focal_class.return: void
focal_class.signature: void adjust(IDoubleBondStereochemistry dbs)
focal_class.class_method_signature: CorrectGeometricConfiguration.adjust(ExtendedCisTrans elem)
focal_class.full_signature: private void adjust(ExtendedCisTrans elem)
focal_class.identifier: adjust
focal_class.modifiers: private
focal_class.parameters: (ExtendedCisTrans elem)
focal_class.return: void
focal_class.signature: void adjust(ExtendedCisTrans elem)
focal_class.class_method_signature: CorrectGeometricConfiguration.getAtoms(IAtom focus, IAtom substituent, IAtom otherFocus)
focal_class.full_signature: private IAtom[] getAtoms(IAtom focus, IAtom substituent, IAtom otherFocus)
focal_class.identifier: getAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom focus, IAtom substituent, IAtom otherFocus)
focal_class.return: IAtom[]
focal_class.signature: IAtom[] getAtoms(IAtom focus, IAtom substituent, IAtom otherFocus)
focal_class.class_method_signature: CorrectGeometricConfiguration.parity(IStereoElement element)
focal_class.full_signature: private static int parity(IStereoElement element)
focal_class.identifier: parity
focal_class.modifiers: private static
focal_class.parameters: (IStereoElement element)
focal_class.return: int
focal_class.signature: int parity(IStereoElement element)
focal_class.class_method_signature: CorrectGeometricConfiguration.parity(IAtom[] atoms)
focal_class.full_signature: private static int parity(IAtom[] atoms)
focal_class.identifier: parity
focal_class.modifiers: private static
focal_class.parameters: (IAtom[] atoms)
focal_class.return: int
focal_class.signature: int parity(IAtom[] atoms)
focal_class.class_method_signature: CorrectGeometricConfiguration.parity(Point2d a, Point2d b, Point2d c)
focal_class.full_signature: private static int parity(Point2d a, Point2d b, Point2d c)
focal_class.identifier: parity
focal_class.modifiers: private static
focal_class.parameters: (Point2d a, Point2d b, Point2d c)
focal_class.return: int
focal_class.signature: int parity(Point2d a, Point2d b, Point2d c)
focal_class.class_method_signature: CorrectGeometricConfiguration.reflect(int v, IBond bond)
focal_class.full_signature: private void reflect(int v, IBond bond)
focal_class.identifier: reflect
focal_class.modifiers: private
focal_class.parameters: (int v, IBond bond)
focal_class.return: void
focal_class.signature: void reflect(int v, IBond bond)
focal_class.class_method_signature: CorrectGeometricConfiguration.reflect(Point2d p, IBond bond)
focal_class.full_signature: private Point2d reflect(Point2d p, IBond bond)
focal_class.identifier: reflect
focal_class.modifiers: private
focal_class.parameters: (Point2d p, IBond bond)
focal_class.return: Point2d
focal_class.signature: Point2d reflect(Point2d p, IBond bond)
focal_class.class_method_signature: CorrectGeometricConfiguration.reflect(Point2d p, double x0, double y0, double x1, double y1)
focal_class.full_signature: private Point2d reflect(Point2d p, double x0, double y0, double x1, double y1)
focal_class.identifier: reflect
focal_class.modifiers: private
focal_class.parameters: (Point2d p, double x0, double y0, double x1, double y1)
focal_class.return: Point2d
focal_class.signature: Point2d reflect(Point2d p, double x0, double y0, double x1, double y1)
focal_method.body: public static IAtomContainer correct(IAtomContainer container) {
          if (!Iterables.isEmpty(container.stereoElements())) new CorrectGeometricConfiguration(container);
          return container;
      }
focal_method.class_method_signature: CorrectGeometricConfiguration.correct(IAtomContainer container)
focal_method.full_signature: public static IAtomContainer correct(IAtomContainer container)
focal_method.identifier: correct
focal_method.invocations: isEmpty stereoElements
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer container)
focal_method.return: IAtomContainer
focal_method.signature: IAtomContainer correct(IAtomContainer container)