test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
test_class.identifier: NonPlanarBondsTest
test_case.body: @Test public void dontCrossEtheneDoubleBond() {
          IAtomContainer m = new AtomContainer();
          m.addAtom(atom("C", 2, 0.000, 0.000));
          m.addAtom(atom("C", 2, 1.299, -0.750));
          m.addBond(0, 1, IBond.Order.DOUBLE);
          NonplanarBonds.assign(m);
          assertThat(m.getBond(0).getStereo(), is(IBond.Stereo.NONE));
      }
test_case.class_method_signature: NonPlanarBondsTest.dontCrossEtheneDoubleBond()
test_case.full_signature: @Test public void dontCrossEtheneDoubleBond()
test_case.identifier: dontCrossEtheneDoubleBond
test_case.invocations: addAtom atom addAtom atom addBond assign assertThat getStereo getBond is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void dontCrossEtheneDoubleBond()
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: 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: tetrahedralElements
focal_class.modifier: private final
focal_class.original_string: private final ITetrahedralChirality[] tetrahedralElements;
focal_class.type: ITetrahedralChirality[]
focal_class.var_name: tetrahedralElements
focal_class.declarator: doubleBondElements
focal_class.modifier: private final
focal_class.original_string: private final IDoubleBondStereochemistry[] doubleBondElements;
focal_class.type: IDoubleBondStereochemistry[]
focal_class.var_name: doubleBondElements
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: edgeToBond
focal_class.modifier: private final
focal_class.original_string: private final GraphUtil.EdgeToBondMap edgeToBond;
focal_class.type: GraphUtil.EdgeToBondMap
focal_class.var_name: edgeToBond
focal_class.file: tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
focal_class.identifier: NonplanarBonds
focal_class.class_method_signature: NonplanarBonds.assign(final IAtomContainer container)
focal_class.full_signature: public static IAtomContainer assign(final IAtomContainer container)
focal_class.identifier: assign
focal_class.modifiers: public static
focal_class.parameters: (final IAtomContainer container)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer assign(final IAtomContainer container)
focal_class.class_method_signature: NonplanarBonds.NonplanarBonds(final IAtomContainer container, final int[][] g, final GraphUtil.EdgeToBondMap edgeToBond)
focal_class.full_signature:   NonplanarBonds(final IAtomContainer container, final int[][] g, final GraphUtil.EdgeToBondMap edgeToBond)
focal_class.identifier: NonplanarBonds
focal_class.parameters: (final IAtomContainer container, final int[][] g, final GraphUtil.EdgeToBondMap edgeToBond)
focal_class.signature:  NonplanarBonds(final IAtomContainer container, final int[][] g, final GraphUtil.EdgeToBondMap edgeToBond)
focal_class.class_method_signature: NonplanarBonds.rotate(Point2d p, Point2d pivot, double cos, double sin)
focal_class.full_signature: private void rotate(Point2d p, Point2d pivot, double cos, double sin)
focal_class.identifier: rotate
focal_class.modifiers: private
focal_class.parameters: (Point2d p, Point2d pivot, double cos, double sin)
focal_class.return: void
focal_class.signature: void rotate(Point2d p, Point2d pivot, double cos, double sin)
focal_class.class_method_signature: NonplanarBonds.getRotated(Point2d org, Point2d piviot, double theta)
focal_class.full_signature: private Point2d getRotated(Point2d org, Point2d piviot, double theta)
focal_class.identifier: getRotated
focal_class.modifiers: private
focal_class.parameters: (Point2d org, Point2d piviot, double theta)
focal_class.return: Point2d
focal_class.signature: Point2d getRotated(Point2d org, Point2d piviot, double theta)
focal_class.class_method_signature: NonplanarBonds.snapBondToPosition(IAtom beg, IBond bond, Point2d tP)
focal_class.full_signature: private void snapBondToPosition(IAtom beg, IBond bond, Point2d tP)
focal_class.identifier: snapBondToPosition
focal_class.modifiers: private
focal_class.parameters: (IAtom beg, IBond bond, Point2d tP)
focal_class.return: void
focal_class.signature: void snapBondToPosition(IAtom beg, IBond bond, Point2d tP)
focal_class.class_method_signature: NonplanarBonds.modifyAndLabel(SquarePlanar se)
focal_class.full_signature: private void modifyAndLabel(SquarePlanar se)
focal_class.identifier: modifyAndLabel
focal_class.modifiers: private
focal_class.parameters: (SquarePlanar se)
focal_class.return: void
focal_class.signature: void modifyAndLabel(SquarePlanar se)
focal_class.class_method_signature: NonplanarBonds.doMirror(List<IAtom> atoms)
focal_class.full_signature: private boolean doMirror(List<IAtom> atoms)
focal_class.identifier: doMirror
focal_class.modifiers: private
focal_class.parameters: (List<IAtom> atoms)
focal_class.return: boolean
focal_class.signature: boolean doMirror(List<IAtom> atoms)
focal_class.class_method_signature: NonplanarBonds.modifyAndLabel(TrigonalBipyramidal se)
focal_class.full_signature: private void modifyAndLabel(TrigonalBipyramidal se)
focal_class.identifier: modifyAndLabel
focal_class.modifiers: private
focal_class.parameters: (TrigonalBipyramidal se)
focal_class.return: void
focal_class.signature: void modifyAndLabel(TrigonalBipyramidal se)
focal_class.class_method_signature: NonplanarBonds.modifyAndLabel(Octahedral oc)
focal_class.full_signature: private void modifyAndLabel(Octahedral oc)
focal_class.identifier: modifyAndLabel
focal_class.modifiers: private
focal_class.parameters: (Octahedral oc)
focal_class.return: void
focal_class.signature: void modifyAndLabel(Octahedral oc)
focal_class.class_method_signature: NonplanarBonds.flip(IBond.Stereo disp)
focal_class.full_signature: private IBond.Stereo flip(IBond.Stereo disp)
focal_class.identifier: flip
focal_class.modifiers: private
focal_class.parameters: (IBond.Stereo disp)
focal_class.return: IBond.Stereo
focal_class.signature: IBond.Stereo flip(IBond.Stereo disp)
focal_class.class_method_signature: NonplanarBonds.setBondDisplay(IBond bond, IAtom focus, IBond.Stereo display)
focal_class.full_signature: private void setBondDisplay(IBond bond, IAtom focus, IBond.Stereo display)
focal_class.identifier: setBondDisplay
focal_class.modifiers: private
focal_class.parameters: (IBond bond, IAtom focus, IBond.Stereo display)
focal_class.return: void
focal_class.signature: void setBondDisplay(IBond bond, IAtom focus, IBond.Stereo display)
focal_class.class_method_signature: NonplanarBonds.findBond(IAtom beg1, IAtom beg2, IAtom end)
focal_class.full_signature: private IBond findBond(IAtom beg1, IAtom beg2, IAtom end)
focal_class.identifier: findBond
focal_class.modifiers: private
focal_class.parameters: (IAtom beg1, IAtom beg2, IAtom end)
focal_class.return: IBond
focal_class.signature: IBond findBond(IAtom beg1, IAtom beg2, IAtom end)
focal_class.class_method_signature: NonplanarBonds.setWedge(IBond bond, IAtom end, IBond.Stereo style)
focal_class.full_signature: private void setWedge(IBond bond, IAtom end, IBond.Stereo style)
focal_class.identifier: setWedge
focal_class.modifiers: private
focal_class.parameters: (IBond bond, IAtom end, IBond.Stereo style)
focal_class.return: void
focal_class.signature: void setWedge(IBond bond, IAtom end, IBond.Stereo style)
focal_class.class_method_signature: NonplanarBonds.label(final ExtendedTetrahedral element)
focal_class.full_signature: private void label(final ExtendedTetrahedral element)
focal_class.identifier: label
focal_class.modifiers: private
focal_class.parameters: (final ExtendedTetrahedral element)
focal_class.return: void
focal_class.signature: void label(final ExtendedTetrahedral element)
focal_class.class_method_signature: NonplanarBonds.label(final Atropisomeric element)
focal_class.full_signature: private void label(final Atropisomeric element)
focal_class.identifier: label
focal_class.modifiers: private
focal_class.parameters: (final Atropisomeric element)
focal_class.return: void
focal_class.signature: void label(final Atropisomeric element)
focal_class.class_method_signature: NonplanarBonds.label(final ITetrahedralChirality element)
focal_class.full_signature: private void label(final ITetrahedralChirality element)
focal_class.identifier: label
focal_class.modifiers: private
focal_class.parameters: (final ITetrahedralChirality element)
focal_class.return: void
focal_class.signature: void label(final ITetrahedralChirality element)
focal_class.class_method_signature: NonplanarBonds.assignTwoLabels(IBond[] bonds, IBond.Stereo[] labels)
focal_class.full_signature: private boolean assignTwoLabels(IBond[] bonds, IBond.Stereo[] labels)
focal_class.identifier: assignTwoLabels
focal_class.modifiers: private
focal_class.parameters: (IBond[] bonds, IBond.Stereo[] labels)
focal_class.return: boolean
focal_class.signature: boolean assignTwoLabels(IBond[] bonds, IBond.Stereo[] labels)
focal_class.class_method_signature: NonplanarBonds.countRingBonds(IBond[] bonds)
focal_class.full_signature: private int countRingBonds(IBond[] bonds)
focal_class.identifier: countRingBonds
focal_class.modifiers: private
focal_class.parameters: (IBond[] bonds)
focal_class.return: int
focal_class.signature: int countRingBonds(IBond[] bonds)
focal_class.class_method_signature: NonplanarBonds.indexParity(int x)
focal_class.full_signature: private int indexParity(int x)
focal_class.identifier: indexParity
focal_class.modifiers: private
focal_class.parameters: (int x)
focal_class.return: int
focal_class.signature: int indexParity(int x)
focal_class.class_method_signature: NonplanarBonds.parity(ITetrahedralChirality.Stereo stereo)
focal_class.full_signature: private int parity(ITetrahedralChirality.Stereo stereo)
focal_class.identifier: parity
focal_class.modifiers: private
focal_class.parameters: (ITetrahedralChirality.Stereo stereo)
focal_class.return: int
focal_class.signature: int parity(ITetrahedralChirality.Stereo stereo)
focal_class.class_method_signature: NonplanarBonds.nAdjacentCentres(int i)
focal_class.full_signature: private int nAdjacentCentres(int i)
focal_class.identifier: nAdjacentCentres
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: int
focal_class.signature: int nAdjacentCentres(int i)
focal_class.class_method_signature: NonplanarBonds.priority(int focus, IAtom[] atoms, int n)
focal_class.full_signature: private int[] priority(int focus, IAtom[] atoms, int n)
focal_class.identifier: priority
focal_class.modifiers: private
focal_class.parameters: (int focus, IAtom[] atoms, int n)
focal_class.return: int[]
focal_class.signature: int[] priority(int focus, IAtom[] atoms, int n)
focal_class.class_method_signature: NonplanarBonds.isSp3Carbon(IAtom atom, int deg)
focal_class.full_signature: private boolean isSp3Carbon(IAtom atom, int deg)
focal_class.identifier: isSp3Carbon
focal_class.modifiers: private
focal_class.parameters: (IAtom atom, int deg)
focal_class.return: boolean
focal_class.signature: boolean isSp3Carbon(IAtom atom, int deg)
focal_class.class_method_signature: NonplanarBonds.hasPriority(int focus, int i, int j)
focal_class.full_signature:  boolean hasPriority(int focus, int i, int j)
focal_class.identifier: hasPriority
focal_class.parameters: (int focus, int i, int j)
focal_class.return: boolean
focal_class.signature: boolean hasPriority(int focus, int i, int j)
focal_class.class_method_signature: NonplanarBonds.sortClockwise(int[] indices, IAtom focus, IAtom[] atoms, int n)
focal_class.full_signature: private int sortClockwise(int[] indices, IAtom focus, IAtom[] atoms, int n)
focal_class.identifier: sortClockwise
focal_class.modifiers: private
focal_class.parameters: (int[] indices, IAtom focus, IAtom[] atoms, int n)
focal_class.return: int
focal_class.signature: int sortClockwise(int[] indices, IAtom focus, IAtom[] atoms, int n)
focal_class.class_method_signature: NonplanarBonds.less(int i, int j, IAtom[] atoms, Point2d center)
focal_class.full_signature: static boolean less(int i, int j, IAtom[] atoms, Point2d center)
focal_class.identifier: less
focal_class.modifiers: static
focal_class.parameters: (int i, int j, IAtom[] atoms, Point2d center)
focal_class.return: boolean
focal_class.signature: boolean less(int i, int j, IAtom[] atoms, Point2d center)
focal_class.class_method_signature: NonplanarBonds.labelUnspecified(IBond doubleBond)
focal_class.full_signature: private void labelUnspecified(IBond doubleBond)
focal_class.identifier: labelUnspecified
focal_class.modifiers: private
focal_class.parameters: (IBond doubleBond)
focal_class.return: void
focal_class.signature: void labelUnspecified(IBond doubleBond)
focal_class.class_method_signature: NonplanarBonds.isCisTransEndPoint(int idx)
focal_class.full_signature: private boolean isCisTransEndPoint(int idx)
focal_class.identifier: isCisTransEndPoint
focal_class.modifiers: private
focal_class.parameters: (int idx)
focal_class.return: boolean
focal_class.signature: boolean isCisTransEndPoint(int idx)
focal_class.class_method_signature: NonplanarBonds.getBondTypes(int idx)
focal_class.full_signature: private int getBondTypes(int idx)
focal_class.identifier: getBondTypes
focal_class.modifiers: private
focal_class.parameters: (int idx)
focal_class.return: int
focal_class.signature: int getBondTypes(int idx)
focal_class.class_method_signature: NonplanarBonds.findUnspecifiedDoubleBonds(int[][] adjList)
focal_class.full_signature: private List<IBond> findUnspecifiedDoubleBonds(int[][] adjList)
focal_class.identifier: findUnspecifiedDoubleBonds
focal_class.modifiers: private
focal_class.parameters: (int[][] adjList)
focal_class.return: List<IBond>
focal_class.signature: List<IBond> findUnspecifiedDoubleBonds(int[][] adjList)
focal_class.class_method_signature: NonplanarBonds.hasLinearEqualPaths(int[][] adjList, int start, int prev)
focal_class.full_signature: private boolean hasLinearEqualPaths(int[][] adjList, int start, int prev)
focal_class.identifier: hasLinearEqualPaths
focal_class.modifiers: private
focal_class.parameters: (int[][] adjList, int start, int prev)
focal_class.return: boolean
focal_class.signature: boolean hasLinearEqualPaths(int[][] adjList, int start, int prev)
focal_class.class_method_signature: NonplanarBonds.notEqual(Integer a, Integer b)
focal_class.full_signature: private boolean notEqual(Integer a, Integer b)
focal_class.identifier: notEqual
focal_class.modifiers: private
focal_class.parameters: (Integer a, Integer b)
focal_class.return: boolean
focal_class.signature: boolean notEqual(Integer a, Integer b)
focal_class.class_method_signature: NonplanarBonds.hasOnlyPlainBonds(int v, IBond allowedDoubleBond)
focal_class.full_signature: private boolean hasOnlyPlainBonds(int v, IBond allowedDoubleBond)
focal_class.identifier: hasOnlyPlainBonds
focal_class.modifiers: private
focal_class.parameters: (int v, IBond allowedDoubleBond)
focal_class.return: boolean
focal_class.signature: boolean hasOnlyPlainBonds(int v, IBond allowedDoubleBond)
focal_method.body: public static IAtomContainer assign(final IAtomContainer container) {
          GraphUtil.EdgeToBondMap edgeToBond = GraphUtil.EdgeToBondMap.withSpaceFor(container);
          new NonplanarBonds(container, GraphUtil.toAdjList(container, edgeToBond), edgeToBond);
          return container;
      }
focal_method.class_method_signature: NonplanarBonds.assign(final IAtomContainer container)
focal_method.full_signature: public static IAtomContainer assign(final IAtomContainer container)
focal_method.identifier: assign
focal_method.invocations: withSpaceFor toAdjList
focal_method.modifiers: public static
focal_method.parameters: (final IAtomContainer container)
focal_method.return: IAtomContainer
focal_method.signature: IAtomContainer assign(final IAtomContainer container)