test_class.file: tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
test_class.identifier: NonPlanarBondsTest
test_case.body: @Test
      public void dontUnspecifiedDueToHRepresentation() {
          IAtomContainer m = new AtomContainer();
          m.addAtom(atom("R", 0, 0.00, 0.00));
          m.addAtom(atom("C", 2, 1.30, -0.75));
          m.addAtom(atom("N", 0, 2.60, -0.00));
          m.addAtom(atom("C", 0, 3.90, -0.75));
          m.addAtom(atom("C", 2, 3.90, -2.25));
          m.addAtom(atom("C", 2, 2.60, -3.00));
          m.addAtom(atom("C", 3, 2.60, -4.50));
          m.addAtom(atom("C", 2, 5.20, -0.00));
          m.addAtom(atom("C", 2, 6.50, -0.75));
          m.addAtom(atom("C", 2, 7.79, -0.00));
          m.addAtom(atom("H", 0, 9.09, -0.75));
          m.addBond(0, 1, IBond.Order.SINGLE);
          m.addBond(1, 2, IBond.Order.SINGLE);
          m.addBond(2, 3, IBond.Order.DOUBLE);
          m.addBond(3, 4, IBond.Order.SINGLE);
          m.addBond(4, 5, IBond.Order.SINGLE);
          m.addBond(5, 6, IBond.Order.SINGLE);
          m.addBond(3, 7, IBond.Order.SINGLE);
          m.addBond(7, 8, IBond.Order.SINGLE);
          m.addBond(8, 9, IBond.Order.SINGLE);
          m.addBond(9, 10, IBond.Order.SINGLE);
          NonplanarBonds.assign(m);
          for (IBond bond : m.bonds())
              assertThat(bond.getStereo(), is(IBond.Stereo.NONE));
      }
test_case.class_method_signature: NonPlanarBondsTest.dontUnspecifiedDueToHRepresentation()
test_case.full_signature: @Test public void dontUnspecifiedDueToHRepresentation()
test_case.identifier: dontUnspecifiedDueToHRepresentation
test_case.invocations: addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addBond addBond addBond addBond addBond addBond addBond addBond addBond addBond assign bonds assertThat getStereo is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void dontUnspecifiedDueToHRepresentation()
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)