test_class.file: legacy/src/test/java/org/openscience/cdk/geometry/GeometryToolsTest.java
test_class.identifier: GeometryToolsTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetBestAlignmentForLabelXY() {
          final String TYPE = "C";
          IAtom zero = new Atom("O");
          zero.setPoint2d(new Point2d());
          IAtom pX = new Atom(TYPE);
          pX.setPoint2d(new Point2d(1, 0));
          IAtom nX = new Atom(TYPE);
          nX.setPoint2d(new Point2d(-1, 0));
          IAtom pY = new Atom(TYPE);
          pY.setPoint2d(new Point2d(0, 1));
          IAtom nY = new Atom(TYPE);
          nY.setPoint2d(new Point2d(0, -1));
  
          Assert.assertEquals(-1, alignmentTestHelper(zero, pX));
          Assert.assertEquals(1, alignmentTestHelper(zero, nX));
          Assert.assertEquals(-2, alignmentTestHelper(zero, pY));
          Assert.assertEquals(2, alignmentTestHelper(zero, nY));
  
          Assert.assertEquals(1, alignmentTestHelper(zero, pY, nY));
      }
test_case.class_method_signature: GeometryToolsTest.testGetBestAlignmentForLabelXY()
test_case.full_signature: @Test public void testGetBestAlignmentForLabelXY()
test_case.identifier: testGetBestAlignmentForLabelXY
test_case.invocations: setPoint2d setPoint2d setPoint2d setPoint2d setPoint2d assertEquals alignmentTestHelper assertEquals alignmentTestHelper assertEquals alignmentTestHelper assertEquals alignmentTestHelper assertEquals alignmentTestHelper
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetBestAlignmentForLabelXY()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(GeometryTools.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(GeometryTools.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java
focal_class.identifier: GeometryTools
focal_class.class_method_signature: GeometryTools.translateAllPositive(IAtomContainer atomCon)
focal_class.full_signature: public static void translateAllPositive(IAtomContainer atomCon)
focal_class.identifier: translateAllPositive
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon)
focal_class.return: void
focal_class.signature: void translateAllPositive(IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.translate2D(IAtomContainer atomCon, double transX, double transY)
focal_class.full_signature: public static void translate2D(IAtomContainer atomCon, double transX, double transY)
focal_class.identifier: translate2D
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, double transX, double transY)
focal_class.return: void
focal_class.signature: void translate2D(IAtomContainer atomCon, double transX, double transY)
focal_class.class_method_signature: GeometryTools.scaleMolecule(IAtomContainer atomCon, Dimension areaDim, double fillFactor)
focal_class.full_signature: public static void scaleMolecule(IAtomContainer atomCon, Dimension areaDim, double fillFactor)
focal_class.identifier: scaleMolecule
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, Dimension areaDim, double fillFactor)
focal_class.return: void
focal_class.signature: void scaleMolecule(IAtomContainer atomCon, Dimension areaDim, double fillFactor)
focal_class.class_method_signature: GeometryTools.scaleMolecule(IAtomContainer atomCon, double scaleFactor)
focal_class.full_signature: public static void scaleMolecule(IAtomContainer atomCon, double scaleFactor)
focal_class.identifier: scaleMolecule
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, double scaleFactor)
focal_class.return: void
focal_class.signature: void scaleMolecule(IAtomContainer atomCon, double scaleFactor)
focal_class.class_method_signature: GeometryTools.center(IAtomContainer atomCon, Dimension areaDim)
focal_class.full_signature: public static void center(IAtomContainer atomCon, Dimension areaDim)
focal_class.identifier: center
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, Dimension areaDim)
focal_class.return: void
focal_class.signature: void center(IAtomContainer atomCon, Dimension areaDim)
focal_class.class_method_signature: GeometryTools.translate2D(IAtomContainer atomCon, Vector2d vector)
focal_class.full_signature: public static void translate2D(IAtomContainer atomCon, Vector2d vector)
focal_class.identifier: translate2D
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, Vector2d vector)
focal_class.return: void
focal_class.signature: void translate2D(IAtomContainer atomCon, Vector2d vector)
focal_class.class_method_signature: GeometryTools.rotate(IAtomContainer atomCon, Point2d center, double angle)
focal_class.full_signature: public static void rotate(IAtomContainer atomCon, Point2d center, double angle)
focal_class.identifier: rotate
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, Point2d center, double angle)
focal_class.return: void
focal_class.signature: void rotate(IAtomContainer atomCon, Point2d center, double angle)
focal_class.class_method_signature: GeometryTools.rotate(IAtom atom, Point3d p1, Point3d p2, double angle)
focal_class.full_signature: public static void rotate(IAtom atom, Point3d p1, Point3d p2, double angle)
focal_class.identifier: rotate
focal_class.modifiers: public static
focal_class.parameters: (IAtom atom, Point3d p1, Point3d p2, double angle)
focal_class.return: void
focal_class.signature: void rotate(IAtom atom, Point3d p1, Point3d p2, double angle)
focal_class.class_method_signature: GeometryTools.normalize(Point3d point)
focal_class.full_signature: public static void normalize(Point3d point)
focal_class.identifier: normalize
focal_class.modifiers: public static
focal_class.parameters: (Point3d point)
focal_class.return: void
focal_class.signature: void normalize(Point3d point)
focal_class.class_method_signature: GeometryTools.get2DDimension(IAtomContainer atomCon)
focal_class.full_signature: public static Dimension get2DDimension(IAtomContainer atomCon)
focal_class.identifier: get2DDimension
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon)
focal_class.return: Dimension
focal_class.signature: Dimension get2DDimension(IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.getRectangle2D(IAtomContainer container)
focal_class.full_signature: public static Rectangle2D getRectangle2D(IAtomContainer container)
focal_class.identifier: getRectangle2D
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: Rectangle2D
focal_class.signature: Rectangle2D getRectangle2D(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.getMinMax(IAtomContainer container)
focal_class.full_signature: public static double[] getMinMax(IAtomContainer container)
focal_class.identifier: getMinMax
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: double[]
focal_class.signature: double[] getMinMax(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.translate2DCentreOfMassTo(IAtomContainer atomCon, Point2d p)
focal_class.full_signature: public static void translate2DCentreOfMassTo(IAtomContainer atomCon, Point2d p)
focal_class.identifier: translate2DCentreOfMassTo
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, Point2d p)
focal_class.return: void
focal_class.signature: void translate2DCentreOfMassTo(IAtomContainer atomCon, Point2d p)
focal_class.class_method_signature: GeometryTools.get2DCenter(Iterable<IAtom> atoms)
focal_class.full_signature: public static Point2d get2DCenter(Iterable<IAtom> atoms)
focal_class.identifier: get2DCenter
focal_class.modifiers: public static
focal_class.parameters: (Iterable<IAtom> atoms)
focal_class.return: Point2d
focal_class.signature: Point2d get2DCenter(Iterable<IAtom> atoms)
focal_class.class_method_signature: GeometryTools.get2DCenter(Iterator<IAtom> atoms)
focal_class.full_signature: public static Point2d get2DCenter(Iterator<IAtom> atoms)
focal_class.identifier: get2DCenter
focal_class.modifiers: public static
focal_class.parameters: (Iterator<IAtom> atoms)
focal_class.return: Point2d
focal_class.signature: Point2d get2DCenter(Iterator<IAtom> atoms)
focal_class.class_method_signature: GeometryTools.get2DCenter(IRingSet ringSet)
focal_class.full_signature: public static Point2d get2DCenter(IRingSet ringSet)
focal_class.identifier: get2DCenter
focal_class.modifiers: public static
focal_class.parameters: (IRingSet ringSet)
focal_class.return: Point2d
focal_class.signature: Point2d get2DCenter(IRingSet ringSet)
focal_class.class_method_signature: GeometryTools.get2DCentreOfMass(IAtomContainer ac)
focal_class.full_signature: public static Point2d get2DCentreOfMass(IAtomContainer ac)
focal_class.identifier: get2DCentreOfMass
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer ac)
focal_class.return: Point2d
focal_class.signature: Point2d get2DCentreOfMass(IAtomContainer ac)
focal_class.class_method_signature: GeometryTools.get2DCenter(IAtomContainer container)
focal_class.full_signature: public static Point2d get2DCenter(IAtomContainer container)
focal_class.identifier: get2DCenter
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: Point2d
focal_class.signature: Point2d get2DCenter(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.translate2DCenterTo(IAtomContainer container, Point2d p)
focal_class.full_signature: public static void translate2DCenterTo(IAtomContainer container, Point2d p)
focal_class.identifier: translate2DCenterTo
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, Point2d p)
focal_class.return: void
focal_class.signature: void translate2DCenterTo(IAtomContainer container, Point2d p)
focal_class.class_method_signature: GeometryTools.get3DCentreOfMass(IAtomContainer ac)
focal_class.full_signature: public static Point3d get3DCentreOfMass(IAtomContainer ac)
focal_class.identifier: get3DCentreOfMass
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer ac)
focal_class.return: Point3d
focal_class.signature: Point3d get3DCentreOfMass(IAtomContainer ac)
focal_class.class_method_signature: GeometryTools.get3DCenter(IAtomContainer ac)
focal_class.full_signature: public static Point3d get3DCenter(IAtomContainer ac)
focal_class.identifier: get3DCenter
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer ac)
focal_class.return: Point3d
focal_class.signature: Point3d get3DCenter(IAtomContainer ac)
focal_class.class_method_signature: GeometryTools.getAngle(double xDiff, double yDiff)
focal_class.full_signature: public static double getAngle(double xDiff, double yDiff)
focal_class.identifier: getAngle
focal_class.modifiers: public static
focal_class.parameters: (double xDiff, double yDiff)
focal_class.return: double
focal_class.signature: double getAngle(double xDiff, double yDiff)
focal_class.class_method_signature: GeometryTools.distanceCalculator(int[] coords, double dist)
focal_class.full_signature: public static int[] distanceCalculator(int[] coords, double dist)
focal_class.identifier: distanceCalculator
focal_class.modifiers: public static
focal_class.parameters: (int[] coords, double dist)
focal_class.return: int[]
focal_class.signature: int[] distanceCalculator(int[] coords, double dist)
focal_class.class_method_signature: GeometryTools.distanceCalculator(double[] coords, double dist)
focal_class.full_signature: public static double[] distanceCalculator(double[] coords, double dist)
focal_class.identifier: distanceCalculator
focal_class.modifiers: public static
focal_class.parameters: (double[] coords, double dist)
focal_class.return: double[]
focal_class.signature: double[] distanceCalculator(double[] coords, double dist)
focal_class.class_method_signature: GeometryTools.getBondCoordinates(IBond bond)
focal_class.full_signature: public static int[] getBondCoordinates(IBond bond)
focal_class.identifier: getBondCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IBond bond)
focal_class.return: int[]
focal_class.signature: int[] getBondCoordinates(IBond bond)
focal_class.class_method_signature: GeometryTools.getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.full_signature: public static IAtom getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.identifier: getClosestAtom
focal_class.modifiers: public static
focal_class.parameters: (int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.return: IAtom
focal_class.signature: IAtom getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.getClosestAtom(IAtomContainer atomCon, IAtom atom)
focal_class.full_signature: public static IAtom getClosestAtom(IAtomContainer atomCon, IAtom atom)
focal_class.identifier: getClosestAtom
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomCon, IAtom atom)
focal_class.return: IAtom
focal_class.signature: IAtom getClosestAtom(IAtomContainer atomCon, IAtom atom)
focal_class.class_method_signature: GeometryTools.getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)
focal_class.full_signature: public static IAtom getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)
focal_class.identifier: getClosestAtom
focal_class.modifiers: public static
focal_class.parameters: (double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)
focal_class.return: IAtom
focal_class.signature: IAtom getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)
focal_class.class_method_signature: GeometryTools.getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.full_signature: public static IAtom getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.identifier: getClosestAtom
focal_class.modifiers: public static
focal_class.parameters: (double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.return: IAtom
focal_class.signature: IAtom getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.full_signature: public static IBond getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.identifier: getClosestBond
focal_class.modifiers: public static
focal_class.parameters: (int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.return: IBond
focal_class.signature: IBond getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.full_signature: public static IBond getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.identifier: getClosestBond
focal_class.modifiers: public static
focal_class.parameters: (double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.return: IBond
focal_class.signature: IBond getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)
focal_class.class_method_signature: GeometryTools.sortBy2DDistance(IAtom[] atoms, Point2d point)
focal_class.full_signature: public static void sortBy2DDistance(IAtom[] atoms, Point2d point)
focal_class.identifier: sortBy2DDistance
focal_class.modifiers: public static
focal_class.parameters: (IAtom[] atoms, Point2d point)
focal_class.return: void
focal_class.signature: void sortBy2DDistance(IAtom[] atoms, Point2d point)
focal_class.class_method_signature: GeometryTools.getScaleFactor(IAtomContainer container, double bondLength)
focal_class.full_signature: public static double getScaleFactor(IAtomContainer container, double bondLength)
focal_class.identifier: getScaleFactor
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, double bondLength)
focal_class.return: double
focal_class.signature: double getScaleFactor(IAtomContainer container, double bondLength)
focal_class.class_method_signature: GeometryTools.getBondLengthAverage(IAtomContainer container)
focal_class.full_signature: public static double getBondLengthAverage(IAtomContainer container)
focal_class.identifier: getBondLengthAverage
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: double
focal_class.signature: double getBondLengthAverage(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.getBondLengthMedian(final IAtomContainer container)
focal_class.full_signature: public static double getBondLengthMedian(final IAtomContainer container)
focal_class.identifier: getBondLengthMedian
focal_class.modifiers: public static
focal_class.parameters: (final IAtomContainer container)
focal_class.return: double
focal_class.signature: double getBondLengthMedian(final IAtomContainer container)
focal_class.class_method_signature: GeometryTools.getLength2D(IBond bond)
focal_class.full_signature: public static double getLength2D(IBond bond)
focal_class.identifier: getLength2D
focal_class.modifiers: public static
focal_class.parameters: (IBond bond)
focal_class.return: double
focal_class.signature: double getLength2D(IBond bond)
focal_class.class_method_signature: GeometryTools.has2DCoordinates(IAtomContainer container)
focal_class.full_signature: public static boolean has2DCoordinates(IAtomContainer container)
focal_class.identifier: has2DCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: boolean
focal_class.signature: boolean has2DCoordinates(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.get2DCoordinateCoverage(IAtomContainer container)
focal_class.full_signature: public static CoordinateCoverage get2DCoordinateCoverage(IAtomContainer container)
focal_class.identifier: get2DCoordinateCoverage
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: CoordinateCoverage
focal_class.signature: CoordinateCoverage get2DCoordinateCoverage(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.has2DCoordinatesNew(IAtomContainer container)
focal_class.full_signature: @Deprecated public static int has2DCoordinatesNew(IAtomContainer container)
focal_class.identifier: has2DCoordinatesNew
focal_class.modifiers: @Deprecated public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: int
focal_class.signature: int has2DCoordinatesNew(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.has2DCoordinates(IAtom atom)
focal_class.full_signature: public static boolean has2DCoordinates(IAtom atom)
focal_class.identifier: has2DCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean has2DCoordinates(IAtom atom)
focal_class.class_method_signature: GeometryTools.has2DCoordinates(IBond bond)
focal_class.full_signature: public static boolean has2DCoordinates(IBond bond)
focal_class.identifier: has2DCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IBond bond)
focal_class.return: boolean
focal_class.signature: boolean has2DCoordinates(IBond bond)
focal_class.class_method_signature: GeometryTools.has3DCoordinates(IAtomContainer container)
focal_class.full_signature: public static boolean has3DCoordinates(IAtomContainer container)
focal_class.identifier: has3DCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: boolean
focal_class.signature: boolean has3DCoordinates(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.get3DCoordinateCoverage(IAtomContainer container)
focal_class.full_signature: public static CoordinateCoverage get3DCoordinateCoverage(IAtomContainer container)
focal_class.identifier: get3DCoordinateCoverage
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: CoordinateCoverage
focal_class.signature: CoordinateCoverage get3DCoordinateCoverage(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.calculatePerpendicularUnitVector(Point2d point1, Point2d point2)
focal_class.full_signature: public static Vector2d calculatePerpendicularUnitVector(Point2d point1, Point2d point2)
focal_class.identifier: calculatePerpendicularUnitVector
focal_class.modifiers: public static
focal_class.parameters: (Point2d point1, Point2d point2)
focal_class.return: Vector2d
focal_class.signature: Vector2d calculatePerpendicularUnitVector(Point2d point1, Point2d point2)
focal_class.class_method_signature: GeometryTools.getNormalizationFactor(IAtomContainer container)
focal_class.full_signature: public static double getNormalizationFactor(IAtomContainer container)
focal_class.identifier: getNormalizationFactor
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: double
focal_class.signature: double getNormalizationFactor(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.getBestAlignmentForLabel(IAtomContainer container, IAtom atom)
focal_class.full_signature: public static int getBestAlignmentForLabel(IAtomContainer container, IAtom atom)
focal_class.identifier: getBestAlignmentForLabel
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: int
focal_class.signature: int getBestAlignmentForLabel(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: GeometryTools.getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)
focal_class.full_signature: public static int getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)
focal_class.identifier: getBestAlignmentForLabelXY
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: int
focal_class.signature: int getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: GeometryTools.findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)
focal_class.full_signature: public static List<IAtom> findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)
focal_class.identifier: findClosestInSpace
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IAtom startAtom, int max)
focal_class.return: List<IAtom>
focal_class.signature: List<IAtom> findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)
focal_class.class_method_signature: GeometryTools.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
              IAtomContainer secondAtomContainer, double searchRadius, Map<Integer, Integer> mappedAtoms)
focal_class.full_signature: public static Map<Integer, Integer> mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
              IAtomContainer secondAtomContainer, double searchRadius, Map<Integer, Integer> mappedAtoms)
focal_class.identifier: mapAtomsOfAlignedStructures
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer firstAtomContainer,
              IAtomContainer secondAtomContainer, double searchRadius, Map<Integer, Integer> mappedAtoms)
focal_class.return: Map<Integer, Integer>
focal_class.signature: Map<Integer, Integer> mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
              IAtomContainer secondAtomContainer, double searchRadius, Map<Integer, Integer> mappedAtoms)
focal_class.class_method_signature: GeometryTools.getLargestAtomContainer(IAtomContainer firstAC, IAtomContainer secondAC)
focal_class.full_signature: private static void getLargestAtomContainer(IAtomContainer firstAC, IAtomContainer secondAC)
focal_class.identifier: getLargestAtomContainer
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer firstAC, IAtomContainer secondAC)
focal_class.return: void
focal_class.signature: void getLargestAtomContainer(IAtomContainer firstAC, IAtomContainer secondAC)
focal_class.class_method_signature: GeometryTools.checkAtomMapping(IAtomContainer firstAC, IAtomContainer secondAC, int posFirstAtom,
              int posSecondAtom)
focal_class.full_signature: private static boolean checkAtomMapping(IAtomContainer firstAC, IAtomContainer secondAC, int posFirstAtom,
              int posSecondAtom)
focal_class.identifier: checkAtomMapping
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer firstAC, IAtomContainer secondAC, int posFirstAtom,
              int posSecondAtom)
focal_class.return: boolean
focal_class.signature: boolean checkAtomMapping(IAtomContainer firstAC, IAtomContainer secondAC, int posFirstAtom,
              int posSecondAtom)
focal_class.class_method_signature: GeometryTools.setVisitedFlagsToFalse(IAtomContainer atomContainer)
focal_class.full_signature: private static IAtomContainer setVisitedFlagsToFalse(IAtomContainer atomContainer)
focal_class.identifier: setVisitedFlagsToFalse
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer setVisitedFlagsToFalse(IAtomContainer atomContainer)
focal_class.class_method_signature: GeometryTools.getBondLengthRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.full_signature: public static double getBondLengthRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.identifier: getBondLengthRMSD
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.return: double
focal_class.signature: double getBondLengthRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.class_method_signature: GeometryTools.getAngleRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms)
focal_class.full_signature: public static double getAngleRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms)
focal_class.identifier: getAngleRMSD
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms)
focal_class.return: double
focal_class.signature: double getAngleRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms)
focal_class.class_method_signature: GeometryTools.getAngle(IAtom atom1, IAtom atom2, IAtom atom3)
focal_class.full_signature: private static double getAngle(IAtom atom1, IAtom atom2, IAtom atom3)
focal_class.identifier: getAngle
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom1, IAtom atom2, IAtom atom3)
focal_class.return: double
focal_class.signature: double getAngle(IAtom atom1, IAtom atom2, IAtom atom3)
focal_class.class_method_signature: GeometryTools.getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.full_signature: public static double getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.identifier: getAllAtomRMSD
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.return: double
focal_class.signature: double getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean Coords3d)
focal_class.class_method_signature: GeometryTools.getHeavyAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean hetAtomOnly, boolean Coords3d)
focal_class.full_signature: public static double getHeavyAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean hetAtomOnly, boolean Coords3d)
focal_class.identifier: getHeavyAtomRMSD
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean hetAtomOnly, boolean Coords3d)
focal_class.return: double
focal_class.signature: double getHeavyAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer,
              Map<Integer, Integer> mappedAtoms, boolean hetAtomOnly, boolean Coords3d)
focal_class.class_method_signature: GeometryTools.getBondLengthAverage3D(IAtomContainer container)
focal_class.full_signature: public static double getBondLengthAverage3D(IAtomContainer container)
focal_class.identifier: getBondLengthAverage3D
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: double
focal_class.signature: double getBondLengthAverage3D(IAtomContainer container)
focal_class.class_method_signature: GeometryTools.shiftContainer(IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.full_signature: public static Rectangle2D shiftContainer(IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.identifier: shiftContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.return: Rectangle2D
focal_class.signature: Rectangle2D shiftContainer(IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.class_method_signature: GeometryTools.getBondLengthAverage(IReaction reaction)
focal_class.full_signature: public static double getBondLengthAverage(IReaction reaction)
focal_class.identifier: getBondLengthAverage
focal_class.modifiers: public static
focal_class.parameters: (IReaction reaction)
focal_class.return: double
focal_class.signature: double getBondLengthAverage(IReaction reaction)
focal_class.class_method_signature: GeometryTools.has3DCoordinates(IChemModel chemModel)
focal_class.full_signature: public static boolean has3DCoordinates(IChemModel chemModel)
focal_class.identifier: has3DCoordinates
focal_class.modifiers: public static
focal_class.parameters: (IChemModel chemModel)
focal_class.return: boolean
focal_class.signature: boolean has3DCoordinates(IChemModel chemModel)
focal_class.class_method_signature: GeometryTools.shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.full_signature: public static Rectangle2D shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.identifier: shiftReactionVertical
focal_class.modifiers: public static
focal_class.parameters: (IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap)
focal_class.return: Rectangle2D
focal_class.signature: Rectangle2D shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap)
focal_method.body: public static int getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom) {
          double overallDiffX = 0;
          double overallDiffY = 0;
          for (IAtom connectedAtom : container.getConnectedAtomsList(atom)) {
              overallDiffX += connectedAtom.getPoint2d().x - atom.getPoint2d().x;
              overallDiffY += connectedAtom.getPoint2d().y - atom.getPoint2d().y;
          }
          if (Math.abs(overallDiffY) > Math.abs(overallDiffX)) {
              if (overallDiffY < 0)
                  return 2;
              else
                  return -2;
          } else {
              if (overallDiffX <= 0)
                  return 1;
              else
                  return -1;
          }
      }
focal_method.class_method_signature: GeometryTools.getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)
focal_method.full_signature: public static int getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)
focal_method.identifier: getBestAlignmentForLabelXY
focal_method.invocations: getConnectedAtomsList getPoint2d getPoint2d getPoint2d getPoint2d abs abs
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer container, IAtom atom)
focal_method.return: int
focal_method.signature: int getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)