org.openscience.cdk.stereo

Class StereoTool

java.lang.Object

org.openscience.cdk.stereo.StereoTool

public class StereoTool
extends Object

Methods to determine or check the stereo class of a set of atoms. Some of these methods were adapted from Jmol's smiles search package.

Author:

maclean

Source code:

master

Belongs to CDK module:

standard

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StereoTool.SquarePlanarShape The shape that four atoms take in a plane.
static class	StereoTool.StereoClass Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.
static class	StereoTool.TetrahedralSign The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.

Field Summary

Fields

Modifier and Type	Field and Description
static double	MAX_AXIS_ANGLE The maximum angle in radians for two lines to be 'diaxial'.
static double	MIN_COLINEAR_NORMAL The maximum tolerance for the normal calculated during colinearity.
static double	PLANE_TOLERANCE

Constructor Summary

Constructors

Constructor and Description
StereoTool()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	allCoplanar(javax.vecmath.Vector3d planeNormal, javax.vecmath.Point3d pointInPlane, javax.vecmath.Point3d... points) Check that all the points in the list are coplanar (in the same plane) as the plane defined by the planeNormal and the pointInPlane.
static StereoTool.TetrahedralSign	getHandedness(IAtom baseAtomA, IAtom baseAtomB, IAtom baseAtomC, IAtom apexAtom) Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex.
static javax.vecmath.Vector3d	getNormal(javax.vecmath.Point3d ptA, javax.vecmath.Point3d ptB, javax.vecmath.Point3d ptC) Given three points (A, B, C), makes the vectors A-B and A-C, and makes the cross product of these two vectors; this has the effect of making a third vector at right angles to AB and AC.
static StereoTool.SquarePlanarShape	getSquarePlanarShape(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD) Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.
static ITetrahedralChirality.Stereo	getStereo(IAtom atom1, IAtom atom2, IAtom atom3, IAtom atom4) Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
static boolean	isColinear(javax.vecmath.Point3d ptA, javax.vecmath.Point3d ptB, javax.vecmath.Point3d ptC) Checks the three supplied points to see if they fall on the same line.
static boolean	isOctahedral(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF, IAtom atomG) Checks these 7 atoms to see if they are at the points of an octahedron.
static boolean	isSquarePlanar(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD) Checks these four atoms for square planarity.
static boolean	isTrigonalBipyramidal(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF) Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
static double	signedDistanceToPlane(javax.vecmath.Vector3d planeNormal, javax.vecmath.Point3d pointInPlane, javax.vecmath.Point3d point) Given a normalized normal for a plane, any point in that plane, and a point, will return the distance between the plane and that point.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_AXIS_ANGLE

public static final double MAX_AXIS_ANGLE

The maximum angle in radians for two lines to be 'diaxial'. Where 0.95 is about 172 degrees.

See Also:

Constant Field Values

MIN_COLINEAR_NORMAL

public static final double MIN_COLINEAR_NORMAL

The maximum tolerance for the normal calculated during colinearity.

See Also:

Constant Field Values

PLANE_TOLERANCE

public static final double PLANE_TOLERANCE

See Also:

Constant Field Values

Constructor Detail

StereoTool

public StereoTool()

Method Detail

isSquarePlanar

public static boolean isSquarePlanar(IAtom atomA,
                     IAtom atomB,
                     IAtom atomC,
                     IAtom atomD)

Checks these four atoms for square planarity.

Parameters:

atomA - an atom in the plane

atomB - an atom in the plane

atomC - an atom in the plane

atomD - an atom in the plane

Returns:

true if all the atoms are in the same plane

getSquarePlanarShape

public static StereoTool.SquarePlanarShape getSquarePlanarShape(IAtom atomA,
                                                IAtom atomB,
                                                IAtom atomC,
                                                IAtom atomD)

Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.

The 'shapes' returned represent arrangements that look a little like the characters 'U', '4', and 'Z'.

Parameters:

atomA - an atom in the plane

atomB - an atom in the plane

atomC - an atom in the plane

atomD - an atom in the plane

Returns:

the shape (U/4/Z)

allCoplanar

public static boolean allCoplanar(javax.vecmath.Vector3d planeNormal,
                  javax.vecmath.Point3d pointInPlane,
                  javax.vecmath.Point3d... points)

Check that all the points in the list are coplanar (in the same plane) as the plane defined by the planeNormal and the pointInPlane.

Parameters:

planeNormal - the normal to the plane

pointInPlane - any point know to be in the plane

points - an array of points to test

Returns:

false if any of the points is not in the plane

isOctahedral

public static boolean isOctahedral(IAtom atomA,
                   IAtom atomB,
                   IAtom atomC,
                   IAtom atomD,
                   IAtom atomE,
                   IAtom atomF,
                   IAtom atomG)

Checks these 7 atoms to see if they are at the points of an octahedron.

Parameters:

atomA - one of the axial atoms

atomB - the central atom

atomC - one of the equatorial atoms

atomD - one of the equatorial atoms

atomE - one of the equatorial atoms

atomF - one of the equatorial atoms

atomG - the other axial atom

Returns:

true if the geometry is octahedral

isTrigonalBipyramidal

public static boolean isTrigonalBipyramidal(IAtom atomA,
                            IAtom atomB,
                            IAtom atomC,
                            IAtom atomD,
                            IAtom atomE,
                            IAtom atomF)

Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.

Parameters:

atomA - one of the axial atoms

atomB - the central atom

atomC - one of the equatorial atoms

atomD - one of the equatorial atoms

atomE - one of the equatorial atoms

atomF - the other axial atom

Returns:

true if the geometry is trigonal-bipyramidal

getStereo

public static ITetrahedralChirality.Stereo getStereo(IAtom atom1,
                                     IAtom atom2,
                                     IAtom atom3,
                                     IAtom atom4)

Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE. The first atom is the one pointing towards the observer.

Parameters:

atom1 - the atom pointing towards the observer

atom2 - the second atom (points away)

atom3 - the third atom (points away)

atom4 - the fourth atom (points away)

Returns:

clockwise or anticlockwise

getHandedness

public static StereoTool.TetrahedralSign getHandedness(IAtom baseAtomA,
                                       IAtom baseAtomB,
                                       IAtom baseAtomC,
                                       IAtom apexAtom)

Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex. Note that it assumes a right-handed coordinate system, and that the points {A,B,C} are in a counter-clockwise order in the plane they share.

Parameters:

baseAtomA - the first atom in the base of the tetrahedron

baseAtomB - the second atom in the base of the tetrahedron

baseAtomC - the third atom in the base of the tetrahedron

apexAtom - the atom in the point of the tetrahedron

Returns:

the sign of the tetrahedron

isColinear

public static boolean isColinear(javax.vecmath.Point3d ptA,
                 javax.vecmath.Point3d ptB,
                 javax.vecmath.Point3d ptC)

Checks the three supplied points to see if they fall on the same line. It does this by finding the normal to an arbitrary pair of lines between the points (in fact, A-B and A-C) and checking that its length is 0.

Parameters:

ptA -

ptB -

ptC -

Returns:

true if the tree points are on a straight line

signedDistanceToPlane

public static double signedDistanceToPlane(javax.vecmath.Vector3d planeNormal,
                           javax.vecmath.Point3d pointInPlane,
                           javax.vecmath.Point3d point)

Given a normalized normal for a plane, any point in that plane, and a point, will return the distance between the plane and that point.

Parameters:

planeNormal - the normalized plane normal

pointInPlane - an arbitrary point in that plane

point - the point to measure

Returns:

the signed distance to the plane

getNormal

public static javax.vecmath.Vector3d getNormal(javax.vecmath.Point3d ptA,
                               javax.vecmath.Point3d ptB,
                               javax.vecmath.Point3d ptC)

Given three points (A, B, C), makes the vectors A-B and A-C, and makes the cross product of these two vectors; this has the effect of making a third vector at right angles to AB and AC.

NOTE : the returned normal is normalized; that is, it has been divided by its length.

Parameters:

ptA - the 'middle' point

ptB - one of the end points

ptC - one of the end points

Returns:

the vector at right angles to AB and AC