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 pointplane distance
of three of the corners, compared to the fourth.

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 and Description 

StereoTool() 
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 AB and AC, 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 trigonalbipyramidal 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.

public static final double MAX_AXIS_ANGLE
public static final double MIN_COLINEAR_NORMAL
public static final double PLANE_TOLERANCE
public static boolean isSquarePlanar(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD)
atomA
 an atom in the planeatomB
 an atom in the planeatomC
 an atom in the planeatomD
 an atom in the planepublic 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'.
atomA
 an atom in the planeatomB
 an atom in the planeatomC
 an atom in the planeatomD
 an atom in the planepublic static boolean allCoplanar(javax.vecmath.Vector3d planeNormal, javax.vecmath.Point3d pointInPlane, javax.vecmath.Point3d... points)
planeNormal
 the normal to the planepointInPlane
 any point know to be in the planepoints
 an array of points to testpublic static boolean isOctahedral(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF, IAtom atomG)
atomA
 one of the axial atomsatomB
 the central atomatomC
 one of the equatorial atomsatomD
 one of the equatorial atomsatomE
 one of the equatorial atomsatomF
 one of the equatorial atomsatomG
 the other axial atompublic static boolean isTrigonalBipyramidal(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF)
atomA
 one of the axial atomsatomB
 the central atomatomC
 one of the equatorial atomsatomD
 one of the equatorial atomsatomE
 one of the equatorial atomsatomF
 the other axial atompublic static ITetrahedralChirality.Stereo getStereo(IAtom atom1, IAtom atom2, IAtom atom3, IAtom atom4)
atom1
 the atom pointing towards the observeratom2
 the second atom (points away)atom3
 the third atom (points away)atom4
 the fourth atom (points away)public static StereoTool.TetrahedralSign getHandedness(IAtom baseAtomA, IAtom baseAtomB, IAtom baseAtomC, IAtom apexAtom)
baseAtomA
 the first atom in the base of the tetrahedronbaseAtomB
 the second atom in the base of the tetrahedronbaseAtomC
 the third atom in the base of the tetrahedronapexAtom
 the atom in the point of the tetrahedronpublic static boolean isColinear(javax.vecmath.Point3d ptA, javax.vecmath.Point3d ptB, javax.vecmath.Point3d ptC)
ptA
 ptB
 ptC
 public static double signedDistanceToPlane(javax.vecmath.Vector3d planeNormal, javax.vecmath.Point3d pointInPlane, javax.vecmath.Point3d point)
planeNormal
 the normalized plane normalpointInPlane
 an arbitrary point in that planepoint
 the point to measurepublic 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 AB and AC, 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.
ptA
 the 'middle' pointptB
 one of the end pointsptC
 one of the end pointsCopyright © 2021. All rights reserved.