org.openscience.cdk.modeling.builder3d

Class AtomTetrahedralLigandPlacer3D

java.lang.Object

org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

public class AtomTetrahedralLigandPlacer3D
extends Object

A set of static utility classes for geometric calculations on Atoms.

Author:

Peter Murray-Rust,chhoppe,egonw

Source code:

master

Belongs to CDK module:

builder3d

Created on:

2003-??-??

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_BOND_LENGTH_H
static double	TETRAHEDRAL_ANGLE

Method Summary

Methods

Modifier and Type	Method and Description
void	add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer) Generate coordinates for all atoms which are singly bonded and have no coordinates.
javax.vecmath.Point3d[]	calculate3DCoordinates0(javax.vecmath.Point3d aPoint, int nwanted, double length) Calculates substituent points.
javax.vecmath.Point3d[]	calculate3DCoordinates1(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, int nwanted, double length, double angle) Calculate new point(s) X in a B-A system to form B-A-X.
javax.vecmath.Point3d[]	calculate3DCoordinates2(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, int nwanted, double length, double angle) Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X system.
javax.vecmath.Point3d	calculate3DCoordinates3(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, javax.vecmath.Point3d dPoint, double length) Calculate new point X in a B-A(-D)-C system.
javax.vecmath.Point3d	calculate3DCoordinatesSP2_1(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, double length, double angle) Calculate new point in B-A-C system.
javax.vecmath.Point3d[]	calculate3DCoordinatesSP2_2(javax.vecmath.Point3d aPoint, javax.vecmath.Point3d bPoint, javax.vecmath.Point3d cPoint, double length, double angle) Calculate two new points in B-A system.
javax.vecmath.Point3d[]	get3DCoordinatesForLigands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle) Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
javax.vecmath.Point3d[]	get3DCoordinatesForSP2Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, double length, double angle) Main method for the calculation of the ligand coordinates for sp2 atoms.
javax.vecmath.Point3d[]	get3DCoordinatesForSP3Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle) Main method for the calculation of the ligand coordinates for sp3 atoms.
javax.vecmath.Point3d	get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle)
double	getAngleValue(String id1, String id2, String id3) Gets the angleKey attribute of the AtomPlacer3D object.
IAtomContainer	getPlacedAtomsInAtomContainer(IAtom atom, IAtomContainer ac) Gets all placed neighbouring atoms of a atom.
IAtom	getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac) Returns a placed neighbouring atom of a central atom atomA, which is not atomB.
double	getSpatproduct(javax.vecmath.Vector3d a, javax.vecmath.Vector3d b, javax.vecmath.Vector3d c) Gets the spatproduct of three vectors.
double	getTorsionAngle(javax.vecmath.Point3d a, javax.vecmath.Point3d b, javax.vecmath.Point3d c, javax.vecmath.Point3d d) Calculates the torsionAngle of a-b-c-d.
IAtomContainer	getUnsetAtomsInAtomContainer(IAtom atom, IAtomContainer ac) Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.
boolean	hasUnsetNeighbour(IAtom atom, IAtomContainer ac)
int	makeStereocenter(javax.vecmath.Point3d atomA, IBond ax, javax.vecmath.Point3d atomB, javax.vecmath.Point3d atomC, javax.vecmath.Point3d[] branchPoints) set Atoms in respect to stereoinformation.
javax.vecmath.Point3d	rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2) Rescales Point2 so that length 1-2 is sum of covalent radii.
static javax.vecmath.Vector3d	rotate(javax.vecmath.Vector3d vector, javax.vecmath.Vector3d axis, double angle) Rotates a vector around an axis.
void	setParameterSet(Map moleculeParameter) Constructor for the setParameterSet object.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_BOND_LENGTH_H

public static final double DEFAULT_BOND_LENGTH_H

See Also:

Constant Field Values

TETRAHEDRAL_ANGLE

public static final double TETRAHEDRAL_ANGLE

Method Detail

setParameterSet

public void setParameterSet(Map moleculeParameter)

Constructor for the setParameterSet object.

Parameters:

moleculeParameter - Description of the Parameter

add3DCoordinatesForSinglyBondedLigands

public void add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
                                            throws CDKException

Generate coordinates for all atoms which are singly bonded and have no coordinates. This is useful when hydrogens are present but have no coordinates. It knows about C, O, N, S only and will give tetrahedral or trigonal geometry elsewhere. Bond lengths are computed from covalent radii or taken out of a parameter set if available. Angles are tetrahedral or trigonal

Parameters:

atomContainer - the set of atoms involved

Throws:

CDKException

Keywords:

coordinate calculation, 3D model

rescaleBondLength

public javax.vecmath.Point3d rescaleBondLength(IAtom atom1,
                                      IAtom atom2,
                                      javax.vecmath.Point3d point2)

Rescales Point2 so that length 1-2 is sum of covalent radii. If covalent radii cannot be found, use bond length of 1.0

Parameters:

atom1 - stationary atom

atom2 - movable atom

point2 - coordinates for atom 2

Returns:

new coordinates for atom 2

get3DCoordinatesForLigands

public javax.vecmath.Point3d[] get3DCoordinatesForLigands(IAtom refAtom,
                                                 IAtomContainer noCoords,
                                                 IAtomContainer withCoords,
                                                 IAtom atomC,
                                                 int nwanted,
                                                 double length,
                                                 double angle)
                                                   throws CDKException

Adds 3D coordinates for singly-bonded ligands of a reference atom (A). Initially designed for hydrogens. The ligands of refAtom are identified and those with 3D coordinates used to generate the new points. (This allows structures with partially known 3D coordinates to be used, as when groups are added.) "Bent" and "non-planar" groups can be formed by taking a subset of the calculated points. Thus R-NH2 could use 2 of the 3 points calculated from (1,iii) nomenclature: A is point to which new ones are "attached". A may have ligands B, C... B may have ligands J, K.. points X1, X2... are returned The cases (see individual routines, which use idealised geometry by default): (0) zero ligands of refAtom. The resultant points are randomly oriented: (i) 1 points required; +x,0,0 (ii) 2 points: use +x,0,0 and -x,0,0 (iii) 3 points: equilateral triangle in xy plane (iv) 4 points x,x,x, x,-x,-x, -x,x,-x, -x,-x,x (1a) 1 ligand(B) of refAtom which itself has a ligand (J) (i) 1 points required; vector along AB vector (ii) 2 points: 2 vectors in ABJ plane, staggered and eclipsed wrt J (iii) 3 points: 1 staggered wrt J, the others +- gauche wrt J (1b) 1 ligand(B) of refAtom which has no other ligands. A random J is generated and (1a) applied (2) 2 ligands(B, C) of refAtom A (i) 1 points required; vector in ABC plane bisecting AB, AC. If ABC is linear, no points (ii) 2 points: 2 vectors at angle ang, whose resultant is 2i (3) 3 ligands(B, C, D) of refAtom A (i) 1 points required; if A, B, C, D coplanar, no points. else vector is resultant of BA, CA, DA fails if atom itself has no coordinates or >4 ligands

Parameters:

refAtom - (A) to which new ligands coordinates could be added

length - A-X length

angle - B-A-X angle (used in certain cases)

nwanted - Description of the Parameter

noCoords - Description of the Parameter

withCoords - Description of the Parameter

atomC - Description of the Parameter

Returns:

Point3D[] points calculated. If request could not be fulfilled (e.g. too many atoms, or strange geometry, returns empty array (zero length, not null)

Throws:

CDKException

Keywords:

coordinate generation

get3DCoordinatesForSPLigands

public javax.vecmath.Point3d get3DCoordinatesForSPLigands(IAtom refAtom,
                                                 IAtomContainer withCoords,
                                                 double length,
                                                 double angle)

get3DCoordinatesForSP2Ligands

public javax.vecmath.Point3d[] get3DCoordinatesForSP2Ligands(IAtom refAtom,
                                                    IAtomContainer noCoords,
                                                    IAtomContainer withCoords,
                                                    IAtom atomC,
                                                    double length,
                                                    double angle)

Main method for the calculation of the ligand coordinates for sp2 atoms. Decides if one or two coordinates should be created

Parameters:

refAtom - central atom (Atom)

noCoords - Description of the Parameter

withCoords - Description of the Parameter

atomC - Description of the Parameter

length - Description of the Parameter

angle - Description of the Parameter

Returns:

coordinates as Points3d []

get3DCoordinatesForSP3Ligands

public javax.vecmath.Point3d[] get3DCoordinatesForSP3Ligands(IAtom refAtom,
                                                    IAtomContainer noCoords,
                                                    IAtomContainer withCoords,
                                                    IAtom atomC,
                                                    int nwanted,
                                                    double length,
                                                    double angle)

Main method for the calculation of the ligand coordinates for sp3 atoms. Decides how many coordinates should be created

Parameters:

refAtom - central atom (Atom)

nwanted - how many ligands should be created

length - bond length

angle - angle in a B-A-(X) system; a=central atom; x=ligand with unknown coordinates

noCoords - Description of the Parameter

withCoords - Description of the Parameter

atomC - Description of the Parameter

Returns:

Description of the Return Value

calculate3DCoordinates0

public javax.vecmath.Point3d[] calculate3DCoordinates0(javax.vecmath.Point3d aPoint,
                                              int nwanted,
                                              double length)

Calculates substituent points. Calculate substituent points for (0) zero ligands of aPoint. The resultant points are randomly oriented: (i) 1 points required; +x,0,0 (ii) 2 points: use +x,0,0 and -x,0,0 (iii) 3 points: equilateral triangle in the xy plane (iv) 4 points x,x,x, x,-x,-x, -x,x,-x, -x,-x,x where 3x**2 = bond length

Parameters:

aPoint - to which substituents are added

nwanted - number of points to calculate (1-4)

length - from aPoint

Returns:

Point3d[] nwanted points (or zero if failed)

calculate3DCoordinates1

public javax.vecmath.Point3d[] calculate3DCoordinates1(javax.vecmath.Point3d aPoint,
                                              javax.vecmath.Point3d bPoint,
                                              javax.vecmath.Point3d cPoint,
                                              int nwanted,
                                              double length,
                                              double angle)

Calculate new point(s) X in a B-A system to form B-A-X. Use C as reference for * staggering about the B-A bond (1a) 1 ligand(B) of refAtom (A) which itself has a ligand (C) (i) 1 points required; vector along AB vector (ii) 2 points: 2 vectors in ABC plane, staggered and eclipsed wrt C (iii) 3 points: 1 staggered wrt C, the others +- gauche wrt C If C is null, a random non-colinear C is generated

Parameters:

aPoint - to which substituents are added

nwanted - number of points to calculate (1-3)

length - A-X length

angle - B-A-X angle

bPoint - Description of the Parameter

cPoint - Description of the Parameter

Returns:

Point3d[] nwanted points (or zero if failed)

calculate3DCoordinates2

public javax.vecmath.Point3d[] calculate3DCoordinates2(javax.vecmath.Point3d aPoint,
                                              javax.vecmath.Point3d bPoint,
                                              javax.vecmath.Point3d cPoint,
                                              int nwanted,
                                              double length,
                                              double angle)

Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X system. (2) 2 ligands(B, C) of refAtom A (i) 1 points required; vector in ABC plane bisecting AB, AC. If ABC is linear, no points (ii) 2 points: 2 points X1, X2, X1-A-X2 = angle about 2i vector

Parameters:

aPoint - to which substituents are added

bPoint - first ligand of A

cPoint - second ligand of A

nwanted - number of points to calculate (1-2)

length - A-X length

angle - B-A-X angle

Returns:

Point3d[] nwanted points (or zero if failed)

calculate3DCoordinates3

public javax.vecmath.Point3d calculate3DCoordinates3(javax.vecmath.Point3d aPoint,
                                            javax.vecmath.Point3d bPoint,
                                            javax.vecmath.Point3d cPoint,
                                            javax.vecmath.Point3d dPoint,
                                            double length)

Calculate new point X in a B-A(-D)-C system. It forms a B-A(-D)(-C)-X system. (3) 3 ligands(B, C, D) of refAtom A (i) 1 points required; if A, B, C, D coplanar, no points. else vector is resultant of BA, CA, DA

Parameters:

aPoint - to which substituents are added

bPoint - first ligand of A

cPoint - second ligand of A

dPoint - third ligand of A

length - A-X length

Returns:

Point3d nwanted points (or null if failed (coplanar))

calculate3DCoordinatesSP2_1

public javax.vecmath.Point3d calculate3DCoordinatesSP2_1(javax.vecmath.Point3d aPoint,
                                                javax.vecmath.Point3d bPoint,
                                                javax.vecmath.Point3d cPoint,
                                                double length,
                                                double angle)

Calculate new point in B-A-C system. It forms B-A(-X)-C system, where A is sp2

Parameters:

aPoint - central point A (Point3d)

bPoint - B (Point3d)

cPoint - C (Point3d)

length - bond length

angle - angle between B(C)-A-X

Returns:

new Point (Point3d)

calculate3DCoordinatesSP2_2

public javax.vecmath.Point3d[] calculate3DCoordinatesSP2_2(javax.vecmath.Point3d aPoint,
                                                  javax.vecmath.Point3d bPoint,
                                                  javax.vecmath.Point3d cPoint,
                                                  double length,
                                                  double angle)

Calculate two new points in B-A system. It forms B-A(-X)(-X) system, where A is sp2

Parameters:

aPoint - central point A (Point3d)

bPoint - B (Point3d)

cPoint - C (Point3d)

length - bond length

angle - angle between B(C)-A-X

Returns:

new Points (Point3d [])

rotate

public static javax.vecmath.Vector3d rotate(javax.vecmath.Vector3d vector,
                            javax.vecmath.Vector3d axis,
                            double angle)

Rotates a vector around an axis.

Parameters:

vector - vector to be rotated around axis

axis - axis of rotation

angle - angle to vector rotate around

Returns:

rotated vector author: egonw

getAngleValue

public double getAngleValue(String id1,
                   String id2,
                   String id3)

Gets the angleKey attribute of the AtomPlacer3D object.

Parameters:

id1 - Description of the Parameter

id2 - Description of the Parameter

id3 - Description of the Parameter

Returns:

The angleKey value

makeStereocenter

public int makeStereocenter(javax.vecmath.Point3d atomA,
                   IBond ax,
                   javax.vecmath.Point3d atomB,
                   javax.vecmath.Point3d atomC,
                   javax.vecmath.Point3d[] branchPoints)

set Atoms in respect to stereoinformation. take placed neighbours to stereocenter create a x b if right handed system (spatproduct >0) if unplaced is not up (relative to stereocenter) n=b x a Determine angle between n and possible ligand place points if angle smaller than 90 degrees take this branch point

Parameters:

atomA - placed Atom - stereocenter

ax - bond between stereocenter and unplaced atom

atomB - neighbour of atomA (in plane created by atomA, atomB and atomC)

atomC - neighbour of atomA

branchPoints - the two possible placement points for unplaced atom (up and down)

Returns:

int value of branch point position

getSpatproduct

public double getSpatproduct(javax.vecmath.Vector3d a,
                    javax.vecmath.Vector3d b,
                    javax.vecmath.Vector3d c)

Gets the spatproduct of three vectors.

Parameters:

a - vector a

b - vector b

c - vector c

Returns:

double value of the spatproduct

getTorsionAngle

public double getTorsionAngle(javax.vecmath.Point3d a,
                     javax.vecmath.Point3d b,
                     javax.vecmath.Point3d c,
                     javax.vecmath.Point3d d)

Calculates the torsionAngle of a-b-c-d.

Parameters:

a - Point3d

b - Point3d

c - Point3d

d - Point3d

Returns:

The torsionAngle value

getPlacedAtomsInAtomContainer

public IAtomContainer getPlacedAtomsInAtomContainer(IAtom atom,
                                           IAtomContainer ac)

Gets all placed neighbouring atoms of a atom.

Parameters:

atom - central atom (Atom)

ac - the molecule

Returns:

all connected and placed atoms to the central atom ((AtomContainer)

getUnsetAtomsInAtomContainer

public IAtomContainer getUnsetAtomsInAtomContainer(IAtom atom,
                                          IAtomContainer ac)

Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.

Parameters:

atom - Description of the Parameter

ac - Description of the Parameter

Returns:

The unsetAtomsInAtomContainer value

hasUnsetNeighbour

public boolean hasUnsetNeighbour(IAtom atom,
                        IAtomContainer ac)

getPlacedHeavyAtomInAtomContainer

public IAtom getPlacedHeavyAtomInAtomContainer(IAtom atomA,
                                      IAtom atomB,
                                      IAtomContainer ac)

Returns a placed neighbouring atom of a central atom atomA, which is not atomB.

Parameters:

atomA - central atom (Atom)

atomB - atom connected to atomA (Atom)

ac - molecule

Returns:

returns a connected atom (Atom)