org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D Maven / Gradle / Ivy
/* Copyright (C) 2005-2007 Christian Hoppe
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.modeling.builder3d;
import java.util.List;
import java.util.Map;
import javax.vecmath.AxisAngle4d;
import javax.vecmath.Matrix3d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
/**
* A set of static utility classes for geometric calculations on Atoms.
*
*@author Peter Murray-Rust,chhoppe,egonw
*@cdk.created 2003-??-??
* @cdk.module builder3d
* @cdk.githash
*/
public class AtomTetrahedralLigandPlacer3D {
private Map pSet = null;
public final static double DEFAULT_BOND_LENGTH_H = 1.0;
public final static double TETRAHEDRAL_ANGLE = 2.0 * Math.acos(1.0 / Math.sqrt(3.0));
private final static double SP2_ANGLE = 120 * Math.PI / 180;
private final static double SP_ANGLE = Math.PI;
final static Vector3d XV = new Vector3d(1.0, 0.0, 0.0);
final static Vector3d YV = new Vector3d(0.0, 1.0, 0.0);
/**
* Constructor for the AtomTetrahedralLigandPlacer3D object.
*/
AtomTetrahedralLigandPlacer3D() {}
/**
* Constructor for the setParameterSet object.
*
*@param moleculeParameter Description of the Parameter
*/
public void setParameterSet(Map moleculeParameter) {
pSet = moleculeParameter;
}
/**
* 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
*
*@param atomContainer the set of atoms involved
* @throws CDKException
*@cdk.keyword coordinate calculation
*@cdk.keyword 3D model
*/
public void add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer) throws CDKException {
IAtom refAtom = null;
IAtom atomC = null;
int nwanted = 0;
for (int i = 0; i < atomContainer.getAtomCount(); i++) {
refAtom = atomContainer.getAtom(i);
if (!refAtom.getSymbol().equals("H") && hasUnsetNeighbour(refAtom, atomContainer)) {
IAtomContainer noCoords = getUnsetAtomsInAtomContainer(refAtom, atomContainer);
IAtomContainer withCoords = getPlacedAtomsInAtomContainer(refAtom, atomContainer);
if (withCoords.getAtomCount() > 0) {
atomC = getPlacedHeavyAtomInAtomContainer(withCoords.getAtom(0), refAtom, atomContainer);
}
if (refAtom.getFormalNeighbourCount() == 0 && refAtom.getSymbol().equals("C")) {
nwanted = noCoords.getAtomCount();
} else if (refAtom.getFormalNeighbourCount() == 0 && !refAtom.getSymbol().equals("C")) {
nwanted = 4;
} else {
nwanted = refAtom.getFormalNeighbourCount() - withCoords.getAtomCount();
}
Point3d[] newPoints = get3DCoordinatesForLigands(refAtom, noCoords, withCoords, atomC, nwanted,
DEFAULT_BOND_LENGTH_H, -1);
for (int j = 0; j < noCoords.getAtomCount(); j++) {
IAtom ligand = noCoords.getAtom(j);
Point3d newPoint = rescaleBondLength(refAtom, ligand, newPoints[j]);
ligand.setPoint3d(newPoint);
ligand.setFlag(CDKConstants.ISPLACED, true);
}
noCoords.removeAllElements();
withCoords.removeAllElements();
}
}
}
/**
* Rescales Point2 so that length 1-2 is sum of covalent radii.
* If covalent radii cannot be found, use bond length of 1.0
*
*@param atom1 stationary atom
*@param atom2 movable atom
*@param point2 coordinates for atom 2
*@return new coordinates for atom 2
*@exception Exception Description of the Exception
*/
public Point3d rescaleBondLength(IAtom atom1, IAtom atom2, Point3d point2) {
Point3d point1 = atom1.getPoint3d();
Double d1 = atom1.getCovalentRadius();
Double d2 = atom2.getCovalentRadius();
// in case we have no covalent radii, set to 1.0
double distance = (d1 == null || d2 == null) ? 1.0 : d1 + d2;
if (pSet != null) {
distance = getDistanceValue(atom1.getAtomTypeName(), atom2.getAtomTypeName());
}
Vector3d vect = new Vector3d(point2);
vect.sub(point1);
vect.normalize();
vect.scale(distance);
Point3d newPoint = new Point3d(point1);
newPoint.add(vect);
return newPoint;
}
/**
* 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
*
*@param refAtom (A) to which new ligands coordinates could be added
*@param length A-X length
*@param angle B-A-X angle (used in certain cases)
*@param nwanted Description of the Parameter
*@param noCoords Description of the Parameter
*@param withCoords Description of the Parameter
*@param atomC Description of the Parameter
*@return 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
*@cdk.keyword coordinate generation
*/
public Point3d[] get3DCoordinatesForLigands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords,
IAtom atomC, int nwanted, double length, double angle) throws CDKException {
Point3d newPoints[] = new Point3d[1];
if (noCoords.getAtomCount() == 0 && withCoords.getAtomCount() == 0) {
return newPoints;
}
// too many ligands at present
if (withCoords.getAtomCount() > 3) {
return newPoints;
}
IBond.Order refMaxBondOrder = refAtom.getMaxBondOrder();
if (refAtom.getFormalNeighbourCount() == 1) {
// WTF???
} else if (refAtom.getFormalNeighbourCount() == 2 || refMaxBondOrder == IBond.Order.TRIPLE) {
//sp
if (angle == -1) {
angle = SP_ANGLE;
}
newPoints[0] = get3DCoordinatesForSPLigands(refAtom, withCoords, length, angle);
} else if (refAtom.getFormalNeighbourCount() == 3 || (refMaxBondOrder == IBond.Order.DOUBLE)) {
//sp2
if (angle == -1) {
angle = SP2_ANGLE;
}
try {
newPoints = get3DCoordinatesForSP2Ligands(refAtom, noCoords, withCoords, atomC, length, angle);
} catch (Exception ex1) {
// logger.debug("Get3DCoordinatesForLigandsERROR: Cannot place SP2 Ligands due to:" + ex1.toString());
throw new CDKException("Cannot place sp2 substituents\n" + ex1.getMessage(), ex1);
}
} else {
//sp3
try {
newPoints = get3DCoordinatesForSP3Ligands(refAtom, noCoords, withCoords, atomC, nwanted, length, angle);
} catch (Exception ex1) {
// logger.debug("Get3DCoordinatesForLigandsERROR: Cannot place SP3 Ligands due to:" + ex1.toString());
throw new CDKException("Cannot place sp3 substituents\n" + ex1.getMessage(), ex1);
}
}
//logger.debug("...Ready "+newPoints.length+" "+newPoints[0].toString());
return newPoints;
}
public Point3d get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle) {
//logger.debug(" SP Ligands start "+refAtom.getPoint3d()+" "+(withCoords.getAtomAt(0)).getPoint3d());
Vector3d ca = new Vector3d(refAtom.getPoint3d());
ca.sub((withCoords.getAtom(0)).getPoint3d());
ca.normalize();
ca.scale(length);
Point3d newPoint = new Point3d(refAtom.getPoint3d());
newPoint.add(ca);
return newPoint;
}
/**
* Main method for the calculation of the ligand coordinates for sp2 atoms.
* Decides if one or two coordinates should be created
*
*@param refAtom central atom (Atom)
*@param noCoords Description of the Parameter
*@param withCoords Description of the Parameter
*@param atomC Description of the Parameter
*@param length Description of the Parameter
*@param angle Description of the Parameter
*@return coordinates as Points3d []
*/
public Point3d[] get3DCoordinatesForSP2Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords,
IAtom atomC, double length, double angle) {
//logger.debug(" SP2 Ligands start");
Point3d newPoints[] = new Point3d[1];
if (angle < 0) {
angle = SP2_ANGLE;
}
if (withCoords.getAtomCount() >= 2) {
//logger.debug("Wanted:1 "+noCoords.getAtomCount());
newPoints[0] = calculate3DCoordinatesSP2_1(refAtom.getPoint3d(), (withCoords.getAtom(0)).getPoint3d(),
(withCoords.getAtom(1)).getPoint3d(), length, -1 * angle);
} else if (withCoords.getAtomCount() <= 1) {
//logger.debug("NoCoords 2:"+noCoords.getAtomCount());
newPoints = calculate3DCoordinatesSP2_2(refAtom.getPoint3d(), (withCoords.getAtom(0)).getPoint3d(),
(atomC != null) ? atomC.getPoint3d() : null, length, angle);
}
//logger.debug("Ready SP2");
return newPoints;
}
/**
* Main method for the calculation of the ligand coordinates for sp3 atoms.
* Decides how many coordinates should be created
*
*@param refAtom central atom (Atom)
*@param nwanted how many ligands should be created
*@param length bond length
*@param angle angle in a B-A-(X) system; a=central atom;
* x=ligand with unknown coordinates
*@param noCoords Description of the Parameter
*@param withCoords Description of the Parameter
*@param atomC Description of the Parameter
*@return Description of the Return Value
*/
public Point3d[] get3DCoordinatesForSP3Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords,
IAtom atomC, int nwanted, double length, double angle) {
//logger.debug("SP3 Ligands start ");
Point3d newPoints[] = new Point3d[0];
Point3d aPoint = refAtom.getPoint3d();
int nwithCoords = withCoords.getAtomCount();
if (angle < 0) {
angle = TETRAHEDRAL_ANGLE;
}
if (nwithCoords == 0) {
newPoints = calculate3DCoordinates0(refAtom.getPoint3d(), nwanted, length);
} else if (nwithCoords == 1) {
newPoints = calculate3DCoordinates1(aPoint, (withCoords.getAtom(0)).getPoint3d(),
(atomC != null) ? atomC.getPoint3d() : null, nwanted, length, angle);
} else if (nwithCoords == 2) {
Point3d bPoint = withCoords.getAtom(0).getPoint3d();
Point3d cPoint = withCoords.getAtom(1).getPoint3d();
newPoints = calculate3DCoordinates2(aPoint, bPoint, cPoint, nwanted, length, angle);
} else if (nwithCoords == 3) {
Point3d bPoint = withCoords.getAtom(0).getPoint3d();
Point3d cPoint = withCoords.getAtom(1).getPoint3d();
newPoints = new Point3d[1];
Point3d dPoint = withCoords.getAtom(2).getPoint3d();
newPoints[0] = calculate3DCoordinates3(aPoint, bPoint, cPoint, dPoint, length);
}
//logger.debug("...Ready");
return newPoints;
}
/**
* 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
*
*@param aPoint to which substituents are added
*@param nwanted number of points to calculate (1-4)
*@param length from aPoint
*@return Point3d[] nwanted points (or zero if failed)
*/
public Point3d[] calculate3DCoordinates0(Point3d aPoint, int nwanted, double length) {
Point3d points[] = new Point3d[0];
if (nwanted == 1) {
points = new Point3d[1];
points[0] = new Point3d(aPoint);
points[0].add(new Vector3d(length, 0.0, 0.0));
} else if (nwanted == 2) {
points = new Point3d[2];
points[0] = new Point3d(aPoint);
points[0].add(new Vector3d(length, 0.0, 0.0));
points[1] = new Point3d(aPoint);
points[1].add(new Vector3d(-length, 0.0, 0.0));
} else if (nwanted == 3) {
points = new Point3d[3];
points[0] = new Point3d(aPoint);
points[0].add(new Vector3d(length, 0.0, 0.0));
points[1] = new Point3d(aPoint);
points[1].add(new Vector3d(-length * 0.5, -length * 0.5 * Math.sqrt(3.0), 0.0f));
points[2] = new Point3d(aPoint);
points[2].add(new Vector3d(-length * 0.5, length * 0.5 * Math.sqrt(3.0), 0.0f));
} else if (nwanted == 4) {
points = new Point3d[4];
double dx = length / Math.sqrt(3.0);
points[0] = new Point3d(aPoint);
points[0].add(new Vector3d(dx, dx, dx));
points[1] = new Point3d(aPoint);
points[1].add(new Vector3d(dx, -dx, -dx));
points[2] = new Point3d(aPoint);
points[2].add(new Vector3d(-dx, -dx, dx));
points[3] = new Point3d(aPoint);
points[3].add(new Vector3d(-dx, dx, -dx));
}
return points;
}
/**
* 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
*
*@param aPoint to which substituents are added
*@param nwanted number of points to calculate (1-3)
*@param length A-X length
*@param angle B-A-X angle
*@param bPoint Description of the Parameter
*@param cPoint Description of the Parameter
*@return Point3d[] nwanted points (or zero if failed)
*/
public Point3d[] calculate3DCoordinates1(Point3d aPoint, Point3d bPoint, Point3d cPoint, int nwanted,
double length, double angle) {
Point3d points[] = new Point3d[nwanted];
// BA vector
Vector3d ba = new Vector3d(aPoint);
ba.sub(bPoint);
ba.normalize();
// if no cPoint, generate a random reference
if (cPoint == null) {
Vector3d cVector = getNonColinearVector(ba);
cPoint = new Point3d(cVector);
}
// CB vector
Vector3d cb = new Vector3d(bPoint);
cb.sub(cPoint);
cb.normalize();
// if A, B, C colinear, replace C by random point
double cbdotba = cb.dot(ba);
if (cbdotba > 0.999999) {
Vector3d cVector = getNonColinearVector(ba);
cPoint = new Point3d(cVector);
cb = new Vector3d(bPoint);
cb.sub(cPoint);
}
// cbxba = c x b
Vector3d cbxba = new Vector3d();
cbxba.cross(cb, ba);
cbxba.normalize();
// create three perp axes ba, cbxba, and ax
Vector3d ax = new Vector3d();
ax.cross(cbxba, ba);
ax.normalize();
double drot = Math.PI * 2.0 / (double) nwanted;
for (int i = 0; i < nwanted; i++) {
double rot = (double) i * drot;
points[i] = new Point3d(aPoint);
Vector3d vx = new Vector3d(ba);
vx.scale(-Math.cos(angle) * length);
Vector3d vy = new Vector3d(ax);
vy.scale(Math.cos(rot) * length);
Vector3d vz = new Vector3d(cbxba);
vz.scale(Math.sin(rot) * length);
points[i].add(vx);
points[i].add(vy);
points[i].add(vz);
}
/*
* ax = null; cbxba = null; ba = null; cb = null;
*/
return points;
}
/**
* 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
*
*@param aPoint to which substituents are added
*@param bPoint first ligand of A
*@param cPoint second ligand of A
*@param nwanted number of points to calculate (1-2)
*@param length A-X length
*@param angle B-A-X angle
*@return Point3d[] nwanted points (or zero if failed)
*/
public Point3d[] calculate3DCoordinates2(Point3d aPoint, Point3d bPoint, Point3d cPoint, int nwanted,
double length, double angle) {
//logger.debug("3DCoordinates2");
Point3d newPoints[] = new Point3d[0];
double ang2 = angle / 2.0;
Vector3d ba = new Vector3d(aPoint);
ba.sub(bPoint);
Vector3d ca = new Vector3d(aPoint);
ca.sub(cPoint);
Vector3d baxca = new Vector3d();
baxca.cross(ba, ca);
if (baxca.length() < 0.00000001) {
;
// linear
} else if (nwanted == 1) {
newPoints = new Point3d[1];
Vector3d ax = new Vector3d(ba);
ax.add(ca);
ax.normalize();
ax.scale(length);
newPoints[0] = new Point3d(aPoint);
newPoints[0].add(ax);
} else if (nwanted >= 2) {
newPoints = new Point3d[2];
Vector3d ax = new Vector3d(ba);
ax.add(ca);
ax.normalize();
baxca.normalize();
baxca.scale(Math.sin(ang2) * length);
ax.scale(Math.cos(ang2) * length);
newPoints[0] = new Point3d(aPoint);
newPoints[0].add(ax);
newPoints[0].add(baxca);
newPoints[1] = new Point3d(aPoint);
newPoints[1].add(ax);
newPoints[1].sub(baxca);
}
baxca = null;
ba = null;
ca = null;
return newPoints;
}
/**
* 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
*
*@param aPoint to which substituents are added
*@param bPoint first ligand of A
*@param cPoint second ligand of A
*@param dPoint third ligand of A
*@param length A-X length
*@return Point3d nwanted points (or null if failed (coplanar))
*/
public Point3d calculate3DCoordinates3(Point3d aPoint, Point3d bPoint, Point3d cPoint, Point3d dPoint, double length) {
//logger.debug("3DCoordinates3");
Vector3d bc = new Vector3d(bPoint);
bc.sub(cPoint);
Vector3d dc = new Vector3d(dPoint);
dc.sub(cPoint);
Vector3d ca = new Vector3d(cPoint);
ca.sub(aPoint);
Vector3d n1 = new Vector3d();
Vector3d n2 = new Vector3d();
n1.cross(bc, dc);
n1.normalize();
n1.scale(length);
Vector3d ax = new Vector3d(aPoint);
ax.add(n1);
ax.sub(aPoint);
Vector3d ax2 = new Vector3d(aPoint);
ax2.add(n2);
ax2.sub(aPoint);
Point3d point = new Point3d(aPoint);
double dotProduct = ca.dot(ax);
double angle = Math.acos((dotProduct) / (ax.length() * ca.length()));
if (angle < 1.5) {
n2.cross(dc, bc);
n2.normalize();
n2.scale(length);
point.add(n2);
} else {
point.add(n1);
}
bc = null;
dc = null;
ca = null;
n1 = null;
n2 = null;
return point;
}
/**
* Calculate new point in B-A-C system. It forms B-A(-X)-C system, where A is
* sp2
*
*@param aPoint central point A (Point3d)
*@param bPoint B (Point3d)
*@param cPoint C (Point3d)
*@param length bond length
*@param angle angle between B(C)-A-X
*@return new Point (Point3d)
*/
public Point3d calculate3DCoordinatesSP2_1(Point3d aPoint, Point3d bPoint, Point3d cPoint, double length,
double angle) {
//logger.debug("3DCoordinatesSP2_1");
Vector3d ba = new Vector3d(bPoint);
ba.sub(aPoint);
Vector3d ca = new Vector3d(cPoint);
ca.sub(aPoint);
Vector3d n1 = new Vector3d();
n1.cross(ba, ca);
n1.normalize();
Vector3d n2 = rotate(ba, n1, angle);
n2.normalize();
n2.scale(length);
Point3d point = new Point3d(aPoint);
point.add(n2);
n1 = null;
n2 = null;
ba = null;
ca = null;
return point;
}
/**
* Calculate two new points in B-A system. It forms B-A(-X)(-X) system, where
* A is sp2
*
*@param aPoint central point A (Point3d)
*@param bPoint B (Point3d)
*@param cPoint C (Point3d)
*@param length bond length
*@param angle angle between B(C)-A-X
*@return new Points (Point3d [])
*/
public Point3d[] calculate3DCoordinatesSP2_2(Point3d aPoint, Point3d bPoint, Point3d cPoint, double length,
double angle) {
//logger.debug("3DCoordinatesSP_2");
Vector3d ca = new Vector3d();
Point3d newPoints[] = new Point3d[2];
Vector3d ba = new Vector3d(bPoint);
ba.sub(aPoint);
if (cPoint != null) {
ca.x = cPoint.x - aPoint.x;
ca.y = cPoint.y - aPoint.y;
ca.z = cPoint.z - aPoint.z;
} else {
ca.x = -1 * ba.x;
ca.y = -1 * ba.y;
ca.z = -1.5 * ba.z;
}
Vector3d crossProduct = new Vector3d();
crossProduct.cross(ba, ca);
Vector3d n1 = rotate(ba, crossProduct, 2 * angle);
n1.normalize();
n1.scale(length);
newPoints[0] = new Point3d(aPoint);
newPoints[0].add(n1);
Vector3d n2 = rotate(n1, ba, Math.PI);
n2.normalize();
n2.scale(length);
newPoints[1] = new Point3d(aPoint);
newPoints[1].add(n2);
n1 = null;
n2 = null;
ba = null;
ca = null;
return newPoints;
}
/**
* Gets the nonColinearVector attribute of the AtomLigandPlacer3D class
*
*@param ab Description of the Parameter
*@return The nonColinearVector value
*/
private Vector3d getNonColinearVector(Vector3d ab) {
Vector3d cr = new Vector3d();
cr.cross(ab, XV);
if (cr.length() > 0.00001) {
return XV;
} else {
return YV;
}
}
/**
* Rotates a vector around an axis.
*
*@param vector vector to be rotated around axis
*@param axis axis of rotation
*@param angle angle to vector rotate around
*@return rotated vector
*author: egonw
*/
public static Vector3d rotate(Vector3d vector, Vector3d axis, double angle) {
Matrix3d rotate = new Matrix3d();
rotate.set(new AxisAngle4d(axis.x, axis.y, axis.z, angle));
Vector3d result = new Vector3d();
rotate.transform(vector, result);
return result;
}
/**
* Gets the distance between two atoms out of the parameter set.
*
*@param id1 id of the parameter set for atom1 (atom1.getAtomTypeName())
*@param id2 id of the parameter set for atom2
*@return The distanceValue value
*@exception Exception Description of the Exception
*/
private double getDistanceValue(String id1, String id2) {
String dkey = "";
if (pSet.containsKey(("bond" + id1 + ";" + id2))) {
dkey = "bond" + id1 + ";" + id2;
} else if (pSet.containsKey(("bond" + id2 + ";" + id1))) {
dkey = "bond" + id2 + ";" + id1;
} else {
// logger.debug("DistanceKEYError:pSet has no key:" + id2 + " ; " + id1 + " take default bond length:" + DEFAULT_BOND_LENGTH_H);
return DEFAULT_BOND_LENGTH_H;
}
return ((Double) (((List) pSet.get(dkey)).get(0))).doubleValue();
}
/**
* Gets the angleKey attribute of the AtomPlacer3D object.
*
*@param id1 Description of the Parameter
*@param id2 Description of the Parameter
*@param id3 Description of the Parameter
*@return The angleKey value
*@exception Exception Description of the Exception
*/
public double getAngleValue(String id1, String id2, String id3) {
String akey = "";
if (pSet.containsKey(("angle" + id1 + ";" + id2 + ";" + id3))) {
akey = "angle" + id1 + ";" + id2 + ";" + id3;
} else if (pSet.containsKey(("angle" + id3 + ";" + id2 + ";" + id1))) {
akey = "angle" + id3 + ";" + id2 + ";" + id1;
} else if (pSet.containsKey(("angle" + id2 + ";" + id1 + ";" + id3))) {
akey = "angle" + id2 + ";" + id1 + ";" + id3;
} else if (pSet.containsKey(("angle" + id1 + ";" + id3 + ";" + id2))) {
akey = "angle" + id1 + ";" + id3 + ";" + id2;
} else if (pSet.containsKey(("angle" + id3 + ";" + id1 + ";" + id2))) {
akey = "angle" + id3 + ";" + id1 + ";" + id2;
} else if (pSet.containsKey(("angle" + id2 + ";" + id3 + ";" + id1))) {
akey = "angle" + id2 + ";" + id3 + ";" + id1;
} else {
System.out.println("AngleKEYError:Unknown angle " + id1 + " " + id2 + " " + id3 + " take default angle:"
+ TETRAHEDRAL_ANGLE);
return TETRAHEDRAL_ANGLE;
}
return ((Double) (((List) pSet.get(akey)).get(0))).doubleValue();
}
/**
* 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
*
*@param atomA placed Atom - stereocenter
*@param ax bond between stereocenter and unplaced atom
*@param atomB neighbour of atomA (in plane created by atomA, atomB and atomC)
*@param atomC neighbour of atomA
*@param branchPoints the two possible placement points for unplaced atom (up and down)
*@return int value of branch point position
*/
public int makeStereocenter(Point3d atomA, IBond ax, Point3d atomB, Point3d atomC, Point3d[] branchPoints) {
Vector3d b = new Vector3d((atomB.x - atomA.x), (atomB.y - atomA.y), (atomB.z - atomA.z));
Vector3d c = new Vector3d((atomC.x - atomA.x), (atomC.y - atomA.y), (atomC.z - atomA.z));
Vector3d n1 = new Vector3d();
Vector3d n2 = null;
n1.cross(b, c);
n1.normalize();
if (getSpatproduct(b, c, n1) >= 0) {
if (ax.getStereo() != IBond.Stereo.UP_INVERTED) {
n1.cross(c, b);
n1.normalize();
}
}
double dotProduct = 0;
for (int i = 0; i < branchPoints.length; i++) {
n2 = new Vector3d(branchPoints[0].x, branchPoints[0].y, branchPoints[0].z);
dotProduct = n1.dot(n2);
if (Math.acos(dotProduct / (n1.length() * n2.length())) < 1.6) {
return i;
}
}
return -1;
}
/**
* Gets the spatproduct of three vectors.
*
*@param a vector a
*@param b vector b
*@param c vector c
*@return double value of the spatproduct
*/
public double getSpatproduct(Vector3d a, Vector3d b, Vector3d c) {
return (c.x * (b.y * a.z - b.z * a.y) + c.y * (b.z * a.x - b.x * a.z) + c.z * (b.x * a.y - b.y * a.x));
}
/**
* Calculates the torsionAngle of a-b-c-d.
*
*@param a Point3d
*@param b Point3d
*@param c Point3d
*@param d Point3d
*@return The torsionAngle value
*/
public double getTorsionAngle(Point3d a, Point3d b, Point3d c, Point3d d) {
Vector3d ab = new Vector3d(a.x - b.x, a.y - b.y, a.z - b.z);
Vector3d cb = new Vector3d(c.x - b.x, c.y - b.y, c.z - b.z);
Vector3d dc = new Vector3d(d.x - c.x, d.y - c.y, d.z - c.z);
Vector3d bc = new Vector3d(b.x - c.x, b.y - c.y, b.z - c.z);
Vector3d n1 = new Vector3d();
Vector3d n2 = new Vector3d();
n1.cross(ab, cb);
if (getSpatproduct(ab, cb, n1) > 0) {
n1.cross(cb, ab);
}
n1.normalize();
n2.cross(dc, bc);
if (getSpatproduct(dc, bc, n2) < 0) {
n2.cross(bc, dc);
}
n2.normalize();
return n1.dot(n2);
}
/**
* Gets all placed neighbouring atoms of a atom.
*
*@param atom central atom (Atom)
*@param ac the molecule
*@return all connected and placed atoms to the central atom
* ((AtomContainer)
*/
public IAtomContainer getPlacedAtomsInAtomContainer(IAtom atom, IAtomContainer ac) {
List bonds = ac.getConnectedBondsList(atom);
IAtomContainer connectedAtoms = atom.getBuilder().newInstance(IAtomContainer.class);
IAtom connectedAtom = null;
for (int i = 0; i < bonds.size(); i++) {
connectedAtom = ((IBond) bonds.get(i)).getConnectedAtom(atom);
if (connectedAtom.getFlag(CDKConstants.ISPLACED)) {
connectedAtoms.addAtom(connectedAtom);
}
}
return connectedAtoms;
}
/**
* Gets the unsetAtomsInAtomContainer attribute of the
* AtomTetrahedralLigandPlacer3D object.
*
*@param atom Description of the Parameter
*@param ac Description of the Parameter
*@return The unsetAtomsInAtomContainer value
*/
public IAtomContainer getUnsetAtomsInAtomContainer(IAtom atom, IAtomContainer ac) {
List atoms = ac.getConnectedAtomsList(atom);
IAtomContainer connectedAtoms = atom.getBuilder().newInstance(IAtomContainer.class);
for (int i = 0; i < atoms.size(); i++) {
IAtom curAtom = (IAtom) atoms.get(i);
if (!curAtom.getFlag(CDKConstants.ISPLACED)) {//&& atoms[i].getPoint3d() == null) {
connectedAtoms.addAtom(curAtom);
}
}
return connectedAtoms;
}
public boolean hasUnsetNeighbour(IAtom atom, IAtomContainer ac) {
List atoms = ac.getConnectedAtomsList(atom);
for (int i = 0; i < atoms.size(); i++) {
IAtom curAtom = (IAtom) atoms.get(i);
if (!curAtom.getFlag(CDKConstants.ISPLACED)) {//&& atoms[i].getPoint3d() == null) {
return true;
}
}
return false;
}
/**
* Returns a placed neighbouring atom of a central atom atomA, which is not
* atomB.
*
*@param atomA central atom (Atom)
*@param atomB atom connected to atomA (Atom)
*@param ac molecule
*@return returns a connected atom (Atom)
*/
public IAtom getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac) {
List atoms = ac.getConnectedAtomsList(atomA);
IAtom atom = null;
for (int i = 0; i < atoms.size(); i++) {
IAtom curAtom = (IAtom) atoms.get(i);
if (curAtom.getFlag(CDKConstants.ISPLACED) && !curAtom.getSymbol().equals("H") && curAtom != atomB) {
return curAtom;
}
}
return atom;
}
}
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