/**
* 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 moveable atom
* @param point2 coordinates for atom 2
* @return new coords for atom 2
*/
public static 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 < 0.1 || d2 < 0.1) ? 1.0 : atom1.getCovalentRadius() + atom2.getCovalentRadius();
Vector3d vect = new Vector3d(point2);
vect.sub(point1);
vect.normalize();
vect.scale(distance);
Point3d newPoint = new Point3d(point1);
newPoint.add(vect);
return newPoint;
}
