private static double getAngle(IAtom atom1, IAtom atom2, IAtom atom3)
{
Vector3d centerAtom = new Vector3d();
centerAtom.x = atom1.X3d;
centerAtom.y = atom1.Y3d;
centerAtom.z = atom1.Z3d;
Vector3d firstAtom = new Vector3d();
Vector3d secondAtom = new Vector3d();
firstAtom.x = atom2.X3d;
firstAtom.y = atom2.Y3d;
firstAtom.z = atom2.Z3d;
secondAtom.x = atom3.X3d;
secondAtom.y = atom3.Y3d;
secondAtom.z = atom3.Z3d;
firstAtom.sub(centerAtom);
secondAtom.sub(centerAtom);
return firstAtom.angle(secondAtom);
}
/// <cdk.dictref> blue-obelisk:convertCartesianIntoNotionalCoordinates </cdk.dictref>
public static double[] cartesianToNotional(Vector3d aAxis, Vector3d bAxis, Vector3d cAxis)
{
double[] notionalCoords = new double[6];
notionalCoords[0] = aAxis.length();
notionalCoords[1] = bAxis.length();
notionalCoords[2] = cAxis.length();
notionalCoords[3] = bAxis.angle(cAxis) * 180.0 / System.Math.PI;
notionalCoords[4] = aAxis.angle(cAxis) * 180.0 / System.Math.PI;
notionalCoords[5] = aAxis.angle(bAxis) * 180.0 / System.Math.PI;
return notionalCoords;
}