/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2008 Rajarshi Guha <rajarshi.guha@gmail.com>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.
*
* 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.pharmacophore;
import org.openscience.cdk.Bond;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
/**
* Represents an angle relationship between three pharmacophore groups.
*
* @author Rajarshi Guha
* @cdk.module pcore
* @cdk.githash
* @cdk.keyword pharmacophore
* @cdk.keyword 3D isomorphism
* @see PharmacophoreAtom
*/
@TestClass("org.openscience.cdk.pharmacophore.PharmacophoreAngleBondTest")
public class PharmacophoreAngleBond extends Bond {
/**
* Create a pharmacophore distance constraint.
*
* @param patom1 The first pharmacophore group
* @param patom2 The second pharmacophore group
* @param patom3 The third pharmacophore group
*/
public PharmacophoreAngleBond(PharmacophoreAtom patom1, PharmacophoreAtom patom2, PharmacophoreAtom patom3) {
super(new PharmacophoreAtom[] {patom1, patom2, patom3});
}
/**
* Get the angle between the three pharmacophore groups that make up the constraint.
*
* @return The angle in degrees between the two groups
*/
@TestMethod("testGetAngle1,testGetAngle2,testGetAngle3,testGetAngle4,testGetAngle5")
public double getBondLength() {
double epsilon = 1e-3;
PharmacophoreAtom atom1 = (PharmacophoreAtom) getAtom(0);
PharmacophoreAtom atom2 = (PharmacophoreAtom) getAtom(1);
PharmacophoreAtom atom3 = (PharmacophoreAtom) getAtom(2);
double a2 = atom3.getPoint3d().distanceSquared(atom1.getPoint3d());
double b2 = atom3.getPoint3d().distanceSquared(atom2.getPoint3d());
double c2 = atom2.getPoint3d().distanceSquared(atom1.getPoint3d());
double cosangle = (b2+c2-a2) / (2*Math.sqrt(b2)*Math.sqrt(c2));
if (-1.0-epsilon < cosangle && -1.0+epsilon > cosangle) return 180.0;
if (1.0-epsilon < cosangle && 1.0+epsilon > cosangle) return 0.0;
return Math.acos(cosangle) * 180.0 / Math.PI;
}
}