/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* 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.
* 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.geometry;
import javax.vecmath.AxisAngle4d;
import javax.vecmath.Matrix3d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
/**
* A set of static utility classes for dealing with Z matrices.
*
* @cdk.module io
* @cdk.githash
* @cdk.keyword Z-matrix
*
* @cdk.created 2004-02-09
* @cdk.bug 1653028
*/
public class ZMatrixTools {
/**
* Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
* The first Atom end up in the origin, the second on on the x axis, and the third
* one in the XY plane. The rest is added by applying the Zmatrix distances, angles
* and dihedrals. Angles are in degrees.
*
* @param distances Array of distance variables of the Z matrix
* @param angles Array of angle variables of the Z matrix
* @param dihedrals Array of distance variables of the Z matrix
* @param first_atoms Array of atom ids of the first invoked atom in distance, angle and dihedral
* @param second_atoms Array of atom ids of the second invoked atom in angle and dihedral
* @param third_atoms Array of atom ids of the third invoked atom in dihedral
*
* @cdk.dictref blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates
*/
public static Point3d[] zmatrixToCartesian(double[] distances, int[] first_atoms,
double[] angles, int[] second_atoms,
double[] dihedrals, int[] third_atoms) {
Point3d[] cartesianCoords = new Point3d[distances.length];
for (int index=0; index<distances.length; index++) {
if (index==0) {
cartesianCoords[index] = new Point3d(0d,0d,0d);
} else if (index==1) {
cartesianCoords[index] = new Point3d(distances[1],0d,0d);
} else if (index==2) {
cartesianCoords[index] = new Point3d(-Math.cos((angles[2]/180)*Math.PI)*distances[2]+distances[1],
Math.sin((angles[2]/180)*Math.PI)*distances[2],
0d);
if (first_atoms[index] == 0)
cartesianCoords[index].x = (cartesianCoords[index].x - distances[1]) * -1;
} else {
Vector3d cd = new Vector3d();
cd.sub(cartesianCoords[third_atoms[index]], cartesianCoords[second_atoms[index]]);
Vector3d bc = new Vector3d();
bc.sub(cartesianCoords[second_atoms[index]], cartesianCoords[first_atoms[index]]);
Vector3d n1 = new Vector3d();
n1.cross(cd, bc);
Vector3d n2 = rotate(n1,bc,-dihedrals[index]);
Vector3d ba = rotate(bc,n2,-angles[index]);
ba.normalize();
ba.scale(distances[index]);
Point3d result = new Point3d();
result.add(cartesianCoords[first_atoms[index]], ba);
cartesianCoords[index] = result;
}
}
return cartesianCoords;
}
private static Vector3d rotate(Vector3d vector, Vector3d axis, double angle) {
Matrix3d rotate = new Matrix3d();
rotate.set(new AxisAngle4d(axis, Math.toRadians(angle)));
Vector3d result = new Vector3d();
rotate.transform(vector, result);
return result;
}
}