/* $Revision: 8712 $ $Author: egonw $ $Date: 2007-08-28 10:12:57 +0200 (Tue, 28 Aug 2007) $ * * 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.keyword Z Matrix * * @cdk.created 2004-02-09 * @cdk.bug 1653028 */ 00041 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 involed atom in distance, angle and dihedral * @param second_atoms Array of atom ids of the second involed atom in angle and dihedral * @param third_atoms Array of atom ids of the third involed atom in dihedral * * @cdk.dictref blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates */ 00058 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; } }

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