/* 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.
 *
 *  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.graph.matrix;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

/**
 * Calculator for a adjacency matrix representation of this AtomContainer. An
 * adjacency matrix is a matrix of quare NxN matrix, where N is the number of
 * atoms in the AtomContainer. The element i,j of the matrix is 1, if the i-th
 * and the j-th atom in the atomcontainer share a bond. Otherwise it is zero.
 * See {@cdk.cite TRI92}.
 *
 * @cdk.module  core
 * @cdk.githash
 * @cdk.keyword adjacency matrix
 *
 * @author      steinbeck
 * @cdk.created 2004-07-04
 * @cdk.dictref blue-obelisk:calculateAdjecencyMatrix
 */
public class AdjacencyMatrix implements IGraphMatrix {

    /**
     * Returns the adjacency matrix for the given AtomContainer.
     *
     * @param  container The AtomContainer for which the matrix is calculated
     * @return           An adjacency matrix representing this AtomContainer
     */
    public static int[][] getMatrix(IAtomContainer container) {
        IBond bond;
        int indexAtom1;
        int indexAtom2;
        int[][] conMat = new int[container.getAtomCount()][container.getAtomCount()];
        for (int f = 0; f < container.getBondCount(); f++) {
            bond = container.getBond(f);
            indexAtom1 = container.indexOf(bond.getBegin());
            indexAtom2 = container.indexOf(bond.getEnd());
            conMat[indexAtom1][indexAtom2] = 1;
            conMat[indexAtom2][indexAtom1] = 1;
        }
        return conMat;
    }

}
