package com.actelion.research.chem.descriptor.flexophore.generator;

import com.actelion.research.chem.descriptor.flexophore.MolDistHist;
import com.actelion.research.chem.descriptor.flexophore.PPNode;

/**
 * Copyright (c) 2024-2026
 * Alipheron AG
 * Hochbergerstrasse 60C
 * CH-4057 Basel
 * Switzerland
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the copyright holder nor the
 *    names of its contributors may be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * @author Modest v. Korff
 */
public class SubFlexophoreExtractorHelper {

    public static MolDistHist getSubFragment(MolDistHist mdh, int [] arrIndices){

        MolDistHist frag = new MolDistHist(arrIndices.length);

        for (int i = 0; i < arrIndices.length; i++) {
            PPNode node = new PPNode(mdh.getNode(arrIndices[i]));
            frag.addNode(node);
        }

        for (int i = 0; i < arrIndices.length; i++) {
            for (int j = i+1; j < arrIndices.length; j++) {
                byte [] arrHist = mdh.getDistHist(arrIndices[i],arrIndices[j]);
                frag.setDistHist(i,j,arrHist);
            }
        }

        frag.realize();
        return frag;
    }

}
