org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory Maven / Gradle / Ivy

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/*
 * Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
 *                    John May 
 *
 * Contact: [email protected]
 *
 * 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 U
 */

package org.openscience.cdk.hash.stereo;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.ITetrahedralChirality;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import static org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo.CLOCKWISE;

/**
 * Defines a stereo encoder factory for the hash code. The factory allows the
 * generation of stereo hash codes for molecules with predefined
 * {@link ITetrahedralChirality} stereo elements.
 *
 * @author John May
 * @cdk.module hash
 */
public final class TetrahedralElementEncoderFactory implements StereoEncoderFactory {

    /**
     * @inheritDoc
     */
    @Override
    public StereoEncoder create(IAtomContainer container, int[][] graph) {

        // index atoms for quick lookup - wish we didn't have to do this
        // but the it's better than calling getAtomNumber every time - we use
        // a lazy creation so it's only created if there was a need for it
        Map atomToIndex = null;

        List encoders = new ArrayList();

        // for each tetrahedral element - create a new encoder
        for (IStereoElement se : container.stereoElements()) {
            if (se instanceof ITetrahedralChirality) {
                encoders.add(encoder((ITetrahedralChirality) se, atomToIndex = indexMap(atomToIndex, container)));
            }
        }

        return encoders.isEmpty() ? StereoEncoder.EMPTY : new MultiStereoEncoder(encoders);
    }

    /**
     * Create an encoder for the {@link ITetrahedralChirality} element.
     *
     * @param tc          stereo element from an atom container
     * @param atomToIndex map of atoms to indices
     * @return a new geometry encoder
     */
    private static GeometryEncoder encoder(ITetrahedralChirality tc, Map atomToIndex) {

        IAtom[] ligands = tc.getLigands();

        int centre = atomToIndex.get(tc.getChiralAtom());
        int[] indices = new int[4];

        int offset = -1;

        for (int i = 0; i < ligands.length; i++) {
            indices[i] = atomToIndex.get(ligands[i]);
            if (indices[i] == centre) offset = i;
        }

        // convert clockwise/anticlockwise to -1/+1
        int parity = tc.getStereo() == CLOCKWISE ? -1 : 1;

        // now if any atom is the centre (indicating an implicit
        // hydrogen) we need to adjust the indicies and the parity
        if (offset >= 0) {

            // remove the 'implicit' central from the first 3 vertices
            for (int i = offset; i < indices.length - 1; i++) {
                indices[i] = indices[i + 1];
            }

            // we now take how many vertices we moved which is
            // 3 (last index) minus the index where we started. if the
            // value is odd we invert the parity (odd number of
            // inversions)
            if (Integer.lowestOneBit(3 - offset) == 0x1) parity *= -1;

            // trim the array to size we don't include the last (implicit)
            // vertex when checking the invariants
            indices = Arrays.copyOf(indices, indices.length - 1);
        }

        return new GeometryEncoder(centre, new BasicPermutationParity(indices), GeometricParity.valueOf(parity));
    }

    /**
     * Lazy creation of an atom index map.
     *
     * @param map       existing map (possibly null)
     * @param container the container we want the map for
     * @return a usable atom to index map for the given container
     */
    private static Map indexMap(Map map, IAtomContainer container) {
        if (map != null) return map;
        map = new HashMap();
        for (IAtom a : container.atoms()) {
            map.put(a, map.size());
        }
        return map;
    }
}