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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, 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 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
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.chem.descriptor;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.BurtleHasher;

import java.nio.charset.StandardCharsets;
import java.util.Arrays;

public class DescriptorHandlerSkeletonSpheres implements DescriptorHandler {
    private static final double CORRECTION_FACTOR = 0.7;

    private static final byte[] FAILED_OBJECT = new byte[0];
    private static final int MAX_SPHERE_COUNT = 5;
    private static final int EXACT_SPHERE_COUNT = 4;
    private static final int SKELETON_SPHERE_COUNT = 5;
    private static final int HASH_BITS = 10;
    private static final int HASH_INIT = 13;
    private static final int DESCRIPTOR_SIZE = (1 << HASH_BITS);

    private static DescriptorHandlerSkeletonSpheres sDefaultInstance;

    public static DescriptorHandlerSkeletonSpheres getDefaultInstance() {
    	synchronized(DescriptorHandlerSkeletonSpheres.class) {
    		if (sDefaultInstance == null) {
        		sDefaultInstance = new DescriptorHandlerSkeletonSpheres();
        		}
        	}
        return sDefaultInstance;
    	}

    public boolean calculationFailed(byte[] o) {
        return o==null || o.length == 0;
        }

    /**
     * This descriptor requires proper up/down bonds, because it encodes stereo parities.
     * If a passed molecule is generated from idcode parsing, make sure that coordinates
     * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with
     * the respective option.
     */
    public byte[] createDescriptor(StereoMolecule mol) {
	    if (mol == null)
		    return null;

        mol.ensureHelperArrays(Molecule.cHelperRings);
        StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());

		byte[] descriptor = new byte[DESCRIPTOR_SIZE];

//System.out.println("descriptor skeleton spheres:");
        int[] atomList = new int[mol.getAtoms()];
        boolean[] atomMask = new boolean[mol.getAtoms()];
        for (int rootAtom=0; rootAtom 0.8) {
    System.out.print("i:");
    for (int i=0; i= 1.0f ? 1.0f
			 : (float)(1.0-Math.pow(1-Math.pow(value, CORRECTION_FACTOR) ,1.0/CORRECTION_FACTOR));
		}

    public DescriptorHandler getThreadSafeCopy() {
		return this;
    	}
	}