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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
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.chem;

import com.actelion.research.chem.coords.CoordinateInventor;

import java.util.ArrayList;

public class MarkushStructure implements java.io.Serializable {
	static final long serialVersionUID = 0x20080515;

	private static final int MAX_RGROUP_DEPTH = 5;

	private	ArrayList   mCoreList;
	private	ArrayList   mRGroupList;
	private StereoMolecule[][]          mSubstituent;
	private int                         mCoreIndex;
	private int[]                       mSubstituentCount,mSubstituentIndex;
	private int[][]                     mCoreRGroup;
	private int[][][]                   mSubstituentRGroup;

	public MarkushStructure() {
	    mCoreList = new ArrayList();
	    mRGroupList = new ArrayList();
		}

	public MarkushStructure(StereoMolecule[] fragment, int coreCount) {
		this();
		if (fragment != null) {
			for (int i=0; i rGroupList = new ArrayList();
			for (int atom=0; atom= mRGroupList.size())
            throw new Exception("Not all used R-groups are defined.");

        String warning = null;
        if (rGroupCount < mRGroupList.size())
            warning = "One or more defined R-group(s) are unreferenced.";

        mSubstituent = new StereoMolecule[mRGroupList.size()][];
        mSubstituentRGroup = new int[mRGroupList.size()][][];
        for (int i=0; i rGroupList = new ArrayList();
                for (int atom=0; atom 1) {
                if (mSubstituentIndex[rGroup]+1 < mSubstituentCount[rGroup]) {
                    mSubstituentIndex[rGroup]++;
                    incrementCoreIndex = false;
                    break;
                    }
                else {
                    mSubstituentIndex[rGroup] = 0;
                    }
                }
            }
        if (incrementCoreIndex)
            mCoreIndex++;

        return mol;
        }

    private int getRGroupIndex(int atomicNo) {
        if (atomicNo < 129 || atomicNo > 144)
            return -1;
        return (atomicNo >= 142) ? atomicNo - 142 : atomicNo - 126;
        }

    private StereoMolecule createCurrentEnumeration() {
        StereoMolecule mol = new StereoMolecule();

        mol.addMolecule(mCoreList.get(mCoreIndex));
        for (int atom=0; atom