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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.
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*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
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*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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package com.actelion.research.chem.forcefield.mmff;

import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.RingCollection;

/**
 * MMFF molecule is a wrapper class for the ExtendedMolecule. It holds some
 * additional data such as a cache of the atom types, whether the molecule is
 * valid for MMFF and the ring mmff aromaticity property.
 */
public final class MMFFMolecule extends StereoMolecule  {
    private RingBoolean[] mRingArom;
    private int[] mAtomTypes;
    private int[] mHydrogenMap;

    public MMFFMolecule(StereoMolecule mol) throws BadAtomTypeException,
                                                 BadRingAromException
    {
    	super(mol);
        mHydrogenMap = getHandleHydrogenMap();
        RingCollection rings = getRingSet();
        mRingArom = new RingBoolean[rings.getSize()];
        for (int i=0; i




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