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• Separation.java

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com.actelion.research.chem.forcefield.mmff.Separation Maven / Gradle / Ivy

/*
* 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.forcefield.mmff;

import java.util.Hashtable;

/**
 * The Separation class is an efficient storage of an adjacency matrix
 * representing how many degrees of separation there are between any two
 * atoms. The Relations enum marks the relationship between two atoms. A
 * HashTable is used to store the relations between atoms. Atom pairs with
 * ONE_X relations are not stored (this is assumed to be the default case).
 */
public class Separation {
    /**
     * Relation class shows the relationship between two atoms A1 and A2.
     */
    public enum Relation {
        ONE_ONE,   // A1 is A2, an atom has a ONE_ONE relation with itself.
        ONE_TWO,   // A1 is directly bonded to A2.
        ONE_THREE, // A1 is indirectly bonded to A2 via one intermediary atom.
        ONE_FOUR,  // A1 is indirectly bonded to A2 via two intermediary atoms.
        ONE_X;     // (Default) A1 and A2 are separated by more than two atoms.
    }

    public Hashtable table =
        new Hashtable();

    /**
     * Constructs a new separation table for a molecule.
     *  @param mol The molecule that the table will describe.
     */
    public Separation(MMFFMolecule mol) {
        for (int atom=0; atom