content: /*
  * 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<SortedPair, Relation> table =
          new Hashtable<SortedPair, Relation>();
  
      /**
       * 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<mol.getAllAtoms(); atom++) {
              table.put(new SortedPair(atom, atom), Relation.ONE_ONE);
  
              for (int i=0; i<mol.getAllConnAtoms(atom); i++) {
                  int nbr1 = mol.getConnAtom(atom, i);
                  SortedPair keytwo = new SortedPair(atom, nbr1);
  
                  table.put(keytwo, Relation.ONE_TWO);
  
                  for (int j=0; j<mol.getAllConnAtoms(nbr1); j++) {
                      int nbr2 = mol.getConnAtom(nbr1, j);
                      SortedPair keythree = new SortedPair(atom, nbr2);
  
                      if (!table.containsKey(keythree)
                              || table.get(keythree) == Relation.ONE_FOUR)
                          table.put(keythree, Relation.ONE_THREE);
  
                      for (int k=0; k<mol.getAllConnAtoms(nbr2); k++) {
                          int nbr3 = mol.getConnAtom(nbr2, k);
                          SortedPair keyfour = new SortedPair(atom, nbr3);
  
                          if (!table.containsKey(keyfour))
                              table.put(keyfour, Relation.ONE_FOUR);
                      }
                  }
              }
          }
      }
  
      /**
       * Returns the relation of a given pair of atoms. If no key was found
       * that is an indication that there is a ONE_X relationship between
       * the two atoms.
       *  @param key The sorted pair of atoms.
       *  @return The separation relationship between the two atoms.
       */
      public Relation get(SortedPair key) {
          return table.get(key) != null ? table.get(key) : Relation.ONE_X;
      }
  
      public Relation get(int a1, int a2) {
          return get(new SortedPair(a1, a2));
      }
  }
  