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.
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  package com.actelion.research.chem.forcefield.mmff.type;
  
  import com.actelion.research.chem.RingCollection;
  import com.actelion.research.chem.forcefield.mmff.MMFFMolecule;
  import com.actelion.research.chem.forcefield.mmff.Tables;
  
  /**
   * The bond type class provides static functions for getting the MMFF bond
   * type (either by bond or by the atoms of a bond).
   */
  public class Bond {
      /**
       * Returns the MMFF bond type of a bond on a molecule. This function
       * assumes that a valid bond is passed for the molecule.
       *  @param mol The molecule that contains the bond.
       *  @param bond The bond to be typed.
       *  @return The MMFF bond type.
       */
      public static int getType(Tables table, MMFFMolecule mol, int bond) {
          return getType(table, mol, mol.getBondAtom(0, bond),
                  mol.getBondAtom(1, bond));
      }
  
      /**
       * Returns the MMFF bond type of a bond on a molecule. This function
       * assumes that both atoms passed are valid and have a valid bond
       * between them.
       *  @param mol The molecule that contains the bond.
       *  @param atom1 The first atom of the bond.
       *  @param atom2 The second atom of the bond.
       *  @return The MMFF bond type.
       */
      public static int getType(Tables table, MMFFMolecule mol, int atom1,
                                int atom2) {
          int a1t = mol.getAtomType(atom1);
          int a2t = mol.getAtomType(atom2);
          int bond = mol.getBond(atom1, atom2);
  
          boolean notInAromaticRing = true;
  
          RingCollection rings = mol.getRingSet();
          for (int r=0; r<rings.getSize() && notInAromaticRing; r++) {
              for (int b : rings.getRingBonds(r)) {
                  if (b == bond && mol.ringIsMMFFAromatic(r)) {
                      notInAromaticRing = false;
                      break;
                  }
              }
          }
  
          return (mol.getBondOrder(bond) == 1)
              && notInAromaticRing
              && (table.atom.arom(a1t) && table.atom.arom(a2t)
              || table.atom.sbmb(a1t) && table.atom.sbmb(a2t)) ? 1 : 0;
      }
  }
  