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.type;
  
  import com.actelion.research.chem.RingCollection;
  import com.actelion.research.chem.forcefield.mmff.MMFFMolecule;
  import com.actelion.research.chem.forcefield.mmff.Tables;
  
  import java.util.HashSet;
  
  /**
   * The torsion type class provides a static function for getting the
   * torsion type of a torsion angle.
   */
  public final class Torsion {
      /**
       * Returns the torsion type of a torsion angle.
       *  @param mol The molecule that the atoms are in.
       *  @param a1 Atom 1.
       *  @param a2 Atom 2.
       *  @param a3 Atom 3.
       *  @param a4 Atom 4.
       *  @return The torsion type (combined tortype and secondary tortype).
       */
      public static int getType(Tables table, MMFFMolecule mol, int a1, int a2, int a3,
                                int a4) {
          int bond_jk = mol.getBond(a2, a3);
  
          int bijt = Bond.getType(table, mol, a1, a2);
          int bjkt = Bond.getType(table, mol, a2, a3);
          int bklt = Bond.getType(table, mol, a3, a4);
          int tort = bjkt;
  
          if (bjkt == 0 && mol.getBondOrder(bond_jk) == 1
                  && (bijt == 1 || bklt == 1))
              tort = 2;
  
          int size = inRingOfSize(mol, a1, a2, a3, a4);
  
          if (size == 4 && mol.getBond(a1, a3) == -1
                  && mol.getBond(a2, a4) == -1)
              return 40 + tort;
  
          if (size == 5 && (mol.getAtomType(a1) == 1
                      || mol.getAtomType(a2) == 1
                      || mol.getAtomType(a3) == 1
                      || mol.getAtomType(a4) == 1))
              return 50 + tort;
  
          return tort;
      }
  
      /**
       * Checks and returns the minimum ring size that a torsion is
       * contained in. Only checks rings of size 4 and 5.
       *  @param mol The molecule that the atoms are in.
       *  @param a1 Atom 1.
       *  @param a2 Atom 2.
       *  @param a3 Atom 3.
       *  @param a4 Atom 4.
       */
      public static int inRingOfSize(MMFFMolecule mol, int a1, int a2,
                                     int a3, int a4) {
  
          // If any of the four atoms don't have bonds between them, then they
          // don't form a torsion angle and there fore this invalid torsion
          // cannot be in a ring.
          if (mol.getBond(a1, a2) == -1 || mol.getBond(a2, a3) == -1
                  || mol.getBond(a3, a4) == -1)
              return 0;
  
          // If atom 4 is connected to atom 1, then the torsion loops back on to
          // itself and is in a ring of size 4.
          if (mol.getBond(a4, a1) >= 0)
              return 4;
  
  
          RingCollection rings = mol.getRingSet();
          HashSet<Integer> tor = new HashSet<Integer>();
          tor.add(a1);
          tor.add(a2);
          tor.add(a3);
          tor.add(a4);
  
          // Loop over all the molecule rings, for all rings of size 5 check if
          // the set of ring atoms contains the torsion angle atoms with a set
          // intersection. If true then the ring contains the torsion.
          for (int r=0; r<rings.getSize(); r++)
              if (rings.getRingSize(r) == 5) {
                  HashSet<Integer> ring = new HashSet<Integer>();
  
                  for (int a : rings.getRingAtoms(r))
                      ring.add(a);
  
                  if (ring.containsAll(tor))
                      return 5;
              }
  
          return 0;
      }
  }
  