/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  This program is distributed in the hope that it will be useful,       *
*  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
*  GNU General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package com.act.biointerpretation.sars;

import chemaxon.struc.Molecule;
import com.chemaxon.search.mcs.MaxCommonSubstructure;
import com.chemaxon.search.mcs.McsSearchOptions;
import com.chemaxon.search.mcs.RingHandlingMode;

import java.util.List;

public class McsCalculator {

  /**
   * Bond matching = true --> only bonds of same order will match
   * connectedMode = true --> only return one fragment
   * ringHandlingMode = KEEP_RINGS --> don't allow a ring to be only partially matched by substructure; all or nothing
   * We do not match bond type because it throws off a lot of matches on benzene rings with bonds shifted.
   * TODO: further investigate bond type regarding aromatization and rings.
   */
  public static final McsSearchOptions REACTION_BUILDING_OPTIONS =
      new McsSearchOptions.Builder()
          .bondTypeMatching(true)
          .connectedMode(false)
          .ringHandlingMode(RingHandlingMode.KEEP_RINGS)
          .build();
  public static final McsSearchOptions SAR_OPTIONS =
      new McsSearchOptions.Builder()
          .bondTypeMatching(false)
          .connectedMode(false)
          .ringHandlingMode(RingHandlingMode.KEEP_RINGS)
          .build();


  private final MaxCommonSubstructure mcs;

  public McsCalculator(McsSearchOptions mcsOptions) {
    this.mcs = MaxCommonSubstructure.newInstance(mcsOptions);
  }

  /**
   * Gets MCS of any number of molecules by iteratively applying Chemaxon's MCS search to all substrates.
   * For an array of n molecules, this will use n-1 MCS operations.
   * TODO: experiment with LibraryMcs instead of MaxCommonSubstructure here; it may find a better overall match.
   *
   * @param molecules The molecules to get the MCS of.
   * @return The MCS of all input molecules.
   */
  public Molecule getMCS(List<Molecule> molecules) {
    if (molecules.isEmpty()) {
      throw new IllegalArgumentException("Cannot get MCS of empty list of molecules.");
    }

    Molecule substructure = molecules.get(0);
    for (Molecule mol : molecules.subList(1, molecules.size())) {
      substructure = getMcsOfPair(substructure, mol);
    }
    return substructure;
  }

  /**
   * Helper method to find MCS of exactly two molecules.
   */
  private Molecule getMcsOfPair(Molecule moleculeA, Molecule moleculeB) {
    mcs.setMolecules(moleculeA, moleculeB);
    return mcs.nextResult().getAsMolecule();
  }
}