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.
   *
   * @author Thomas Sander, Modest v. Korff
   */
  
  package com.actelion.research.chem.prediction;
  
  import com.actelion.research.chem.Canonizer;
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  
  import java.util.TreeSet;
  
  /**
   * This is a fast version of the MolecularComplexityCalculator in the com.actelion.chem.properties.complexity
   * package. It determines the number of distinct fragments within the given molecule up to a bod count of 7.
   */
  public class FastMolecularComplexityCalculator {
  	protected static final int MAX_BOND_COUNT = 7;
  
  	/**
  	 * Before calculating any kind of property, make sure that the molecule's structure is standardized.
  	 * Typically, molecules created by an IDCodeParser are standardized. Molecules generated from a
  	 * SmilesParser or MolfileParser, or just drawn within an editor, should be standardized using the
  	 * MoleculeStandardizer.
  	 * @param mol
  	 * @return complexity value estimated from the number of distinct small fragments
  	 */
  	public static float assessComplexity(StereoMolecule mol) {
  		int bondCount = Math.min(mol.getBonds()/2, MAX_BOND_COUNT);
  
  		if (bondCount < 2)
  			return 0;
  
  		mol.ensureHelperArrays(Molecule.cHelperSymmetrySimple);
  		StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());
  		TreeSet<String> fragmentSet = new TreeSet<>();
  		int[] atomMap = new int[mol.getAllAtoms()];
  
  		boolean[][] bondsTouch = new boolean[mol.getBonds()][mol.getBonds()];
  		for (int atom=0; atom<mol.getAtoms(); atom++) {
  			for (int i=1; i<mol.getConnAtoms(atom); i++) {
  				for (int j=0; j<i; j++) {
  					int bond1 = mol.getConnBond(atom, i);
  					int bond2 = mol.getConnBond(atom, j);
  					bondsTouch[bond1][bond2] = true;
  					bondsTouch[bond2][bond1] = true;
  				}
  			}
  		}
  
  		boolean[] bondIsMember = new boolean[mol.getBonds()];
  		int maxLevel = bondCount - 2;
  		int[] levelBond = new int[maxLevel+1];
  		for (int rootBond=0; rootBond<mol.getBonds(); rootBond++) {
  			bondIsMember[rootBond] = true;
  			int level = 0;
  			levelBond[0] = rootBond;
  			while (true) {
  				boolean levelBondFound = false;
  				while (!levelBondFound && levelBond[level] < mol.getBonds()-1) {
  					levelBond[level]++;
  					if (!bondIsMember[levelBond[level]]) {
  						for (int bond=rootBond; bond<mol.getBonds(); bond++) {
  							if (bondIsMember[bond] && bondsTouch[bond][levelBond[level]]) {
  								levelBondFound = true;
  								break;
  							}
  						}
  					}
  				}
  
  				if (levelBondFound) {
  					bondIsMember[levelBond[level]] = true;
  					if (level == maxLevel) {
  						mol.copyMoleculeByBonds(fragment, bondIsMember, true, atomMap);
  						fragmentSet.add(new Canonizer(fragment).getIDCode());
  						bondIsMember[levelBond[level]] = false;
  					}
  					else {
  						level++;
  						levelBond[level] = rootBond;
  					}
  				}
  				else {
  					if (--level < 0)
  						break;
  					bondIsMember[levelBond[level]] = false;
  				}
  			}
  			bondIsMember[rootBond] = false;
  		}
  
  		return (float)Math.log(fragmentSet.size()) / bondCount;
  	}
  }
  