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/*
 * Copyright 2017 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
 *
 * This file is part of DataWarrior.
 *
 * DataWarrior 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.
 *
 * DataWarrior 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 DataWarrior.
 * If not, see http://www.gnu.org/licenses/.
 *
 * @author Thomas Sander,Modest von 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 {
	/**
	 * Ambiguous bonds are normalized.
	 * @param mol
	 * @return
	 */
	public static float assessComplexity(StereoMolecule mol) {
		final int MAX_BOND_COUNT = 7;
		int bondCount = Math.min(mol.getBonds()/2, MAX_BOND_COUNT);

		if (bondCount < 2)
			return 0;

		mol.ensureHelperArrays(Molecule.cHelperRings);
		StereoMolecule fragment = new StereoMolecule(mol.getAtoms(), mol.getBonds());
		TreeSet fragmentSet = new TreeSet();
		int[] atomMap = new int[mol.getAllAtoms()];

		boolean[][] bondsTouch = new boolean[mol.getBonds()][mol.getBonds()];
		for (int atom=0; atom