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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
 */

package com.actelion.research.chem.prediction;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;

public class MolecularShapeCalculator {
	/**
	 * Returns the number of bonds of the shortest path between those two atoms
	 * with the largest topological distance divided by the number of non-hydrogen atoms.
	 * @param mol
	 * @return
	 */
	public static float assessShape(StereoMolecule mol) {
		mol.ensureHelperArrays(Molecule.cHelperRings);
		if (mol.getAtoms() == 0)
			return -1;
		if (mol.getBonds() == 0)
			return 0;

		int maxLength = 0;
		for (int atom=0; atom