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
   */
  
  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<mol.getAtoms(); atom++)
  			if (mol.getConnAtoms(atom) == 1 || mol.isRingAtom(atom))
  				maxLength = Math.max(maxLength, findHighestAtomDistance(mol, atom));
  
  		return (float)(maxLength+1) / (float)mol.getAtoms();
  	}
  
  	/**
  	 * Calculates the topological distance to the topologically most remote atom.
  	 * @param mol
  	 * @param startAtom
  	 * @return number of bonds from startAtom to remote atom
  	 */
  	private static int findHighestAtomDistance(StereoMolecule mol, int startAtom) {
  		int[] graphLevel = new int[mol.getAtoms()];
  		int[] graphAtom = new int[mol.getAtoms()];
  
  		graphAtom[0] = startAtom;
  		graphLevel[startAtom] = 1;
  
  		int current = 0;
  		int highest = 0;
  		while (current <= highest /* && graphLevel[current] <= maxLength */) {
  			int parent = graphAtom[current];
  			for (int i=0; i<mol.getConnAtoms(parent); i++) {
  				int candidate = mol.getConnAtom(parent, i);
  				if (graphLevel[candidate] == 0) {
  					graphAtom[++highest] = candidate;
  					graphLevel[candidate] = graphLevel[parent]+1;
  				}
  			}
  			current++;
  		}
  		return graphLevel[graphAtom[highest]] - 1;
  	}
  }
  