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.conf;
  
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  
  public class TorsionRelevanceHelper {
  	/**
  	 * The relevance of a rotatable bond and its torsion angle for creating substantially different conformers
  	 * depends on how close the bond is to the center of the molecule. Bond relevance values range from
  	 * 1.0/atomCount (e.g. bond to methyl group) to 1.0 (bond dividing molecule into two equally large parts).
  	 * Ring bonds are assigned a relevance value of 0.33 independent of their location.
  	 * @param mol
  	 * @param rotatableBond array containing bond indexes for which to calculate relevance values
  	 * @return
  	 */
  	public static final float[] getRelevance(StereoMolecule mol, int[] rotatableBond) {
  		mol.ensureHelperArrays(Molecule.cHelperRings);
  
  		float[] bondWeight = new float[rotatableBond.length];
  		for (int i=0; i<bondWeight.length; i++) {
  			if (mol.isRingBond(rotatableBond[i])) {
  				bondWeight[i] = 0.33f;
  				}
  			else {
  				int atom1 = mol.getBondAtom(0, rotatableBond[i]);
  				int atom2 = mol.getBondAtom(1, rotatableBond[i]);
  				if (mol.getConnAtoms(atom1) == 1 || mol.getConnAtoms(atom2) == 1) {
  					bondWeight[i] = 1f / mol.getAtoms();	// rotates hydrogens only
  					}
  				else {
  					int atomCount = mol.getSubstituentSize(atom1, atom2);
  					bondWeight[i] = 2f * Math.min(atomCount, mol.getAtoms() - atomCount) / mol.getAtoms();
  					}
  				}
  			}
  		return bondWeight;
  	}
  
  	/**
  	 * The relevance of a rotatable bond and its torsion angle for creating substantially different conformers
  	 * depends on how close the bond is to the center of the molecule. Bond relevance values range from
  	 * 1.0/atomCount (e.g. bond to methyl group) to 1.0 (bond dividing molecule into two equally large parts).
  	 * @param mol
  	 * @param isRotatableBond if null, then the relevance is calculated for every non-H-bond
  	 * @return array with bond relevance values for all rotatable or all non-H-bonds
  	 */
  	public static final float[] getRelevance(StereoMolecule mol, boolean[] isRotatableBond) {
  		mol.ensureHelperArrays(Molecule.cHelperRings);
  
  		float[] bondWeight = new float[mol.getBonds()];
  		for (int bond=0; bond<mol.getBonds(); bond++) {
  			if (isRotatableBond == null || isRotatableBond[bond]) {
  				if (mol.isRingBond(bond)) {
  					bondWeight[bond] = 0.33f;
  					}
  				else {
  					int atom1 = mol.getBondAtom(0, bond);
  					int atom2 = mol.getBondAtom(1, bond);
  					if (mol.getConnAtoms(atom1) == 1 || mol.getConnAtoms(atom2) == 1) {
  						bondWeight[bond] = 1f / mol.getAtoms();	// rotates hydrogens only
  						}
  					else {
  						int atomCount = mol.getSubstituentSize(atom1, atom2);
  						bondWeight[bond] = 2f * Math.min(atomCount, mol.getAtoms() - atomCount) / mol.getAtoms();
  						}
  					}
  				}
  			}
  		return bondWeight;
  		}
  	}
  