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.StereoMolecule;
  import com.actelion.research.util.Angle;
  import com.actelion.research.util.DoubleFormat;
  
  public class TorsionDescriptor implements Comparable<TorsionDescriptor> {
  	private static final float TORSION_EQUIVALENCE_TOLERANCE = (float)Math.PI / 12f;
  
  	private float[] mTorsion;
  	private float[] mMaxTorsion;
  
  	/**
  	 *
  	 * @param torsion torsion angles of rotatable bonds from 0 to maxTorsion
  	 * @param maxTorsion maximum torsions of rotatable bonds defining individual symmetry dependent range
  	 */
  	public TorsionDescriptor(float[] torsion, float[] maxTorsion) {
  		mTorsion = torsion;
  		mMaxTorsion = maxTorsion;
  		}
  
  	/**
  	 * Creates a TorsionDescriptor from conformer's coordinates
  	 * drawing atom connectivity from the conformer's molecule.
  	 * The torsion descriptor is not canonical, unless the passed molecule is canonical.
  	 * Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
  	 * @param conformer
  	 *
  	public TorsionDescriptor(Conformer conformer, int[] rotatableBond) {
  		mTorsion = new float[rotatableBond.length];
  		StereoMolecule mol = conformer.getMolecule();
  		mol.ensureHelperArrays(Molecule.cHelperSymmetrySimple);
  		int[] atom = new int[4];
  		for (int i=0; i<rotatableBond.length; i++) {
  			for (int j=0; j<2; j++) {
  				atom[j+1] = mol.getBondAtom(j, rotatableBond[i]);
  				for (int k=0; k<mol.getConnAtoms(atom[j+1]); k++) {
  					int refAtom = mol.getConnAtom(atom[j+1], k);
  					if (refAtom != mol.getBondAtom(1-j, rotatableBond[i])) {
  						atom[3*j] = refAtom;
  						break;
  						}
  					}
  				}
  			mTorsion[i] = (float)getNormalizedTorsion(conformer.calculateTorsion(atom), getSymmetryClass());
  			}
  		}*/
  
  	/**
  	 * Returns true, if none of the torsion angles are more different
  	 * than TORSION_EQUIVALENCE_TOLERANCE;
  	 * @param td
  	 * @return
  	 */
  	public boolean equals(TorsionDescriptor td) {
  		for (int i=0; i<mTorsion.length; i++) {
  			float dif = Math.abs(mTorsion[i] - td.mTorsion[i]);
  			if (dif > TORSION_EQUIVALENCE_TOLERANCE
  			 && dif < mMaxTorsion[i] - TORSION_EQUIVALENCE_TOLERANCE)
  				return false;
  			}
  		return true;
  		}
  
  	/**
  	 * Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
  	 * Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
  	 * @param td
  	 * @return
  	 */
  	@Override
  	public int compareTo(TorsionDescriptor td) {
  		for (int i=0; i<mTorsion.length; i++) {
  			float dif = Math.abs(mTorsion[i] - td.mTorsion[i]);
  			if (dif > TORSION_EQUIVALENCE_TOLERANCE
  			 && dif < mMaxTorsion[i] - TORSION_EQUIVALENCE_TOLERANCE)
  				return (dif < mMaxTorsion[i]/2) ^ (mTorsion[i] < td.mTorsion[i]) ? 1 : -1;
  			}
  		return 0;
  		}
  
  	/**
  	 * 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
  	 * @return
  	 */
  	public static float[] getRotatableBondWeights(StereoMolecule mol, int[] rotatableBond) {
  		return TorsionRelevanceHelper.getRelevance(mol, rotatableBond);
  		}
  
  	/**
  	 * Calculates a similarity value between td and this considering
  	 * individual torsion values, the importance of the rotatable bond,
  	 * and the ratio of rotatable/non-rotatable bonds.
  	 * @param td
  	 * @return
  	 */
  	public float getDissimilarity(TorsionDescriptor td, float[] bondWeight) {
  		assert(mTorsion.length == td.mTorsion.length);
  
  		if (mTorsion.length == 0)
  			return 0.0f;
  
  		float meanAngleDiff = 0f;
  
  		float weightSum = 0f;
  		for (int i=0; i<mTorsion.length; i++) {
  			meanAngleDiff += bondWeight[i] * Math.abs(Angle.difference(mTorsion[i], td.mTorsion[i]));
  			weightSum += bondWeight[i];
  			}
  		return meanAngleDiff / ((float)Math.PI * weightSum);
  		}
  
  	@Override
  	public String toString() {
  		StringBuilder sb = new StringBuilder();
  		for (int i=0; i<mTorsion.length; i++) {
  			sb.append(i == 0? "Torsions: " : ", ");
  			sb.append(DoubleFormat.toString(mTorsion[i], 3)+"("+Math.round(mMaxTorsion[i]+0.5f)+")");
  			}
  		return sb.toString();
  		}
  	}
  