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• 2024.9.3
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• TorsionRelevanceHelper.java

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com.actelion.research.chem.conf.TorsionRelevanceHelper Maven / Gradle / Ivy

/*
 * 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