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Open Source Chemistry Library
/*
* Copyright 2013-2020 Thomas Sander, openmolecules.org
*
* 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 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 HOLDER 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 org.openmolecules.chem.conf.gen;
import java.util.Random;
public class TorsionSetStrategyRandom extends TorsionSetStrategy {
private static final int MAX_TRIES_FOR_NEW = 64;
private Random mRandom;
private boolean mPreferLikelyTorsions;
/**
* This simple TorsionSetStrategy produces random sets of torsion indexes in a loop.
* If it finds a new torsion set within a reasonable number of cycles, the set is returned.
* If this is not successful or if all permutations of torsion indexes was already delivered,
* then it stops creating new permutations and returns null.
* Torsion indices are chosen either pure randomly or optionally with a bias
* towards those torsion angles, that are more frequently populated in the CSD
* and cause less collision strain.
* @param conformerGenerator
* @param preferLikelyTorsions if set then more frequent angles are picked with higher probability
* @param seed
*/
public TorsionSetStrategyRandom(ConformerGenerator conformerGenerator, boolean preferLikelyTorsions, long seed) {
super(conformerGenerator);
mPreferLikelyTorsions = preferLikelyTorsions;
mRandom = (seed == 0) ? new Random() : new Random(seed);
}
public Random getRandom() {
return mRandom;
}
/**
* Build a new set of torsion angles by pure or biased random picking.
* @param previousTorsionSet is not used
* @return a random and new torsion index set.
*/
@Override
public TorsionSet createTorsionSet(TorsionSet previousTorsionSet) {
if (getTorsionSetCount() == getPermutationCount())
return null; // if we have found all permutations
int[] torsionIndex = new int[mRotatableBond.length];
int[] conformerIndex = new int[mRigidFragment.length];
TorsionSet ts;
int count = 0;
do {
if (count++ == MAX_TRIES_FOR_NEW)
return null;
if (mPreferLikelyTorsions) {
double progress = (double)count/(double)MAX_TRIES_FOR_NEW;
for (int rf=0; rf