org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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.Arrays;
public class TorsionSetStrategyAdaptiveRandom extends TorsionSetStrategyRandom {
private static final int MAX_TRIES_FOR_NEW = 64;
private boolean mStartWithMostProbable;
/**
* This torsion set strategy produces random sets of torsion indices until a torsion set
* collides. Then it updates individual torsion indices of those rotatable bonds
* that connect colliding fragments.
* Torsion indices are picked either by pure random or with a twisted likelyhood
* towards towards those angles, that show higher frequencies in the CSD.
* @param conformerGenerator
* @param preferLikelyTorsions if set then more frequent torsions are picked with higher probability
* @param startWithMostProbable if true then the first torsion set returned contains for every bond the most frequent torsion
* @param seed
* @return
*/
public TorsionSetStrategyAdaptiveRandom(ConformerGenerator conformerGenerator, boolean preferLikelyTorsions, boolean startWithMostProbable, long seed) {
super(conformerGenerator, preferLikelyTorsions, seed);
mStartWithMostProbable = startWithMostProbable;
}
@Override
public TorsionSet createTorsionSet(TorsionSet previousTorsionSet) {
if (previousTorsionSet == null) {
if (mStartWithMostProbable)
return createTorsionSet(new int[mRotatableBond.length], new int[mRigidFragment.length]);
else
return super.createTorsionSet(null);
}
if (previousTorsionSet.getCollisionStrainSum() == 0.0)
return super.createTorsionSet(previousTorsionSet);
double[] collisionIntensitySum = getBondAndFragmentCollisionIntensities(previousTorsionSet);
int[] collidingTorsionIndex = previousTorsionSet.getTorsionIndexes();
int[] collidingConformerIndex = previousTorsionSet.getConformerIndexes();
boolean[] indexTried = new boolean[collisionIntensitySum.length];
for (int count=0; count