Package org.openmolecules.chem.conf.gen
Class TorsionSetStrategyAdaptiveRandom
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- org.openmolecules.chem.conf.gen.TorsionSetStrategy
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- org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
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- org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
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public class TorsionSetStrategyAdaptiveRandom extends TorsionSetStrategyRandom
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Field Summary
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Fields inherited from class org.openmolecules.chem.conf.gen.TorsionSetStrategy
MAX_ALLOWED_COLLISION_INTENSITY, mRigidFragment, mRotatableBond
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Constructor Summary
Constructors Constructor Description TorsionSetStrategyAdaptiveRandom(RotatableBond[] rotatableBond, RigidFragment[] fragment, boolean preferLikelyTorsions, boolean startWithMostProbable, long seed)
This torsion set strategy produces random sets of torsion indices until a torsion set collides.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description TorsionSet
createTorsionSet(TorsionSet previousTorsionSet)
Build a new set of torsion angles by pure or biased random picking.-
Methods inherited from class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
getRandom
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Methods inherited from class org.openmolecules.chem.conf.gen.TorsionSetStrategy
calculateCollisionTolerance, createTorsionSet, eliminationRuleString, getBestCollidingTorsionIndexes, getBondAndFragmentCollisionIntensities, getBondsBetweenFragments, getContribution, getEliminationRuleList, getFailureCount, getNextTorsionSet, getPermutationCount, getTorsionSetCount, isNewTorsionSet, setMaxTotalCount
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Constructor Detail
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TorsionSetStrategyAdaptiveRandom
public TorsionSetStrategyAdaptiveRandom(RotatableBond[] rotatableBond, RigidFragment[] fragment, boolean preferLikelyTorsions, boolean startWithMostProbable, long seed)
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.- Parameters:
rotatableBond
-preferLikelyTorsions
- if set then more frequent torsions are picked with higher probabilitystartWithMostProbable
- if true then the first torsion set returned contains for every bond the most frequent torsionseed
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Method Detail
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createTorsionSet
public TorsionSet createTorsionSet(TorsionSet previousTorsionSet)
Description copied from class:TorsionSetStrategyRandom
Build a new set of torsion angles by pure or biased random picking.- Overrides:
createTorsionSet
in classTorsionSetStrategyRandom
- Parameters:
previousTorsionSet
- is not used- Returns:
- a random and new torsion index set.
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