int |
TorsionSet.compareTo(TorsionSet ts) |
Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.
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abstract TorsionSet |
TorsionSetStrategy.createTorsionSet(TorsionSet previousTorsionSet) |
Provide the next set of torsion angles using a specific strategy and
considering, which angle combinations were already tried, which had failed, and
(depending on the strategy) considering the likelyhoods of particular torsions.
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TorsionSet |
TorsionSetStrategyAdaptiveRandom.createTorsionSet(TorsionSet previousTorsionSet) |
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TorsionSet |
TorsionSetStrategyLikelySystematic.createTorsionSet(TorsionSet previousTorsionSet) |
Determine the next likely set of torsion angles and return the TorsionSet
containing an array of indexes referring to the torsion value in the
RotatableBond and containing the contribution of this conformer to all
non colliding ones.
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TorsionSet |
TorsionSetStrategyRandom.createTorsionSet(TorsionSet previousTorsionSet) |
Build a new set of torsion angles by pure or biased random picking.
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Conformer |
ConformerGenerator.generateConformerFromTorsionSet(TorsionSet torsionset) |
Computes a conformer from a TorsionSet object.
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protected double[] |
TorsionSetStrategy.getBondAndFragmentCollisionIntensities(TorsionSet collidingTorsionSet) |
Calculates for every rotatable bond and for every rigid fragment a collision intensity sum
for the given torsion/conformer state from the collision rules already known.
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double |
TorsionSetStrategy.getContribution(TorsionSet torsionSet) |
With best current knowledge about colliding torsion combinations
and based on the individual frequencies of currently active torsions
this method returns the conformers's overall contribution to the
total set of non colliding conformers.
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Conformer |
ConformerGenerator.getNextConformer(TorsionSet[] torsion_set_out) |
Creates the next random, likely or systematic new(!) conformer of the molecule
that was passed when calling initializeConformers().
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TorsionSet |
TorsionSetStrategy.getNextTorsionSet(TorsionSet previousTorsionSet) |
Creates the next set of torsion indexes to be tried by the ConformerGenerator.
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protected boolean |
TorsionSetStrategy.isNewTorsionSet(TorsionSet ts) |
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