Index

A

addBarostat() (openmmslicer.smc.SequentialSampler class method) alch_system (openmmslicer.smc.SequentialSampler attribute) alchemical_atoms (openmmslicer.moves.DihedralMove attribute) (openmmslicer.moves.MoveList property) (openmmslicer.moves.RotationMove attribute) (openmmslicer.moves.TranslationMove attribute) (openmmslicer.smc.SequentialSampler property)

AlchemicalEnergyEvaluator (class in openmmslicer.integrators) AlchemicalGeodesicBAOABIntegrator (class in openmmslicer.integrators) AlchemicalLangevinIntegrator (class in openmmslicer.integrators) applyMove() (openmmslicer.moves.DihedralMove method) (openmmslicer.moves.Move method) (openmmslicer.moves.MoveList method) (openmmslicer.moves.RotationMove method) (openmmslicer.moves.TranslationMove method)

C

calculateStateEnergies() (openmmslicer.smc.SequentialSampler method)

coordinates (openmmslicer.smc.SequentialSampler attribute) current_states (openmmslicer.smc.SequentialSampler attribute)

D

defaultTol() (openmmslicer.resampling_metrics.EffectiveSampleSize class method) defaultValue() (openmmslicer.resampling_metrics.EffectiveSampleSize class method)

deltaE_history (openmmslicer.smc.SequentialSampler attribute) DihedralMove (class in openmmslicer.moves)

E

E_after (openmmslicer.sampling_metrics.EnergyCorrelation attribute) E_before (openmmslicer.sampling_metrics.EnergyCorrelation attribute) EffectiveSampleSize (class in openmmslicer.resampling_metrics) EnergyCorrelation (class in openmmslicer.sampling_metrics) ensemble (openmmslicer.sampling_metrics.EnergyCorrelation attribute) equilibrate() (openmmslicer.smc.SequentialSampler method) evaluate() (openmmslicer.resampling_metrics.EffectiveSampleSize class method) (openmmslicer.resampling_metrics.ExpectedSampleSize class method) (openmmslicer.resampling_metrics.ExpWeightEntropy class method) (openmmslicer.resampling_metrics.WorstCaseSampleSize class method) (openmmslicer.resampling_metrics.WorstCaseSystematicSampleSize class method)

evaluateAfter() (openmmslicer.sampling_metrics.EnergyCorrelation method) evaluateBefore() (openmmslicer.sampling_metrics.EnergyCorrelation method) ExpectedSampleSize (class in openmmslicer.resampling_metrics) ExpWeightEntropy (class in openmmslicer.resampling_metrics)

G

generateAlchemicalRegion() (openmmslicer.smc.SequentialSampler method) generateAlchSystem() (openmmslicer.smc.SequentialSampler static method) generateMoves() (openmmslicer.moves.DihedralMove method) (openmmslicer.moves.Move method) (openmmslicer.moves.MoveList method) (openmmslicer.moves.RotationMove method) (openmmslicer.moves.TranslationMove method)

generateSimFromStruct() (openmmslicer.smc.SequentialSampler class method) generateSystem() (openmmslicer.smc.SequentialSampler static method) getPotentialEnergyFromLambda() (openmmslicer.integrators.AlchemicalEnergyEvaluator method) GreedyBisectingMinimiser (class in openmmslicer.minimise)

I

integrator (openmmslicer.smc.SequentialSampler attribute)

K

kT (openmmslicer.smc.SequentialSampler property)

L

lambda_ (openmmslicer.smc.SequentialSampler attribute)

lambda_history (openmmslicer.smc.SequentialSampler attribute) logZ (openmmslicer.smc.SequentialSampler attribute)

M

make_alchemical() (in module openmmslicer.integrators) masses (openmmslicer.moves.RotationMove attribute) (openmmslicer.moves.TranslationMove attribute) max (openmmslicer.sampling_metrics.EnergyCorrelation property) metric (openmmslicer.sampling_metrics.EnergyCorrelation property) min (openmmslicer.sampling_metrics.EnergyCorrelation property) minimise() (openmmslicer.minimise.GreedyBisectingMinimiser class method) module openmmslicer.integrators openmmslicer.minimise openmmslicer.moves openmmslicer.resampling_methods openmmslicer.resampling_metrics openmmslicer.sampling_metrics openmmslicer.smc

movable_atoms (openmmslicer.moves.DihedralMove attribute) (openmmslicer.moves.RotationMove attribute) (openmmslicer.moves.TranslationMove attribute) Move (class in openmmslicer.moves) MoveList (class in openmmslicer.moves) moves (openmmslicer.moves.MoveList attribute) (openmmslicer.smc.SequentialSampler attribute) (openmmslicer.smc.SequentialSampler property) MultinomialResampler (class in openmmslicer.resampling_methods)

N

n_walkers (openmmslicer.smc.SequentialSampler property)

O

openmmslicer.integrators module openmmslicer.minimise module openmmslicer.moves module openmmslicer.resampling_methods module

openmmslicer.resampling_metrics module openmmslicer.sampling_metrics module openmmslicer.smc module origins (openmmslicer.moves.TranslationMove attribute)

P

platform (openmmslicer.smc.SequentialSampler attribute)

platform_properties (openmmslicer.smc.SequentialSampler attribute)

R

radii (openmmslicer.moves.TranslationMove attribute) (openmmslicer.moves.TranslationMove property) region (openmmslicer.moves.TranslationMove attribute) reporter_history (openmmslicer.smc.SequentialSampler attribute) requireNextLambda (openmmslicer.sampling_metrics.EnergyCorrelation property) resample() (openmmslicer.resampling_methods.MultinomialResampler static method) (openmmslicer.resampling_methods.SystematicResampler static method)

reset() (openmmslicer.sampling_metrics.EnergyCorrelation method) rotatable_bond (openmmslicer.moves.DihedralMove attribute) RotationMove (class in openmmslicer.moves) run() (openmmslicer.smc.SequentialSampler method) runSingleIteration() (openmmslicer.smc.SequentialSampler method)

S

sampler() (openmmslicer.moves.Move static method) sampling (openmmslicer.moves.DihedralMove attribute) (openmmslicer.moves.RotationMove attribute) (openmmslicer.moves.TranslationMove attribute) saveCheckpoint() (openmmslicer.smc.SequentialSampler method) SequentialSampler (class in openmmslicer.smc)

serialise() (openmmslicer.sampling_metrics.EnergyCorrelation method) setState() (openmmslicer.smc.SequentialSampler method) simulation (openmmslicer.smc.SequentialSampler attribute) structure (openmmslicer.smc.SequentialSampler attribute) system (openmmslicer.smc.SequentialSampler attribute) SystematicResampler (class in openmmslicer.resampling_methods)

T

temperature (openmmslicer.smc.SequentialSampler property) terminateSampling (openmmslicer.sampling_metrics.EnergyCorrelation property)

total_sampling_steps (openmmslicer.smc.SequentialSampler attribute) TranslationMove (class in openmmslicer.moves)

W

weight_history (openmmslicer.smc.SequentialSampler attribute)

WorstCaseSampleSize (class in openmmslicer.resampling_metrics) WorstCaseSystematicSampleSize (class in openmmslicer.resampling_metrics)