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vvoelz / biceps

Bayesian inference of conformational populations
https://github.com/vvoelz/biceps
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Cleanup with tests #83

Closed robraddi closed 3 years ago

robraddi commented 3 years ago

Now passes the ensemble object to PosterSampler without converting to a list. 

ensemble = biceps.Ensemble(float(lam), list(energies))
ensemble.initialize_restraints(list(input_data))
sampler = biceps.PosteriorSampler(object(ensemble))

Also added a burn-in time for the sample(). Default burn-in time is set to zero.

sampler.sample(int(nsteps), int(burn))
sampler.traj.process_results()

Lastly, the sampler object is automatically saved when calling on process_results

Tests were performed for all systems and notebooks were edited to reflect the alterations in the code.

Fixes #78 #71 #33 #21