API Reference

Preparation

.. currentmodule:: biceps

.. autoclass:: biceps.Restraint.Preparation

.. automethod:: biceps.Restraint.Preparation.prep_cs

.. automethod:: biceps.Restraint.Preparation.prep_J

.. automethod:: biceps.Restraint.Preparation.prep_noe

.. automethod:: biceps.Restraint.Preparation.prep_pf

.. currentmodule:: biceps

.. autoclass:: biceps.Ensemble

.. automethod:: biceps.Ensemble.initialize_restraints

.. automethod:: biceps.Ensemble.to_list

.. currentmodule:: biceps

.. autoclass:: biceps.Restraint.Restraint

.. automethod:: biceps.Restraint.Restraint_cs.init_restraint

.. automethod:: biceps.Restraint.Restraint_J.init_restraint

.. automethod:: biceps.Restraint.Restraint_noe.init_restraint

.. automethod:: biceps.Restraint.Restraint_pf.init_restraint

.. currentmodule:: biceps

.. autoclass:: biceps.PosteriorSampler

.. automethod:: biceps.PosteriorSampler.neglogP

.. automethod:: biceps.PosteriorSampler.sample

.. autoclass:: biceps.PosteriorSamplingTrajectory

.. automethod:: biceps.PosteriorSamplingTrajectory.process_results

Trajectory information

Key	Short Description
`rest_type`	list of strings for each restraint type.
`ref`	list of strings for each reference potential types
`allowed_parameters`	list of numpy arrays containing the allowed range of nuisance parameters with shape (m,n)
`sampled_parameters`	list of numpy arrays containing the counts of nuisance parameters sampled for each restraint with shape (m,n)
`trajectory_headers`	e.g., [step, energy, accept, state, [nuisance parameter index]]
`trajectory`	list of values—see `trajectory_headers`
`sep_accept`	list of separated acceptance ratios with shape (n+1,)
`traces`	list of sampled nuisance parameters with shape (n)
`state_trace`	list of sampled conformational state index

n is the number of allowed parameters
m is the number of restraints

.. currentmodule:: biceps

.. autoclass:: biceps.Analysis

.. automethod:: biceps.Analysis.plot

.. currentmodule:: biceps

.. autofunction:: biceps.convergence.exponential_fit

.. autofunction:: biceps.convergence.compute_autocorrelation_curves

.. autofunction:: biceps.convergence.g

.. autofunction:: biceps.convergence.compute_autocorrelation_time

.. autofunction:: biceps.convergence.get_blocks

.. autofunction:: biceps.convergence.compute_JSD

.. autoclass:: biceps.Convergence

.. automethod:: biceps.Convergence.plot_traces

.. automethod:: biceps.Convergence.plot_auto_curve

.. automethod:: biceps.Convergence.plot_block_avg

.. automethod:: biceps.Convergence.get_autocorrelation_curves

.. automethod:: biceps.Convergence.process

.. currentmodule:: biceps

.. autofunction:: biceps.toolbox.sort_data

.. autofunction:: biceps.toolbox.get_files

.. autofunction:: biceps.toolbox.list_res

.. autofunction:: biceps.toolbox.list_possible_restraints

.. autofunction:: biceps.toolbox.list_extensions

.. autofunction:: biceps.toolbox.list_possible_extensions

.. autofunction:: biceps.toolbox.npz_to_DataFrame

.. autofunction:: biceps.toolbox.save_object