perses.analysis.Analysis

class perses.analysis.Analysis(storage_filename)

Analysis tools for perses automated design.

Methods

extract_logP_values(environment, …[, …])	Extract the requested logP_accept component from the ExpandedEnsembleSampler in the requested environment
extract_state_trajectory(environment)	Extract the trajectory in chemical state space
get_environments()	Return a list of environments in storage file.
get_free_energies(environment)	Estimate the free energies between all pairs with bidirectional transitions of chemical states in the given environment
plot_chemical_trajectory(environment, filename)	Plot the trajectory through chemical space.
plot_exen_logp_components(environment[, …])	Generate histograms of each component of Expanded Ensemble log acceptance probability
plot_ncmc_work_distributions(environment, …)	Plot the forward and reverse work distributions for NCMC switching in the given environment
plot_ncmc_work_old(filename)	Generate plots of NCMC work.
plot_sams_weights(environment)	Plot the trajectory of SAMS weights :param environment: :return:
plot_work_trajectories(environment, filename)	Plot the NCMC work trajectories for the given environment and each attempted transition
write_trajectory(environmnent, pdb_filename)	Write the trajectory of sampled configurations and chemical states.

__init__(storage_filename)

Open a storage file for analysis.

Methods

__init__(storage_filename)	Open a storage file for analysis.
extract_logP_values(environment, …[, …])	Extract the requested logP_accept component from the ExpandedEnsembleSampler in the requested environment
extract_state_trajectory(environment)	Extract the trajectory in chemical state space
get_environments()	Return a list of environments in storage file.
get_free_energies(environment)	Estimate the free energies between all pairs with bidirectional transitions of chemical states in the given environment
plot_chemical_trajectory(environment, filename)	Plot the trajectory through chemical space.
plot_exen_logp_components(environment[, …])	Generate histograms of each component of Expanded Ensemble log acceptance probability
plot_ncmc_work_distributions(environment, …)	Plot the forward and reverse work distributions for NCMC switching in the given environment
plot_ncmc_work_old(filename)	Generate plots of NCMC work.
plot_sams_weights(environment)	Plot the trajectory of SAMS weights :param environment: :return:
plot_work_trajectories(environment, filename)	Plot the NCMC work trajectories for the given environment and each attempted transition
write_trajectory(environmnent, pdb_filename)	Write the trajectory of sampled configurations and chemical states.

extract_logP_values(environment, logP_accept_component, subtract_sams=False)

Extract the requested logP_accept component from the ExpandedEnsembleSampler in the requested environment

Parameters:

environment : str

The name of the environment

logP_accept_component : str

The name of the component of the acceptance probability that we want

subtract_sams : bool, optional, default False

Whether to subtract the SAMS weights corresponding to the same iteration. Useful for logP_accept.

Returns:

logP_values : dict of (str, str)

A dictionary for each state transition, with a list of the requested logP_accept component

extract_state_trajectory(environment)

Extract the trajectory in chemical state space

Parameters:

environment : str

The environment for which the chemical state is desired

chemical_state_trajectory : list of str

The trajectory in chemical space for the given environment

Returns:

chemical_state_traj : list of str

List of chemical states that were visited

get_environments()

Return a list of environments in storage file.

Returns:

environments : list of str

List of environment names in storage (e.g. []’explicit-complex’, ‘explicit-ligand’])

get_free_energies(environment)

Estimate the free energies between all pairs with bidirectional transitions of chemical states in the given environment

Parameters:

environment : str

The name of the environment for which free energies are desired

Returns:

free_energies : dict of (str, str): [float, float]

Dictionary of pairwaise free energies and their uncertainty, computed with bootstrapping

plot_chemical_trajectory(environment, filename)

Plot the trajectory through chemical space.

Parameters:

environment : str

the name of the environment for which the chemical space trajectory is desired

plot_exen_logp_components(environment, filename_prefix=None, logP_range=20, nbins=20)

Generate histograms of each component of Expanded Ensemble log acceptance probability

plot_ncmc_work_distributions(environment, output_filename)

Plot the forward and reverse work distributions for NCMC switching in the given environment

Parameters:

environment : str

The name of the environment for which NCMC work should be plotted

output_filename : str

The name of the PDF file to output

plot_ncmc_work_old(filename)

Generate plots of NCMC work.

Parameters:

filename : str

File to write PDF of NCMC work plots to.

plot_sams_weights(environment)

Plot the trajectory of SAMS weights :param environment: :return:

plot_work_trajectories(environment, filename)

Plot the NCMC work trajectories for the given environment and each attempted transition

Parameters:

environment : str

Name of environment

filename : str

Name of output file

write_trajectory(environmnent, pdb_filename)

Write the trajectory of sampled configurations and chemical states.

Returns:

environment : str

Environment name to write trajectory for

pdbfile : str

Name of PDB file to generate.