implicit_solvent_ddm.adaptive_restraints

A collection of functions that performs simple iterative proceess to improve space phase overlap between adjecent states.

Functions

adaptive_lambda_windows(job, system_runner, ...)	Simple iterative process to improve poor space phase overlap between restraints and/or ligand charge windows.
bisect_between(start, end)	Perform a bisection search between two numbers.
compute_mbar(simulation_data, temperature, ...)	Execute MBAR analysis.
good_enough(space_phase_overlaps[, min])	Check that all averge degree of overlap are about the minimum criteria.
group_overlap_neighbors(matrix)	Retireve both the foward and reverse degree of overlap between adjacent states.
improve_charge_scaling(job, runner, ...)	Improve poor space overlap of two adjacent states via bisection.
improve_gb_dielectric(job, runner, ...)	_summary_
improve_restraints_overlap(job, runner, ...)	Improve poor space overlap of two adjacent states via bisection.
initilized_jobs(job)	Place holder to schedule jobs for MD and post-processing
overlap_average(overlap_matrix, start[, end])	Compute the average of the degree of space phase overlap between a slice adjacent states.
run_compute_mbar(job, system_runner, config, ...)	Run the compute_mbar function.
run_exponential_averaging(job, ...)	Execute exponential averaging