kperm package¶

Submodules¶

Channel class and core workflow of KPERM

The module contains the class Channel and core functions for analysizing ion permeation events in MD simulations using the KPERM framework.

class kperm.channel.Channel(coord=None, trajs=None)¶

Bases: object

TBA.

compute_stats()¶

Compute statistics of trajectories regarding ion permeation

stats: Pandas dataframe: store statistics of trajectories, such as total time, lag time, current and occupation state populations.
states: Pandas dataframe: point estimate and bootstrap confidence interval for occupation states.

mfpt(paths=None, n_jump_per_cycle=5, backward=False, batch=10000, n_resamples=10000)¶

plot_cycle(state_threshold=0.01, label_threshold=0.15, offset=0.7, scale=0.4, figsize=(6, 6))¶

plot_netflux(weight_threshold=0.1, save=None, data=False, returnGraphData=False)¶

run(perm_count='cross', output='kperm', perm_details=False, sf_diag=False, bs_radius=4.0, check_flip=True, check_water=True)¶

kperm.channel.detect_sf(coord, quiet=False, o_cutoff=5, og1_cutoff=7.0, all_res=False)¶

read coordinate file and return zero-indexed atom indices defining SF

coorstr: The path to the coordinate file containing the ion channel.
quietbool, optional: A flag used to print detailed information about SF (default is False).
o_cutoff: float: Distance cutoff for determining if backbone oxygen atoms are close enough to meet the geometric requirement for being a part of SF. Unit: Angstrom
og1_cutoff: float: Same as o_cutoff, but it is for OG1 atom (like threonine’s OG1). Unit: Angstrom
all_res: boolean: If false, only amino acids GLY VAL TYR THR PHE ILE are considered when determining SF.

sf_layer: dict: consisting of two dictionaries containing atom idx (zero-based) and residue id of SF’s oxygen (backbone and hydroxyl) and CA atoms, respectively.

kperm.channel.run(coord, traj, output='kperm', perm_count='cross', perm_details=False, sf_idx=None, sf_all_res=False, sf_diag=False, check_flip=False, check_water=True, bs_radius=4.0)¶

methods for computing permeation cycles

The module contains the methods used by class Channel for computing permeation cycles.