kperm package¶
Submodules¶
kperm.channel module¶
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
Returns¶
- 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.
- detect_sf()¶
- find_cycle(cycle_state, n_jump_per_cycle=5)¶
- load(results_loc=None, filename='kperm')¶
- 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)¶
- set_coord(coord)¶
- set_trajs(trajs)¶
- 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
Parameters¶
- 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.
Returns¶
- 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)¶
kperm.permeation module¶
methods for computing permeation cycles
The module contains the methods used by class Channel for computing permeation cycles.
kperm.examples module¶
- kperm.examples.download_charge_scaling()¶
kperm.utils module¶
helpers methods