v0.2.0

Changelog

0.2.0 - 2023-08-03

Added

• Command-line interface following GROMACS style
• Two methods, cross and jump, for computing current
• set_coord() and set_trajs() for specifying coordinate and trajectory files
• Channel.detect_sf() for showing the identified constituent atoms for SF
• Users now can adjust the radius of the binding site using keyword bs_radius in Channel.run(). Default: 4.0 (Angstrom)

Changed

• FindCycles renamed to find_cycle
• permeationMFPT renamed to mfpt
• plotCycles renamed to plot_cycle
• plotNetFlux renamed to plotNetFlux
• computeStats renamed to compute_stats
• Charge-scaling tutorial updated

v0.1.1

[0.1.1] - 2023-05-23

Changed

• Removed 1 Angstrom buffer for S0 to improve accuracy of S0 occupancy determination.

v0.1.0

Added

• Calculation of net fluxes for permeation cycles
• Method of calculating current via counting permeation events across S2-S3 interface.
• Option of writing indices of objects in SF or involved in permeation to files.
• Changelog.

Changed

• Charge-scaled tutorial.
• Part of the codes formatted to conform to the PEP 8 style.

Removed

• Obsolete methods for determining SF occupancy and ion jumps in SF.

v0.0.1

Initial release of KPERM.