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CHANGELOG.md

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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

0.1.1 - 2023-05-23

Changed

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

0.1.0 - 2023-05-19

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.

0.0.1 - 2023-03-30

Added

  • Initial release of KPERM