Merge pull request #1 from deGrootLab/development

v0.1.0

Author: tomcklam

.gitignore

@@ -1,6 +1,7 @@
 #
 *.npz
 *.lock
+test/
 
 ## Byte-compiled / optimized / DLL files
 __pycache__/
@@ -141,3 +142,5 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# VS Code
+.vscode/

CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+## [0.1.0] - 2023-05-22
+
+### 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
+
+[0.1.0]: https://github.com/deGrootLab/KPerm/compare/v0.0.1...v0.1.0
+[0.0.1]: https://github.com/deGrootLab/KPerm/releases/tag/v0.0.1

README.md

@@ -1,4 +1,4 @@
-# KPerm - Permeation Cycles in Potassium Channels
+# KPerm - Toolkit for Analysis of Permeation Cycles in Potassium Channels
 This package allows you to identify permeation cycles in potassium channels from molecular dynamics (MD) simulation trajectories.
 
 ## Conda

kperm/__init__.py

@@ -1,3 +1 @@
-from .functions import *
-from .permeation import *
-from .markov import *
+from kperm.channel import Channel, detect_sf, detectSF