https://github.com/adicksonlab/csnanalysis
Tools for creating, analyzing and visualizing Conformation Space Networks
https://github.com/adicksonlab/csnanalysis
Last synced: 29 days ago
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Tools for creating, analyzing and visualizing Conformation Space Networks
- Host: GitHub
- URL: https://github.com/adicksonlab/csnanalysis
- Owner: ADicksonLab
- License: mit
- Created: 2018-03-05T14:55:15.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2022-08-31T20:29:59.000Z (over 3 years ago)
- Last Synced: 2025-09-27T14:13:17.624Z (5 months ago)
- Language: Python
- Size: 695 KB
- Stars: 16
- Watchers: 2
- Forks: 3
- Open Issues: 2
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Metadata Files:
- Readme: README.org
- License: LICENSE.txt
Awesome Lists containing this project
README
* CSNAnalysis: Tools for creating, analyzing and visualizing Conformation Space Networks.
CSNAnalysis is a set of tools for network-based analysis of molecular dynamics trajectories.
To use, initialize a `CSN` object using a matrix of transition counts.
The "killer app" of CSNAnalysis is an easy interface between enhanced sampling algorithms
(e.g. WExplore), molecular clustering programs (e.g. MSMBuilder), graph analysis packages (e.g. networkX)
and graph visualization programs (e.g. Gephi).
CSNAnalysis is currently in beta.
* Installation
To install CSNAnalysis, you can get the latest:
#+begin_src bash
pip install git+https://github.com/ADicksonLab/CSNAnalysis
#+end_src
Or one of the releases:
#+begin_src bash
pip install git+https://github.com/ADicksonLab/CSNAnalysis@v0.3
#+end_src
* Dependencies
- numpy
- scipy
- networkx
* Features
CSNAnalysis has the following capabilities:
- constructing transition probability matrices
- trimming CSNs using a variety of criteria
- computing committor probabilities with an arbitrary number of basins
- export gexf files with custom node colorings
* Tutorial
See the Jupyter Notebook in examples/examples.ipynb
* Misc
** Versioning
See [[http://semver.org/]] for version number meanings.
Version 1.0.0 will be released whenever the abstract layer API is stable. Subsequent 1.X.y releases will be made as applied and porcelain layer features are added.