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:

pip install git+https://github.com/ADicksonLab/CSNAnalysis

Or one of the releases:

pip install git+https://github.com/ADicksonLab/[email protected]

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.