README.md

Distribution package for BaNDyT: Bayesian Network Analysis of Dynamic Trajectories

BaNDyT (Bayesian Network analisis of molecular Dynamic simulation Trajectories): software package that implements the Bayesian Network Modeling specifically attuned to the MD simulation trajectories data.

This package was prepared and released along with the publication: BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories (Journal of Chemical Information and Modeling)

Tutorial on how to use BaNDyT can be found here: BaNDyT tutorial

Installing Requirements

Following Python packages are required: numpy,pandas,seaborn,matplotlib,pydot,igraph, networkx. We recommend using pip to install them on your local machine:

pip install pandas
pip install seaborn
pip install matplotlib
pip install pydot
pip install igraph
pip install networkx

Optional (recommended): for built-in graph visualization in PDF format, graphviz is required.

Installation

No particular installation procedure is necessary. However to enable faster compute routines compilation of cpp source in the folder containing this project is necessary. The folder contains Makefile that will tell the compiler what to do as long as 'make' utility and g++ compiler are present.

In the BaNDyT folder execute following commands:

touch ofext.cpp
make

This procedure should update C++ extension to the current architechture and make optimized routines available.