MD-States is a python package for the analysis and visualization of networks (e.g. chemical reaction networks) from molecular dynamics (MD) trajectories based on the work done by Wang et al. (doi: 10.1021/acs.jctc.5b00830). This package is developed and maintained by members of the Pfaendtner Research Group in the Department of Chemical Engineering at the University of Washington in Seattle.
Documentation coming soon.
- python (>=3.6)
- mdtraj (>=1.9.1)
- rdkit (>=2017.09.3)
- networkx (>=2.1)
- graphviz (>=2.38)
- pygraphviz (>=1.4rc1)
- aggdraw (>=1.3.4.dev0)
$ git clone https://github.com/ldgibson/mdstates.git
$ cd mdstates
$ conda env create # Make sure the 'environment.yml' is present.
$ source activate mdstates
$ python setup.py install