PyGT : Graph transformation and reduction in Python

Tom Swinburne, CNRS-CINaM, thomas dor swinburne at cnrs.fr

Deepti Kannan, Wales Group, Cambridge, dk588 at cam.ac.uk

v0.3.0 ©️ TD Swinburne and D Kannan 2020

Quick installation

pip install PyGT

If this looks unfamiliar, please see below

Beta version of code used in the following papers : T.D. Swinburne and D.J. Wales, Defining, Calculating, and Converging Observables of a Kinetic Transition Network, J. Chemical Theory and Computation (2020), link

T.D. Swinburne, D. Kannan, D.J. Sharpe and D.J. Wales, Rare Events and First Passage Time Statistics From the Energy Landscape, Submitted to J. Chemical Physics (2020)

More functionality will be added soon.

Documentation and online examples

• Example notebooks can be run online with binder:

• Please see full documentation at readthedocs

Recommended installation with pip

• We recommend using a virtualenv with e.g. conda-

	conda create --name PyGTenv python=3.5
	conda activate PyGTenv

• One can then safely install PyGT using pip with

	pip install PyGT

Run the examples locally

• Install jupyter notebook if required, inside the same virtualenv

	conda install -c conda-forge notebook

• Open the example notebook

  cd examples
  jupyter-notebook basic_functions.ipynb