Introduction¶

GitHub: https://www.github.com/andrewtarzia/CGExplore

cgexplore or cgx is a general toolkit built on stk for constructing, optimising and exploring molecular coarse-grained models.

Tip

⭐ Star us on GitHub! ⭐

Important

Warning: This package is still very much underdevelopment and many changes are expected.

In particular, if you are trying to reproduce exactly DOI: 10.26434/chemrxiv-2025-f034c, then you should install an old version of the code (cgexplore==2025.2.5.1) alongside the topology_scrambler code and use these docs. Note, however, that the recipes actually reproduce that work with the updated interface.

Installation¶

cgexplore can be installed with pip:

pip install cgexplore

Then, update directory structure in env_set.py if using example code.

The library implements some analysis that uses Shape 2.1. Follow the instructions to download and installed at Shape

Developer Setup¶

To develop with cgexplore, you can clone the repo and use just and uv to setup the dev environment:

just setup

Examples¶

We are moving toward implementing a recipe list, which can be found in the recipe page.

The main series of examples are in First Paper Example. In that page you will find all the information necessary to reproduce the work in 10.1039/D3SC03991A

With each pull request a test is run as a GitHub Action connected to this repository. This ensures that the results obtained for a subset of the original data set do not change with changes to this library.

Note

cg_model_test is a good example of usage too!

How To Cite¶

If you use cgexplore, please cite this paper

Predicting stable cage structures by enumerating stoichiometry and topology

and reference this URL

https://github.com/andrewtarzia/CGExplore

If you use our minimial model, please cite this paper

Systematic exploration of accessible topologies of cage molecules via minimalistic models

Publications using CGExplore¶

Using stk for constructing larger numbers of coarse-grained models: Systematic exploration of accessible topologies of cage molecules via minimalistic models.
Starship structure prediction: (Adjacent backbone interactions control self-sorting of chiral heteroleptic Pd3A2B4 isosceles triangles and Pd4A4C4 pseudo-tetrahedra)
Structure prediction: (Predicting stable cage structures…)

Acknowledgements¶

Funded by the European Union - Next Generation EU, Mission 4 Component 1 CUP E13C22002930006.

This work is now developed as part of the Tarzia Research Group at the University of Birmingham.