| maintainers: | andrewtarzia |
|---|---|
| documentation: | https://cgexplore.readthedocs.io/en/latest/ |
cgexplore or cgx is a general toolkit built on
stk for constructing,
optimising and exploring molecular coarse-grained models.
Important
Warning: This package is still very much underdevelopment and many changes are expected.
cgexplore can be installed with pip:
pip install cgexploreWith dependancies openmm and openmmtools:
mamba install openmm openmmtoolsThen, 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
To develop with cgexplore, you can clone the repo and use
just to setup the dev environment:
just devTo reproduce data in DOI:
`10.1039/D3SC03991A <https://doi.org/10.1039/D3SC03991A>`_:
Download the source code from first_paper_example - presubmission
release from Releases.I do not guarantee that running the example code
on the current version will work. However, 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. Additionally, the naming
convention has changed and force field xml files should provide the
appropriate information for mapping angles to models.
- The directory
cgexplorecontains the actual source code for the package. - The directory
first_paper_examplecontains the code for 10.1039/D3SC03991A. *generate_XX.pygenerates cage structures for different topology sets *env_set.pysets a specific environment for file outputs *plot_XX.pyproduces images and figures, and performs analysis
Important
Warning: If you have a CUDA-capable GPU and attempt to use CUDA in the
first example, you may get NaN errors due to the torsion restriction for
angles at 180 degrees, which cause problematic forces. This will be handled
in future versions of the code. And logically, I would suggest removing the
torsion restriction for those angles. The platform can be handled through
this argument in build_building_blocks and build_populations, which I
currently set to None, meaning OpenMM will decide for itself.
If you use cgexplore please cite
https://github.com/andrewtarzia/CGExplore
and
https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc03991a
- Using stk for constructing larger numbers of coarse-grained models: Systematic exploration of accessible topologies of cage molecules via minimalistic models.
Funded by the European Union - Next Generation EU, Mission 4 Component 1 CUP E13C22002930006 and the ERC under projects DYNAPOL.