cgexplore 2024.10.10.0

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CGExplore

A general toolkit for working with coarse-grained models.

The library is built off of stk, which comes with the pip install

Installation

CGExplore is a library but contains an example library usage in the first_paper_example directory. I recommend installing the library with the following instructions and then using the example directory in a separate repository or code base of your own.

The code can be installed following these steps:

1. Create a conda or mamba environment:

mamba create -n NAME python=3.11

2. Activate the environment:

conda activate NAME

3. Install CGExplore with pip:

pip install cgexplore

5. Install OpenMM:

mamba install openmm

or

conda install -c conda-forge openmm

6. Install openmmtools:

mamba install openmmtools

or

conda config --add channels omnia --add channels conda-forge
conda install openmmtools

7. 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, replace step 3 above with these steps:

3. clone CGExplore from here

4. From CGExplore directory use just to install a dev environment with:

just dev

Usage

To reproduce data in DOI: 10.1039/D3SC03991A: Download the source code from first_paper_example - presubmission release from Releases instead of the repo in step 1. 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 cgexplore contains the actual source code for the package. Warning: This package is still very much underdevelopment and many changes are expected.
• The directory first_paper_example contains the code to generate the cages and data for DOI: 10.1039/D3SC03991A. This series of examples uses the classes and tools in CGExplore. I would no longer recommend using it as a perfect example as many changes, including using databasing have been introduced without optimising these scripts. This testing repository is a good example.
  • generate_XX.py generates cage structures for different topology sets
  • env_set.py sets a specific environment for file outputs
  • plot_XX.py produces images and figures, and performs analysis

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.

How To Cite

If you use CGExplore please cite:

https://github.com/andrewtarzia/CGExplore

and

https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc03991a

Acknowledgements

This work was completed during my time as a postdoc, and then research fellow in the Pavan group at PoliTO (https://www.gmpavanlab.com/).