First Paper ExampleΒΆ

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.

My first usage of cgexplore was on the systematic modelling of cage molecules is described in this paper: 10.1039/D3SC03991A. The code to reproduce this is available in the directory first_paper_example.

However, as cgexplore is updated, some deviations may occur. 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 forcefield .xml files should provide the appropriate information for mapping angles to models.

Note

The main change is the use of atomlite databasing ( docs)!

I recommend installing cgexplore with the following instructions and then using the example directory in a separate repository or code base of your own.

Download the source code from first_paper_example - presubmission release from Releases instead of the main repository. Then follow the instructions on the main page.

The workflow:

  • 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

To visualise the dataset, you can use my repository cgm.