Jake Anderson
Jake Anderson
This adds a script `paprika_colab_init.ipynb` that can be called from a colab notebook to initialize a tutorial. I modeled it after `openff-evaluator`'s colab tutorials. I didn't change any of the...
As far as I know, pAPRika doesn't provide user-friendly progress bars or time estimates. Would these be possible and/or worth looking into? Maybe the time per window can be recorded...
Random, small fixes of typos and grammar as well as [linkrot](https://en.wikipedia.org/wiki/Link_rot) for the first five pages: Philosophy, Licensing, Structure, Version Control, and Python Conventions.
Hi @diogomart, I'm trying to optimize Vina parameters to get better agreement with experiment for docked binding energies of small molecules to cyclodextrins. To do this, I'd like to be...
## Description This change fixes an error where, for certain host PDBs, pAPRika can lose CONECT bond information during the `release_apply_parameters` windows of APR calculations. The error is given here...
This is less of an issue and more of a question. In running an estimation with two schemas, `SolvationFreeEnergy` and `HostGuestBindingAffinity` here, I'm aware that `HostGuestBindingAffinity` is able to make...
To make paprika_testing work with pydantic version 2.xx, the `root_validator` decorator needs to specify skip_on_failure=True. ## Todos Notable points that this PR has either accomplished or will accomplish. - [X]...
This PR aims to get the lint, ci, and codeql workflows working properly. To do so, it was necessary to introduce logic into `devtools/conda-envs/test_env.yaml` that says if python 3.9 is...
There's a Github Action for Codacy, which is a code analysis tool that identifies security issues, formatting issues, and lack of best practices. It might be useful to identify areas...