Frag

Basic RDKit based Python tools for analysis of protein-ligand interactions.

This was originally the fragalysis GitHub repository, which is now being used for another purpose. All new releases of this package will come from here, with the new name xchem-frag.

Currently contains: -

1. Clustering - based on WONKA method - but separated from that code-base. Cluster waters, residues, ligands and pharmacophores. (Under development)
2. Astex Fragment Network - implementation on the basis of their recent paper
3. Conformer generation code - based on known X-ray structures
4. Support for the neo4j 4.4.2 graph database

Pre-commit

The project uses pre-commit to enforce linting of files prior to committing them to the upstream repository.

To get started review the pre-commit utility and then set-up your local clone by following the Installation and Quick Start sections of the pre-commit documentation.

Ideally from a Python environment...

python -m venv venv
source venv/bin/activate

pip install --upgrade pip
pip install -r build-requirements.txt
pre-commit install -t commit-msg -t pre-commit

Now the project's rules will run on every commit and you can check the state of the repository as it stands with...

pre-commit run --all-files

Publishing (to PyPI)

We rely on out release GitHub workflow to publish to PyPI, something that is done automatically when the repository main branch is tagged.

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