Fragalysis

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

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)

If the repository has been provided with a PYPI_APIKEY Secret the GitHub pip-release workflow action will automatically publish the package to PyPI when you create a new Release. The package version will be set using the release tag_name.

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