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)

The version of the package is hard-coded in setup.py. Change that value to something appropriate and then, armed with PyPi account credentials, ideally from within a Python 3 virtual environment, run the following from the project root: -

export TWINE_USERNAME=PyPiUsername
export TWINE_PASSWORD=PyPiPassword
export FRAGALYSIS_VERSION=1.0.1
pip install -r package-requirements.txt
rm dist/*
python setup.py bdist_wheel
twine upload dist/*