Description

Implemented the Protein docking workflow using the framework.
Note: some settings such as center coordinates and search space have
not been added as input arguments and the implementation is not currently
adaptable to other data, but that just requires a small change.

Fixes

• Fixes New workflow: Protein Docking #17

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactoring (internal implementation changes)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update (no changes to the code)
• CI change (changes to CI workflows, packages, templates, etc.)
• Version changes (changes to the package or dependency versions)

Testing

Ran the following command on a Chameleon instance:

python -m webs.run docking \
    --executor process-pool \
    --max-processes 40 \
    --smi-file-name-ligand ${PWD}/dataset_orz_original_1k.csv \
    --receptor ${PWD}/1iep_receptor.pdbqt \
    --tcl-path ${PWD}/set_element.tcl

Pull Request Checklist

Please confirm the PR meets the following requirements.

• Relevant tags are added (breaking, bug, dependencies, documentation, enhancement, refactor).
• Code changes pass pre-commit (e.g., ruff, mypy, etc.).
• Tests have been added to show the fix is effective or that the new feature works.
• New and existing unit tests pass locally with the changes.
• Docs have been updated and reviewed if relevant.