lignova
Generate high-quality docked protein–ligand complexes at scale.
Documentation
LIGNOVA is an open-source, automated pipeline that pairs bioactive compounds from PubChem with high-resolution protein structures from the PDB to generate large-scale docked protein–ligand complexes using GNINA.
Installation¶
Clone the repository:
Install lignova using pip after moving into the directory.
This will install all dependencies and lignova into your current Python environment.
GNINA is called as a separate executable rather than installed as a Python package, so a pip install alone will not provide it. See the documentation for how to build it, or use the pixi workflow below, which handles it through pixi run setup-gnina.
Development¶
We use pixi to manage Python environments and simplify the developer workflow.
Once you have pixi installed, move into lignova directory (e.g., cd lignova) and install the environment using the command
Now you can activate the new virtual environment using
Our pixi.lock uses lock-file format v7, which older versions of pixi cannot read. If pixi install fails with an error that does not seem to point at the cause, run pixi self-update and try again.
Contributing¶
We are not accepting outside contributions while the project is under active development at the University of Pittsburgh.
License¶
Code contained in this project is released under the Apache-2.0 License as specified in LICENSE.md.
This license grants you the freedom to use, modify, and distribute it as long as you include the original copyright notice contained in LICENSE.md and the following disclaimer.
LIGNOVA does not bundle, vendor, or redistribute its dependencies; pixi resolves them on your machine from conda-forge and PyPI. NOTICE and THIRD_PARTY_LICENSES.md record the license of every package in the environment, and docs/licensing-preamble.md explains how those licenses relate to this one.