luna 0.13.1

LUNA: drug discovery toolkit

LUNA [1] is an object-oriented Python 3 toolkit for drug design that makes it easy to analyze very large data sets of 3D molecular structures and complexes, and that allows identifying, filtering, and visualizing atomic interactions.

LUNA also implements three hashed interaction fingerprints (IFP): Extended Interaction FingerPrint (EIFP), Functional Interaction FingerPrint (FIFP), and Hybrid Interaction FingerPrint (HIFP) – inspired by ECFP [2], FCFP [2], and E3FP [3]. These IFPs encode molecular interactions at different levels of detail, provide several functionalities to trace individual bits back to their original atomic substructures in the context of the binding site, and are RDKit-compatible.

Documentation is hosted by ReadTheDocs, and development occurs on GitHub.

Installation and Usage

The latest stable release (and required dependencies) can be installed as follows:

1. Download LUNA’s environment.yml file.

2. Create the Conda environment using the downloaded file:

   conda env create -f <LUNA-ENV-FILE>

3. After creating the Conda environment, activate it:

   conda activate luna-env

4. Finally, install LUNA from Pip:

   pip install luna

For additional installation options and usage instructions, refer to the documentation.

License

LUNA is available under the MIT License.

References

[1]

Fassio, A. V.; Shub, L.; Ponzoni, L.; McKinley, J.; O’Meara, M. J.; Ferreira, R. S.; Keiser, M. J.; de Melo Minardi, R. C. Prioritizing Virtual Screening with Interpretable Interaction Fingerprints. J. Chem. Inf. Model. 2022.

[2] (1,2)

Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints. J. Chem. Inf. Model. 2010, 50 (5), 742–754.

[3]

Axen, S. D.; Huang, X.-P.; Cáceres, E. L.; Gendelev, L.; Roth, B. L.; Keiser, M. J. A Simple Representation of Three-Dimensional Molecular Structure. J. Med. Chem. 2017, 60 (17), 7393–7409.