prolif-lite 2.1.0

Interaction Fingerprints for protein-ligand docking analysis (MDAnalysis-free version)

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Description

ProLIF (Protein-Ligand Interaction Fingerprints) is a tool designed to generate interaction fingerprints for complexes made of ligands, protein, DNA or RNA molecules extracted from docking simulations and experimental structures.

Note

MDAnalysis Dependency Removed: As of this version, MDAnalysis dependency has been removed to resolve LGPL3 licensing issues. The package now focuses on docking results analysis and no longer supports MD trajectory analysis. This enables use under more permissive licenses.

Supported Features

✅ Currently Supported:

• Protein-ligand interaction analysis from docking results

• PDB protein structure support

• SDF ligand structure support

• MOL2 file support (limited via RDKit)

• All core interaction types (hydrogen bonds, hydrophobic, π-stacking, etc.)

• Interaction fingerprint generation and analysis

• Export to DataFrames and bitvectors

❌ No Longer Supported:

• MD trajectory analysis (XTC, TRR, DCD formats)

• PDBQT file support (requires conversion to PDB/SDF)

• Molecule.from_mda() method

• select_over_trajectory() function

• Advanced water bridge analysis requiring trajectory data

Migration Guide

Old Code:

import MDAnalysis as mda
import prolif

u = mda.Universe("protein.pdb", "trajectory.xtc")
ligand = prolif.Molecule.from_mda(u.select_atoms("resname LIG"))

New Code:

from rdkit import Chem
import prolif

protein = Chem.MolFromPDBFile("protein.pdb", removeHs=False)
protein_mol = prolif.Molecule.from_rdkit(protein)
ligands = prolif.sdf_supplier("ligands.sdf")

Documentation

The installation instructions, documentation and tutorials can be found online on ReadTheDocs.

Issues

If you have found a bug, please open an issue on the GitHub Issues page.

Discussion

If you have questions on how to use ProLIF, or if you want to give feedback or share ideas and new features, please head to the GitHub Discussions page.

Contributing

If you are interested in contributing to the project, please read the Contribution Guidelines.

Citing ProLIF

Please refer to the citation page on the documentation.

License

Unless otherwise noted, all files in this directory and all subdirectories are distributed under the Apache License, Version 2.0

Copyright 2017-2025 Cédric BOUYSSET

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.