prolif

library2.1.0pypypiunverified

ProLIF (PROtein-Ligand Interaction Fingerprints) is a Python library for generating interaction fingerprints from molecular dynamics trajectories or docking poses. It supports both 2D and 3D fingerprints based on pharmacophore-like interaction types (e.g., hydrophobic, H-bond, pi-stacking). The current version is 2.1.0, requiring Python >=3.10. The project is under active development with releases every few months.

ai-ml

pip install prolif

github ↗homepage ↗

INSTALL

IMPORT

SIG · PROLIF

prolif

ai-mlpythonv2.1.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Fingerprint

✓ from prolif import Fingerprint

✗ from prolif import Fingerprint

Basic usage: load a complex, compute interactions, and export to DataFrame.

import prolif as plf from rdkit import Chem # Load protein and ligand from PDB/SDF files protein = Chem.MolFromPDBFile('protein.pdb') ligand = Chem.SDMolSupplier('ligand.sdf')[0] # Create fingerprinter fp = plf.Fingerprint(interactions=['Hydrophobic', 'HBAcceptor']) # Run on a single frame fp.run(protein, ligand) # Access data as DataFrame df = fp.to_dataframe() print(df.head())

Debug

Known issues

breakingIn v2.0, the import paths changed significantly. Functions like `run` are now in the top-level `prolif` module, not `prolif.plot`. Code written for v1.x will break.

fix

Update imports: from prolif import run; also use prolif.Fingerprint instead of prolif.fingerprint.Fingerprint.

affects: <2.0

breakingThe `to_dataframe()` method now returns a pandas DataFrame with a different column structure compared to v1.x. Old scripts relying on specific column names may need adjustment.

fix

Use the new DataFrame columns; run `print(df.columns)` to inspect.

affects: <2.0

deprecatedThe `plot_2D` function is deprecated in favor of the `plot_network` function.

fix

Replace `from prolif.plot import plot_2D` with `from prolif import plot_network` and adjust arguments.

affects: >=2.0

gotchaProLIF requires a protein structure with explicit hydrogens for accurate interaction detection. Many PDB files lack hydrogens. Use RDKit or other tools to add them before fingerprinting.

fix

Add hydrogens using RDKit: `mol = Chem.AddHs(mol)` for both protein and ligand.

affects: all

gotchaThe .sdf files from docking programs often have different atom ordering or missing bond information. Use RDKit to sanitize the molecule: `Chem.SanitizeMol(mol)` if issues arise.

fix

Pre-process with RDKit to ensure proper valence and bond orders.

affects: all

Upgrade

Version history

2.1.0latest on PyPI · released Jan 20, 2026

Audit

Dependencies

rdkitrequiredCore dependency for molecular representation and substructure matching.

numpyrequiredNumerical array operations.

pandasrequiredData manipulation for interaction fingerprints.

matplotliboptionalPlotting interaction networks.

seabornoptionalEnhanced visualization.

Agent activity

19 hits · last 30 days

node

Resources

githubhttps://github.com/chemosim-lab/ProLIF ↗

homepagehttps://github.com/chemosim-lab/ProLIF ↗