molfp

Interpretable molecular fingerprints with SHAP-driven chemical explanations.

A native Python/RDKit library that computes 35 molecular fingerprint types (18 2D + 9 3D + 8 graph-based) and provides built-in tools for interpretation, visualization, collision detection, activity cliff analysis, bioactivity profiling, and SHAP-based feature explanation.

Install

pip install molfp

Requires Python 3.9+. RDKit is installed automatically. See Getting Started for optional dependencies and troubleshooting.

Quick Example

import molfp

# Compute fingerprints
fp = molfp.maccs("CC(=O)Oc1ccccc1C(=O)O")
fps = molfp.ecfp4(["CCO", "c1ccccc1"], collision_free=True)

# Explain which atoms set which bits
molfp.explain("CCO", "ecfp4")

# SHAP interpretation with chemical meaning
result = molfp.interpret(smiles, activities, fp_type="ecfp4", collision_aware=True)

# Scaffold-aware train/test split
result = molfp.scaffold_split(smiles, test_size=0.2)

Features

• 35 fingerprint types — 18 2D, 9 3D, 8 graph-based
• Bit-level explainability — atom attribution for every ON bit
• Chemical annotation — human-readable names for fingerprint bits
• SHAP interpretation — collision-aware feature importance with chemical meaning
• Collision handling — detect, remove, or avoid hash collisions entirely
• Scaffold analysis — Murcko scaffolds with ~130 named ring systems, scaffold-aware splitting
• Activity cliffs — detect structurally similar molecules with different activities
• Bioactivity profiling — enriched/depleted bit analysis
• Isomer discrimination — test whether fingerprints distinguish structural isomers
• Graph representations — 4 graph types with PyG/DGL converters
• sklearn compatible — 27 transformers + GraphTransformer

For molecule visualization (2D drawing, 3D viewing, attribution maps), see molviewer: pip install molviewer

35 Fingerprint Types

2D Fingerprints (18 types)

Type	Bits	Function
MACCS Keys	166	maccs()
ECFP4 (Morgan)	1024	ecfp4()
PubChem/CACTVS	881	pubchem()
Substructure FP	307	substructure()
Substructure Count	307	substructure_count()
Klekota-Roth	4860	klekota_roth()
Klekota-Roth Count	4860	klekota_roth_count()
E-State	79	estate()
AtomPairs2D	780	atompairs2d()
AtomPairs2D Count	780	atompairs2d_count()
RDK	1024	rdk()
RDK Extended	1024	rdk_ext()
RDK GraphOnly	1024	rdk_graphonly()
FCFP4 (Feature Morgan)	1024	fcfp4()
Lingo	1024	lingo()
Shortest Path	1024	shortest_path()
Hybridization	1024	hybridization()
Signature	1024	signature()

3D Fingerprints (9 types)

Type	Dims	Function
AtomPairs3D	780	atompairs3d()
AtomPairs3D Count	780	atompairs3d_count()
USR	12	usr()
USRCAT	60	usrcat()
Autocorr3D	80	autocorr3d()
RDF	210	rdf()
MORSE	224	morse()
WHIM	114	whim()
GETAWAY	273	getaway()

Graph Fingerprints (8 types)

Type	Function
Standard	mol_graph(type="standard")
Standard Enriched	mol_graph(type="standard", enriched=True)
Distance	mol_graph(type="distance")
Distance Enriched	mol_graph(type="distance", enriched=True)
Line	mol_graph(type="line")
Line Enriched	mol_graph(type="line", enriched=True)
Fragment	mol_graph(type="fragment")
Fragment Enriched	mol_graph(type="fragment", enriched=True)