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, collision detection, activity cliff analysis, bioactivity profiling, and SHAP-based feature explanation.

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

Features

35 Fingerprint Types

2D Fingerprints (18 types)

3D Fingerprints (9 types)

3D fingerprints use adaptive conformer optimization with MMFF94, where iteration counts are estimated from molecular complexity via a regression model trained on 1,420 FDA-approved drugs.

Graph Fingerprints (8 types)

Enriched variants add Morgan environment hashes, functional group membership, and neighbor type counts per atom. Base variants use atom-level properties only (type, degree, charge, hybridization, aromaticity, ring).

Versatile Input Handling

Every fingerprint function accepts any of these input types:

molfp.ecfp4("c1ccccc1")                  # single SMILES → list
molfp.ecfp4(["CCO", "c1ccccc1"])          # list → numpy array
molfp.ecfp4(pd.Series(["CCO", "c1c..."]))  # Series → numpy array
molfp.ecfp4(df, column="SMILES")           # DataFrame → numpy array (auto-detects column)

Bit-Level Explainability

Map each ON bit to the atoms/bonds that triggered it — across all 13 2D FP types:

molfp.explain("CC(=O)Oc1ccccc1C(=O)O", "ecfp4")
# {11: [(1, 1)], 33: [(0, 0)], 64: [(6, 1), (7, 1)], ...}
# bit 64 → center atoms 6 and 7 at radius 1

Chemical Annotation

Human-readable names for every fingerprint bit:

molfp.annotate("substructure", 83)
# {'name': 'Carboxylic_acid', 'smarts': '[CX3...](=[OX1])...', 'category': 'functional_group'}

molfp.annotate("pubchem", 9)
# {'description': 'Element count: C >= 2', 'category': 'element_count'}

SHAP Interpretation with Chemical Meaning

One call: fingerprint → model → SHAP → chemical annotation → per-class SAR:

result = molfp.interpret(smiles, activities, fp_type="maccs", metric="pchembl")

# Per-class drivers with present/absent effect:
# ACTIVE:
#   ↑ present  methyl group (-CH3)     SHAP +0.004  (freq 23% vs 19%)
#   ↓ present  oxygen atom             SHAP -0.003  (freq 13% vs 17%)

Additional functions for molecule-level analysis:

# Explain a single molecule's prediction
molfp.interpret_molecule(smiles, interpretation_result)

# Compare two molecules' structural differences by importance
molfp.compare_molecules(smiles_a, smiles_b, interpretation_result)

Hash Collision Detection

Detect when different substructures hash to the same bit:

molfp.detect_collisions("c1ccccc1", "ecfp4", n_bits=256)
# {63: [2360741695, 3976623167]}  → 2 hashes collided at bit 63

molfp.collision_rate(smiles_list, "ecfp4", n_bits=1024)
# {'collision_rate': 0.027, 'collided_bits': 15, ...}

Activity Cliff Detection

Find structurally similar molecules with large activity differences:

cliffs = molfp.activity_cliffs(smiles, activities, "maccs",
                                sim_threshold=0.8, activity_threshold=2.0)

Bioactivity Class Profiling

Classify molecules, analyze intra/inter-class similarity, find enriched bits:

labels = molfp.classify(pchembl_values, metric="pchembl")
result = molfp.class_similarity(smiles, labels, "maccs")
enriched = molfp.enriched_bits(smiles, labels, "maccs")

Structure Standardization

Desalt, neutralize, canonicalize tautomers, deduplicate by InChIKey:

molfp.standardize_smiles("CC(=O)Oc1ccccc1C(=O)[O-].[Na+]")
# → "CC(=O)Oc1ccccc1C(=O)O"  (desalted + neutralized)

result = molfp.preprocess(smiles_list)
# n_input: 1000 → n_after_standardization: 985 → n_after_deduplication: 923

Distance Functions

Vectorized Tanimoto, Dice, Cosine, Sokal-Michener, Russel-Rao:

molfp.tanimoto(fp_a, fp_b)           # single pair → float
molfp.pairwise(X, metric="tanimoto") # (N, N_bits) → (N, N) matrix (vectorized)

scikit-learn Compatible

All 35 FP types as sklearn transformers with Pipeline, GridSearchCV, and FeatureUnion support:

from sklearn.pipeline import make_pipeline
from sklearn.ensemble import RandomForestClassifier

pipe = make_pipeline(
    molfp.ECFPTransformer(n_bits=2048, n_jobs=-1),
    RandomForestClassifier()
)
pipe.fit(smiles_train, y_train)

Sparse Matrix & Parallelism

molfp.klekota_roth(smiles_list, sparse=True, n_jobs=-1)
# → scipy.sparse.csr_matrix, 97% memory savings for KR 4860-bit FPs

Consensus Fingerprints

Build optimal fusion fingerprints from multiple types using mutual information:

molfp.fuse(smiles, activities, ["ecfp4", "maccs", "pubchem"])

Feature Selection

Standalone functions that work with any fingerprint or graph feature output:

# Remove constant/near-constant features (no labels needed)
result = molfp.remove_low_variance(X, threshold=0.01)
X_clean = result["X"]  # filtered matrix

# Select top-k features by mutual information (requires labels)
result = molfp.select_features(X, y, k=500, threshold=0.01)
X_selected = result["X"]       # (n_samples, 500)
result["indices"]               # original column indices
result["scores"]                # mutual information scores

Molecular Graph Representations for Deep Learning

Convert molecules to atom/bond feature matrices for graph neural networks (GCN, GAT, MPNN, etc.). Framework-agnostic core with optional PyTorch Geometric and DGL converters.

# Convert to graph — returns NumPy arrays (no DL framework needed)
g = molfp.mol_graph("c1ccccc1")                      # type="standard" (default)
g = molfp.mol_graph("c1ccccc1", type="distance")     # complete graph with 3D distances
g = molfp.mol_graph("c1ccccc1", type="line")          # bonds as nodes
g = molfp.mol_graph("c1ccccc1", type="fragment")      # functional groups as nodes
g = molfp.mol_graph("c1ccccc1", enriched=True)        # enriched atom features (432 dims)

# g["atom_features"]  → numpy (n_nodes, n_features)
# g["edge_index"]     → numpy (2, n_edges)
# g["edge_features"]  → numpy (n_edges, n_edge_features)

# Batch conversion
graphs = molfp.mol_graph(["CCO", "c1ccccc1", "CC(=O)O"])

# PyTorch Geometric (requires: pip install torch torch_geometric)
data = molfp.to_pyg(g, y=1)                          # single graph → Data
loader = molfp.graphs_to_pyg(graphs, y=labels, batch_size=32)  # → DataLoader

# DGL (requires: pip install dgl torch)
dgl_graph = molfp.to_dgl(g)

# Feature inspection
molfp.atom_feature_names()  # ['atom_type_C', 'atom_type_N', ..., 'is_aromatic', 'in_ring']
molfp.edge_feature_names()  # ['bond_type_single', ..., 'is_conjugated', 'in_ring', ...]

Atom features (20 dims): atom type (one-hot, 10), degree, formal charge, num Hs, hybridization (one-hot, 5), is aromatic, in ring.

Edge features (12 dims): bond type (one-hot, 4), is conjugated, in ring, stereo (one-hot, 6).

Graph Vectors for scikit-learn

# Fixed-length vectors from any graph type
X = molfp.graph_vectors(smiles, type="standard", enriched=True)

# sklearn pipeline
from sklearn.pipeline import make_pipeline
from sklearn.ensemble import RandomForestClassifier
pipe = make_pipeline(molfp.GraphTransformer(enriched=True, type="standard"), RandomForestClassifier())
pipe.fit(smiles_train, y_train)

Collision Handling

Hashed fingerprints (ECFP4, RDK, AtomPairs) fold substructures into fixed-length vectors via modulo, causing hash collisions that corrupt SHAP attributions.

# Detect collisions
molfp.detect_collisions("c1ccccc1", "ecfp4", n_bits=1024)

# Remove colliding bits from feature matrix
result = molfp.remove_collisions(X, smiles, "ecfp4", 1024)

# Collision-free mode (multi-hash Bloom filter approach)
fps = molfp.ecfp4(smiles, collision_free=True)  # works on all 8 hashed FPs

# Collision-aware SHAP interpretation
result = molfp.interpret(smiles, activities, fp_type="ecfp4", collision_aware=True)

Scaffold Analysis

Extract Murcko/generic scaffolds with chemical names from ~130 common ring systems. Scaffold-aware train/test splitting prevents data leakage in QSAR.

molfp.scaffold("CC(=O)Oc1ccccc1C(=O)O")
# {"murcko": "c1ccccc1", "generic": "C1CCCCC1", "name": "Benzene"}

# Scaffold fingerprint — binary membership matrix
result = molfp.scaffold_fingerprint(smiles)

# Scaffold-aware split (no scaffold leakage)
result = molfp.scaffold_split(smiles, test_size=0.2)
train_idx, test_idx = result["train_idx"], result["test_idx"]

License

MIT