chematic-fp 0.2.11

ECFP4/6, MACCS 166-bit and topological path fingerprints with Tanimoto/Dice similarity for chematic
Documentation

chematic-fp

Fast molecular fingerprints for similarity search and clustering. ECFP4/6, RDKit Morgan, MACCS 166-bit, and topological path fingerprints with Tanimoto/Dice similarity. Pure Rust, WASM-compatible.

Features

  • ECFP fingerprints: ECFP4 (default), ECFP6, and configurable radius
  • MACCS 166-bit: public pharmacophore-based bit vector
  • Topological path: branching-aware path enumeration
  • RDKit-compatible Morgan: identical to RDKit's default ECFP (FNV-1a 64-bit hash)
  • Similarity metrics: Tanimoto, Dice, complement similarity
  • Chirality-aware: optional stereo center consideration (R/S, E/Z)
  • WASM-compatible: zero C/C++ dependencies

Quick Start

use chematic_smiles::parse;
use chematic_fp::ecfp4;
use chematic_fp::similarity::tanimoto;

let mol1 = parse("c1ccccc1O").expect("phenol");
let mol2 = parse("c1ccccc1N").expect("aniline");

let fp1 = ecfp4(&mol1);
let fp2 = ecfp4(&mol2);

let similarity = tanimoto(&fp1, &fp2);
println!("Tanimoto similarity: {:.2}", similarity);

API Overview

Fingerprint Generators

  • ecfp4(mol: &Molecule) -> Vec<u64> — 4-bond radius ECFP (most common)
  • ecfp(mol: &Molecule, config: &EcfpConfig) -> Vec<u64> — configurable ECFP
  • maccs_166(mol: &Molecule) -> BitVec — MACCS 166 bit pharmacophore vector
  • topo_path(mol: &Molecule) -> Vec<u64> — topological path fingerprint

Similarity

  • tanimoto(fp1: &[u64], fp2: &[u64]) -> f64 — Jaccard/Tanimoto coefficient
  • dice(fp1: &[u64], fp2: &[u64]) -> f64 — Dice similarity

Configuration

use chematic_fp::EcfpConfig;

let config = EcfpConfig {
    radius: 3,           // 3-bond radius ECFP6
    use_chirality: true, // include R/S, E/Z
    use_bond_types: true,
    min_features: 1,
};
let fp = chematic_fp::ecfp(mol, &config);

Dependencies

References

See Also