molprint

molprint is a high-performance molecular fingerprint computation and similarity search library written in Rust.

The goal is to be fast enough for large-scale virtual screening — targeting 5–10× faster than RDKit for bulk workflows — while remaining accurate enough to match RDKit bit-for-bit on standard benchmarks.

What it does

• Parses SMILES strings into molecular graphs
• Computes MACCS-166 structural key fingerprints (100% RDKit-accurate on ChEMBL 10k)
• Computes Morgan/ECFP circular fingerprints at configurable radius and bit width (512–4096)
• Calculates Tanimoto, Dice, and Cosine similarity using POPCNT on u64 word arrays
• Runs parallel threshold and top-k screening via Rayon
• Reads and writes FPS, SDF, and SMILES file formats (FPS is chemfp-compatible)

Benchmarks

Measured on Apple M-series, Rust 1.94, --release.

Quick example

#![allow(unused)]
fn main() {
use molprint_core::smiles::parse_smiles;
use molprint_fp::{morgan::Morgan, maccs::Maccs166, traits::Fingerprinter};
use molprint_search::metrics::tanimoto;

let mol_a = parse_smiles("c1ccccc1").unwrap();   // benzene
let mol_b = parse_smiles("c1ccncc1").unwrap();   // pyridine

let fp = Morgan::new(2, 2048);
let sim = tanimoto(&fp.fingerprint(&mol_a), &fp.fingerprint(&mol_b));
println!("{:.3}", sim); // 0.600
}

Workspace layout

Crates form a strict dependency chain: molprint-core → molprint-fp → molprint-search + molprint-io → molprint-cli. No cycles, no dev-dependency shortcuts across this chain.

License

MIT