molprint

Molecular fingerprint computation and similarity search in Rust — fast enough for large-scale screening, accurate enough to match RDKit bit-for-bit.

• MACCS-166 structural keys (100% RDKit-accurate on ChEMBL 10k)
• Morgan/ECFP fingerprints (configurable radius, 512–4096 bit)
• Tanimoto, Dice, Cosine similarity via POPCNT
• Parallel threshold and top-k screening via Rayon
• FPS, SDF, SMILES file I/O (chemfp-compatible)

→ Documentation

Install

From a release binary — download from Releases, unpack, and place molprint on your PATH.

macOS note: binaries are ad-hoc signed but not notarized. After downloading, clear the quarantine flag once:

xattr -dr com.apple.quarantine molprint

From source:

cargo install --git https://github.com/mariusrueve/molprint molprint-cli

CLI

# Compute fingerprints
molprint fp --input molecules.smi --output molecules.fps
molprint fp --input molecules.smi --fp-type maccs --output maccs.fps
molprint fp --input molecules.sdf --radius 3 --nbits 4096 --output ecfp6.fps

# Similarity search
molprint search --query "c1ccccc1" --db molecules.fps --threshold 0.4
molprint search --query "c1ccccc1" --db molecules.fps --top-k 20

Output: tab-separated id\tsimilarity, sorted by descending score.

Library

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

Benchmarks

Measured on Apple M-series, Rust 1.94, --release. Run cargo bench to reproduce.

Tanimoto (2048-bit)	36 ns
Morgan ECFP4	~700k mol/s
MACCS-166	~535k mol/s
Screening 100k compounds	826 µs / query

Workspace

Crate	Role
molprint-core	SMILES parser, molecular graph, ring perception, SMARTS
molprint-fp	Morgan and MACCS fingerprint algorithms
molprint-search	Similarity metrics and parallel screening
molprint-io	FPS, SDF, SMILES file I/O
molprint-cli	CLI tool

License

MIT