chematic

日本語

A pure-Rust cheminformatics library targeting RDKit feature parity, with no C/C++ FFI.

Design Goals

Pure Rust, zero C/C++ FFI No rdkit-sys, no openbabel bindings. Every algorithm is implemented in safe Rust.

WASM-compatible and lightweight Core crates compile to wasm32-unknown-unknown without modification. Binary size is in the hundreds of KB range, versus tens of MB for C++ FFI wrappers.

Domain-specific algorithms Rather than wrapping a generic graph library, chematic implements chemistry-specific algorithms directly: Kekulization, Hückel aromaticity, CIP stereochemistry, SSSR ring perception.

Reproducible and deterministic Fingerprints use FNV-1a hashing with a fixed invariant ordering. Given the same SMILES input, the same bits are always produced. No RNG, no platform-specific behavior.

Current Status

Phases 1–3 and Phase 5 (coordinate generation + file I/O) are complete. Phase 4 (MACCS, topological path, MCS, tautomer normalization) is also done. 332 tests, all passing.

cargo test --workspace   # 332 tests, all passing

Quick Start

Using the umbrella crate

# Cargo.toml
[dependencies]
chematic = { git = "https://github.com/kent-tokyo/chematic", features = ["smiles", "fp"] }

// Using the umbrella crate
use chematic::smiles::{parse, canonical_smiles};
use chematic::fp::ecfp4;
// chematic = { version = "0.1.0", features = ["smiles", "fp"] }

Using individual crates

# Cargo.toml
[dependencies]
chematic-smiles     = { git = "https://github.com/kent-tokyo/chematic" }
chematic-perception = { git = "https://github.com/kent-tokyo/chematic" }
chematic-fp         = { git = "https://github.com/kent-tokyo/chematic" }

use chematic_smiles::{parse, canonical_smiles};
use chematic_perception::{find_sssr, assign_aromaticity};
use chematic_fp::{ecfp4, tanimoto_ecfp4};

fn main() {
    let benzene = parse("c1ccccc1").unwrap();
    let toluene = parse("Cc1ccccc1").unwrap();

    // Ring and aromaticity perception
    let rings = find_sssr(&benzene);
    println!("rings: {}", rings.ring_count()); // 1
    let arom = assign_aromaticity(&benzene);
    println!("aromatic atoms: {}", arom.aromatic_atom_count()); // 6

    // Fingerprint similarity
    let sim = tanimoto_ecfp4(&benzene, &toluene);
    println!("Tanimoto(benzene, toluene): {sim:.3}"); // ~0.5

    // Canonical SMILES
    println!("{}", canonical_smiles(&benzene)); // c1ccccc1
}

SMARTS substructure search

use chematic_smiles::parse;
use chematic_smarts::{parse_smarts, find_matches};

let mol = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap(); // aspirin
let query = parse_smarts("C=O").unwrap();
let matches = find_matches(&query, &mol);
println!("C=O groups: {}", matches.len()); // 2

Molecular descriptors

use chematic_smiles::parse;
use chematic_chem::{molecular_weight, tpsa, lipinski_passes};

let aspirin = parse("CC(=O)Oc1ccccc1C(=O)O").unwrap();
println!("MW:    {:.2}", molecular_weight(&aspirin)); // ~180.16
println!("TPSA:  {:.2}", tpsa(&aspirin));             // ~63.6
println!("Lipinski: {}", lipinski_passes(&aspirin));  // true

2D depiction

use chematic_smiles::parse;
use chematic_depict::depict_svg;

let caffeine = parse("Cn1cnc2c1c(=O)n(c(=O)n2C)C").unwrap();
let svg = depict_svg(&caffeine);
std::fs::write("caffeine.svg", svg).unwrap();

Comparison with Other Cheminformatics Libraries

Notes:

• "chematic" column reflects current implementation plus the final planned state.
• Binary sizes are approximate and depend on enabled features.
• chemcore and purr are archived; chematic supersedes their scope.

Roadmap

Phase 1 — Foundation (complete)

Core types, OpenSMILES parse/write, Kekulization, canonical SMILES. 80 tests.

Phase 2 — Molecular Perception (complete)

SSSR, Huckel aromaticity, SDF/MOL V2000+V3000, 2D SVG depiction. 63 tests.

Phase 3 — Chemical Intelligence (complete)

Descriptors (MW, LogP, TPSA, Lipinski), ECFP4/6 fingerprints, SMARTS+VF2, molecular standardization (salt stripping, charge neutralization), Murcko scaffold, CIP R/S and E/Z stereochemistry assignment.

Phase 4 — Similarity and Search (complete)

MACCS 166-bit structural keys ✓, topological path fingerprints ✓, MCS ✓, tautomer normalization ✓.

Phase 5 — 3D Chemistry (partially complete)

Rule-based 3D coordinate generation, PDB/XYZ formats. Remaining: UFF force field minimization.

Phase 6 — RDKit Parity (partially complete)

Reaction SMILES/SMIRKS (chematic-rxn) ✓, umbrella crate with feature flags (chematic) ✓. Remaining: WASM package (npm: chematic), ChEMBL-scale validation.

See tasks/todo.md for the detailed per-task breakdown.

Repository Structure

chematic/
├── Cargo.toml               workspace root
├── CHANGELOG.md             version history
├── crates/
│   ├── chematic-core/       Atom, Bond, Molecule, Element, kekulization
│   ├── chematic-smiles/     OpenSMILES parser, writer, canonical SMILES
│   ├── chematic-perception/ SSSR ring perception, Huckel aromaticity
│   ├── chematic-mol/        MOL/SDF V2000+V3000 parser and writer
│   ├── chematic-depict/     2D SVG depiction engine
│   ├── chematic-chem/       Molecular descriptors, standardization, scaffold
│   ├── chematic-fp/         ECFP4/6 fingerprints, Tanimoto/Dice similarity
│   ├── chematic-smarts/     SMARTS parser + VF2 subgraph isomorphism, MCS
│   ├── chematic-3d/         3D coordinate generation, PDB/XYZ formats
│   ├── chematic-rxn/        Reaction SMILES parser and writer
│   └── chematic/            Umbrella crate with feature flags
└── tasks/
    ├── todo.md              full roadmap checklist (Japanese)
    └── lessons.md           development lessons learned

Development Commands

cargo build --workspace      # build all crates
cargo test --workspace       # run all tests (332+)
cargo check --workspace      # type-check without building
cargo clippy --workspace     # lints

License

Licensed under either of Apache License 2.0 or MIT License, at your option.