chematic-rxn 0.4.29

Reaction SMILES/SMIRKS parser and writer for chematic — pure-Rust RDKit alternative
Documentation

chematic-rxn

Reaction SMILES and SMIRKS parser for Rust. Parses chemical transformations (reactants → products) and reaction patterns (transform rules). Pure Rust, RDKit-compatible, WASM-compatible.

Features

  • Reaction SMILES parsing: parse reaction equations (e.g., CC(C)C>>CC(C)[O])
  • SMIRKS parsing: transform patterns for reaction template matching (run_reactants, run_reactants_strict)
  • Atom mapping: track which atoms in reactants map to which atoms in products
  • Reaction properties: count reactants, products, and agents
  • Stereo-selective SMIRKS: @/@@ in reactant templates filter by absolute configuration using permutation-parity comparison (write-order independent — the same enantiomer is matched regardless of how the reactant SMILES was written)
  • Template-based retrosynthesis (retro_disconnect): 60 retro-SMIRKS templates across 6 classes:
    • AmideBond — amide, sulfonamide, carbamate, urea, hydrazide, imide
    • Ester — ester, thioester, carbonate, anhydride, acetal, lactone
    • Ether — aryl ether (SNAr/Ullmann), Williamson, benzyl, Mitsunobu, silyl
    • CNBond — reductive amination, SNAr, Buchwald, N-alkylation, imine reduction
    • CCBond — Suzuki, Heck, Sonogashira, Negishi, Grignard, aldol, Michael, Wittig
    • CSBond — thioether, disulfide, borylation, halogenation, phosphonate
  • RDKit compatibility: parses RDKit reaction SMILES, produces identical results
  • WASM-compatible: zero C/C++ dependencies

Quick Start

use chematic_rxn::parse_reaction;

// Parse a reaction SMILES
let rxn = parse_reaction("CC(C)Br.[Na+].[OH-]>>CC(C)O.[Na+].[Br-]")
    .expect("bimolecular substitution");

println!("Reactants: {}", rxn.reactant_count());
println!("Products: {}", rxn.product_count());

// Access reactants and products as Molecule objects
for mol in rxn.reactants() {
    println!("Atoms: {}", mol.atom_count());
}

API Overview

Parsing

  • parse_reaction(rxn_smiles: &str) -> Result<Reaction, ParseError> — parse reaction SMILES
  • parse_smirks(pattern: &str) -> Result<ReactionPattern, ParseError> — parse SMIRKS pattern

Retrosynthesis

  • retro_disconnect(mol, templates, max_results) -> Vec<RetroResult> — apply retro-SMIRKS templates
  • DEFAULT_TEMPLATES — 60 built-in retro-SMIRKS templates (6 reaction classes)
  • RetroResult — {template_name, reaction_class, precursors, precursor_smiles, max_sa_score}
use chematic_rxn::{retro_disconnect, DEFAULT_TEMPLATES};
use chematic_smiles::parse;

let mol = parse("CC(=O)Nc1ccccc1")?;  // acetanilide
let results = retro_disconnect(&mol, DEFAULT_TEMPLATES, 10);
for r in &results {
    println!("{}: {:?}", r.template_name, r.precursor_smiles);
}
// amide_secondary: ["CC(=O)O", "Nc1ccccc1"]

Reaction Structure

  • Reaction — contains reactants, agents, products, and optional atom mappings
  • Molecule — each reactant/product is a standard Molecule
  • ReactionPattern — SMIRKS pattern for template matching

Properties

let rxn = parse_reaction("C.C>>CC")?;
assert_eq!(rxn.reactant_count(), 2);
assert_eq!(rxn.product_count(), 1);
assert_eq!(rxn.agent_count(), 0);

// Get individual molecules
let mol1 = rxn.reactant(0).expect("first reactant");
let prod = rxn.product(0).expect("first product");

Dependencies

References

See Also