bigsmiles

A BigSMILES parser for polymer and macromolecule notation in Rust.

What is BigSMILES?

BigSMILES is a line notation for polymers and macromolecules. It extends SMILES with stochastic objects {...} that describe repeat units and end groups.

{[$]CC[$]}                    → polyethylene
{[$]CC[$],[$]CC(C)[$]}        → ethylene-propylene copolymer
CC{[$]CC[$]}CC                → α,ω-dimethyl polyethylene
{[>][<]CC(C)[>][<]}           → isotactic polypropylene
{[$]CC[$];[$]CCO[$]}          → polyethylene with hydroxyl end group

Installation

[dependencies]
bigsmiles = "0.1"

Usage

Basic parsing

use bigsmiles::parse;

let pe = parse("{[$]CC[$]}").unwrap();          // polyethylene
let ps = parse("{[]CC(c1ccccc1)[]}").unwrap();  // polystyrene
let copo = parse("{[$]CC[$],[$]CC(C)[$]}").unwrap(); // copolymer

// Display produces the canonical BigSMILES string
println!("{}", pe);   // {[$]CC[$]}

Inspecting the AST

use bigsmiles::{parse, BigSmilesSegment};

let result = parse("CC{[$]CC[$]}CC").unwrap();

for seg in &result.segments {
    match seg {
        BigSmilesSegment::Smiles(mol) => {
            println!("SMILES fragment: {} atoms", mol.nodes().len());
        }
        BigSmilesSegment::Stochastic(obj) => {
            println!("Stochastic object: {} repeat unit(s)", obj.repeat_units.len());
            for ru in &obj.repeat_units {
                println!("  repeat unit: {}", ru.smiles_raw);
                println!("  left BD: {:?}, right BD: {:?}", ru.left, ru.right);
                println!("  left atom index: {}, right atom index: {}", ru.left_atom, ru.right_atom);
            }
        }
    }
}

Bond descriptors

BigSMILES uses bond descriptors to define how repeat units connect:

Connection atoms

Each stochastic fragment records which atom index bonds to each descriptor:

• left_atom — always 0 (the first written atom)
• right_atom — the last atom on the main chain (depth 0), not counting branch atoms

For CC(C) (polypropylene): left_atom = 0 (C0), right_atom = 1 (C1, backbone). The methyl branch C2 is not the connection atom.

Error handling

use bigsmiles::{parse, ParseError};

match parse("{[$]CC[$]") {
    Ok(mol)  => println!("ok: {}", mol),
    Err(ParseError::UnclosedStochasticObject) => eprintln!("missing closing }"),
    Err(e)   => eprintln!("parse error: {}", e),
}

Supported BigSMILES features

Relationship to opensmiles

bigsmiles depends on opensmiles (also part of this workspace) for parsing the SMILES fragments inside stochastic objects. The opensmiles crate is re-exported as bigsmiles::opensmiles for convenience.

References

• Lin, T.-S. et al. "BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules." ACS Central Science 2019, 5, 1523–1531. https://pubs.acs.org/doi/10.1021/acscentsci.9b00476
• BigSMILES Documentation
• OpenSMILES Specification

License

MIT — see LICENSE.