Crate assembly_theory

assembly_theory is an open-source, high-performance library for computing assembly indices of molecular structures (see, e.g., Sharma et al., 2023; Walker et al., 2024).

This crate is specific to the Rust library; see the GitHub repository for ways to use assembly_theory as a standalone executable or as a Python package.

Example

Install the crate as usual:

cargo add assembly-theory

Load a molecule from a .mol file and calculate its assembly index:

use assembly_theory::{
    assembly::index,
    loader::parse_molfile_str
};

// Load a molecule from a `.mol` file.
let path = PathBuf::from(format!("./data/checks/anthracene.mol"));
let molfile = fs::read_to_string(path)?;
let anthracene = parse_molfile_str(&molfile).expect("Parsing failure.");

// Compute the molecule's assembly index using an efficient algorithm.
assert_eq!(index(&anthracene), 6);

See assembly for more usage examples.

Modules

assembly

Compute assembly indices of molecules.

bounds

Prune assembly states from which the assembly index cannot improve.

canonize

Create canonical labelings for molecular graphs.

enumerate

Enumerate connected, non-induced subgraphs of a molecular graph.

kernels

Kernelize match-compatibility graphs to improve top-down search efficiency.

loader

Parse molecules in the .mol file format.

memoize

Memoize assembly states to avoid redundant recursive search.

molecule

Graph-theoretic representation of a molecule.

python

Expose public assembly_theory functionality to a Python package using pyo3.