assembly-theory 0.5.0

Open, reproducible calculation of assembly indices

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 Python package wraps the functionality of the assembly-theory Rust crate for easier interoperability with existing cheminformatic libraries (e.g., RDKit) and computational pipelines.

If you're looking for the Rust crate or standalone executable versions of assembly-theory, or if you're trying to build this Python package from source, see our GitHub repository.

Installation

Install assembly-theory using a Python virtual environment manager of your choosing:

pip install assembly-theory   # Using pip.
pipx install assembly-theory  # Using pipx.
uv add assembly-theory        # Using uv.

Usage

assembly-theory exposes several functions, all of which expecta "mol block" (i.e., the contents of a .mol file as a string) as input. For example:

import assembly_theory as at  # Note the '_' instead of '-'!

# Load a mol block from file.
with open('anthracene.mol') as f:
    mol_block = f.read()

# Calculate the molecule's assembly index.
at.index(mol_block)  # 6

Combine assembly-theory with RDKit (installed separately) if you need to manipulate molecular representations or incorporate assembly index calculations in a broader cheminformatics pipeline.

import assembly_theory as at
from rdkit import Chem

# Get a mol block from a molecule's SMILES representation.
anthracene = Chem.MolFromSmiles("c1ccc2cc3ccccc3cc2c1")
anthracene = Chem.MolToMolBlock(anthracene)

# Calculate the molecule's assembly index.
at.index(anthracene)  # 6

See the assembly_theory::python documentation for a complete list of functions exposed to this package along with usage examples.

Citation

If you use this package in your own scientific work, please consider citing us:

Coming soon!

License

assembly-theory is licensed under the Apache License, Version 2.0 or the MIT License, at your option.