Binary Releases

oxmol is currently available on test PyPI whilst development is likely to be erratic and API-breaking. Wheels have been compiled for the following versions of Python:

  • Python 3.6
  • Python 3.7
  • Python 3.8
  • PyPy 7.3 (implementing Python 3.6)

These have been compiled against Linux, macOS and Windows, and are not guaranteed to be bug free. These can be installed using the following command (with some exceptions for PyPy below):

pip install --index-url oxmol

PyPy wheels for Linux currently aren’t compatible with the manylinux tag, so these will have to be downloaded from the github releases and installed:

curl "${RELEASE}" --output "${RELEASE}"
pip install "${RELEASE}"

PyPy doesn’t currently support 64-bit Windows, so no Windows PyPy wheels are provided.

Compiling From Source


The easiest way to build the Python wheels is to use Maturin, which can be installed via pip.

pip install maturin

You will also need the nightly Rust compiler. If you have not yet installed the Rust toolchain, see the instructions here. The nightly compiler can then be installed and and enabled by running the following two commands:

rustup install nightly
rustup default nightly

To set the default compiler back to stable, run the following command:

rustup default stable

If compiling on macOS, you will need to create a a file at ~/.cargo/config with the following contents in order to set the linker options:

rustflags = [
"-C", "link-arg=-undefined",
"-C", "link-arg=dynamic_lookup",


The Rust component of oxmol depends upon pyo3, molecule and gamma (a graph library) but these should be automatically fetched by Cargo when compiling so there are no dependencies to install manually.

Compiling Against Python

Clone the repo using git and move into the root folder:

git clone
cd oxmol

Execute the following command from the root of the repo.

maturin build --release

Maturin will compile the Rust component of the library and create a Python wheel containing the Rust and Python components, which are placed in ./target/wheels.

As Maturin will compile a wheel for each interpreter it finds (e.g. the system Python and the interpreter from a Conda environment), there may be multiple versions. You will have to install the version most relevant to your version of Python (e.g. oxmol-0.1.0-cp36... for Python 3.6 and oxmol-0.1.0-cp37... for Python 3.7). The full name of the file will vary depending on your platform.

cd into ./target/wheels and use pip to install the most relevant wheel

cd ./target/wheels
# Update the following command with the most relevant version.
pip install ./oxmol-0.1.0-cp37-cp37m-manylinux1_x86_64.whl

You should now be ready to start using oxmol. If you are interested in compiling against a specific version of Python, you can specify the path to the interetreter using the -i flag for Maturin:

maturin build -i $(which python3) --release

For information about other flags, use the Maturin docs.

Compiling Against PyPy

This is mostly the same as the process for Python.

The latest version of PyPy changed the ABI string format and Maturin hasn’t yet been updated, so you may have to rename the wheel file.

To compile oxmol against PyPy3, use the -i flag for Maturin:

maturin build -i $(which pypy3) --release
cd target/wheels

If you’re using PyPy3 version >= 7.3.1 (where SYSTEM is e.g. linux_x86_64):

mv oxmol-0.1.0-pp3pp73-pypy3_pp73-SYSTEM.whl oxmol-0.1.0-pp36-pypy36_pp73-SYSTEM.whl

Install using PyPy’s pip:

pypy3 -m pip install oxmol-0.1.0-pp36-pypy36_pp73-SYSTEM.whl


To run the tests, use pytest:

pip install pytest
pytest --pyargs oxmol

If these pass, all is well! If not, please post an issue on GitHub.