Installation

Pip

Install DeepMol via pip:

If you intend to install all the deepmol modules’ dependencies:

pip install deepmol[all]

or in MacOS:

pip install "deepmol[all]"

Extra modules:

pip install deepmol[preprocessing]
pip install deepmol[machine-learning]
pip install deepmol[deep-learning]

or in MacOS:

pip install "deepmol[preprocessing]"
pip install "deepmol[machine-learning]"
pip install "deepmol[deep-learning]"

Also, you should install mol2vec and its dependencies:

pip install git+https://github.com/samoturk/mol2vec#egg=mol2vec

Manually

Alternatively, clone the repository and install the dependencies manually:

  1. Clone the repository:

git clone https://github.com/BioSystemsUM/DeepMol.git
  1. Install dependencies:

python setup.py install

Docker

You can also use the provided image to build your own Docker image:

docker pull biosystemsum/deepmol

Disclaimer

If you’d like to use the GPU, make sure to install the versions of TensorFlow and DGL that match the CUDA drivers for your hardware.

Do not install JAX, it will result dependency conflicts.

Loading tensorflow models will be problematic for MacOS users due to a known tensorflow issue 46.