Setup and Installation


E3FP is compatible with Python 3.x. It additionally has the following dependencies:



The following packages are required for the specified features:


The following installation approaches are listed in order of recommendation. All but the first of these approaches requires a prior installation of RDKit.

Option 1: Install with Conda

E3FP is on the Anaconda distribution. Conda is a cross-platform package manager. This approach is highly recommended as it installs all required packages.

  1. Install with

    $ conda create -c conda-forge --name e3fp_env e3fp
    $ conda activate e3fp_env
  2. To install the optional Python dependencies, run

    $ conda install -c conda-forge mpi4py h5py standardiser

To get the latest version of E3FP, follow Option 3: Clone the Repository.

Option 2: Install with Pip

  1. Install with

    $ pip install e3fp
  2. To install the optional Python dependencies, run

    $ pip install mpi4py h5py standardiser

Option 3: Clone the Repository

  1. Download this repository to your machine.

    • Clone this repository to your machine with

      $ git clone
      $ cd e3fp
    • OR download an archive by navigating to the repository and clicking “Download ZIP”. Extract the archive.

  2. Install the optional dependencies and any required ones using pip or conda.


The easiest way to install the dependencies is with

$ conda env create --name e3fp_env --file environment.yml
$ conda activate e3fp_env
  1. Install with

    $ python build_ext --inplace
    $ python install


After installation, it is recommended to run all tests with pytest. After running pip install pytest or conda install -c conda-forge pytest, run

$ pytest e3fp