Anaconda with Conda Installation

The Anaconda package can be downloaded from for Windows, macOS and Linux platforms. Follow the very simple instructions given there for installation. For first time users we also recommend reading Getting started with conda and print out the Conda user cheat sheet reference.


We recommend the installation of PYTHON 3 Anaconda packages. This version will default to Python 3 when creating new environments and building packages.


We recommend using the Anaconda package, which is a complete suite containing hundreds of open source Python packages. If disk-space is limited, we recommend the mini version of Anaconda, namely, Miniconda. Miniconda includes conda, its dependencies and Python.

The Miniconda package can be downloaded from for Windows, macOS and Linux platforms.

After downloading and installing Anaconda, the OpenEye Python Toolkit package can be installed by the following steps:

  1. First create a new conda environment:

    $ conda create -n oepython python=3
    Collecting package metadata (current_repodata.json): done
    Solving environment: done
    ## Package Plan ##
      environment location: /anaconda3/envs/oepython
      added / updated specs:
        - python=3
    The following packages will be downloaded:
        package                    |            build
        libffi-3.2.1               |       h0a44026_6          43 KB
        ncurses-6.2                |       h0a44026_1         749 KB
                                               Total:         792 KB
    The following NEW packages will be INSTALLED:
      ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
      certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py38_0
      libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
      libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
      libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
      libffi             pkgs/main/osx-64::libffi-3.2.1-h0a44026_6
      ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
      openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
      pip                pkgs/main/osx-64::pip-20.0.2-py38_1
      python             pkgs/main/osx-64::python-3.8.2-hc70fcce_0
      readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
      setuptools         pkgs/main/osx-64::setuptools-46.1.3-py38_0
      sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
      tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
      wheel              pkgs/main/osx-64::wheel-0.34.2-py38_0
      xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
      zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
    Proceed ([y]/n)?

    After entering “y” to proceed, a new ‘oepython’ environment will be created with Python 3.8.

  2. Activate the newly created ‘oepython’ environment:

    $ source activate oepython
    (oepython) $


    It is very important to activate a work environment before performing any additional installations, otherwise packages will be installed into the global Python environment.

  3. Install the OpenEye Python Toolkits into the new environment:

    (oepython) $ conda install -c openeye openeye-toolkits
    Solving environment: done
    The following NEW packages will be INSTALLED:
    attrs:            17.3.0-py35h20e33bf_0
    ca-certificates:  2017.08.26-h1d4fec5_0
    coverage:         4.4.2-py35h8fc71f1_0
    hypothesis:       3.38.5-py35h785bf34_0
    libgcc-ng:        7.2.0-h7cc24e2_2
    openeye-toolkits: 2018.2b2-py35_0       openeye
    pluggy:           0.6.0-py35hb428803_0
    py:               1.5.2-py35hfe8c5ce_0
    pympler:          0.5-py35hc09b5c8_0
    pytest:           3.3.2-py35_0
    six:              1.11.0-py35h423b573_1
    zope:             1.0-py35_0
    zope.interface:   4.4.3-py35h9cef842_0
    Proceed ([y]/n)? y
  4. Run the OpenEye example to verify the installation has completed successfully:

    (oepython) $
    Installed OEChem version: |oechemversion| platform: linux-g++4.x-x64 built: |builddate|


Setting the environment variable PYTHONPATH will override the path to the Python modules installed in a conda environment. Make sure PYTHONPATH is not set when using a virtual environment.

See also

See Integration Testing for post-installation testing of the OpenEye Python Toolkits.