Anaconda with Pip InstallationΒΆ

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. The instructions for installation can be found here:

All the instructions for installing the OpenEye Python Toolkits are identical whether using the Anaconda or Miniconda packages.

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 oepython3 python=3
    Using Anaconda Cloud api site
    Fetching package metadata: ....
    Solving package specifications: .........
    Package plan for installation in environment  /home/username/anaconda/envs/oepython3:
    The following NEW packages will be INSTALLED:
     openssl:    1.0.2h-1
     pip:        8.1.2-py35_0
     python:     3.5.2-0
     readline:   6.2-2
     setuptools: 25.1.6-py35_0
     sqlite:     3.13.0-0
     tk:         8.5.18-0
     wheel:      0.29.0-py35_0
     xz:         5.2.2-0
     zlib:       1.2.8-3
    Proceed ([y]/n)? y

    After entering “y” to proceed, a new ‘oepython3’ environment will be created with Python 3.5.

  2. Activate the newly created ‘oepython3’ environment:

    $ source activate oepython3
    (oepython3) $


    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:

    (oepython3) $ 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:

    (oepython3) $
    Installed OEChem version: 2.2.0 platform: linux-g++4.x-x64 built: 20190501


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

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