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PyBioMed provides various user-friendly and highly customized APIs to calculate various features(descriptors) of biological molecules(chemicals, proteins and DNA/RNA descriptors) and complex interaction samples conveniently, which aims at building integrated analysis pipelines from data acquisition, data checking, and descriptor calculation to modeling.


Install Pybel and RDKit

Install PyBioMed

PyBioMed has been successfully tested on Linux and Windows systems. After installing RDKit and pybel successfully, The author could download the PyBioMed package via GitHub.

The install process of PyBioMed is very easy:

On Windows

  1. download the
  2. extract or uncompress the file
  3. cd PyBioMed-1.0
  4. python install

On Linux

  1. download the PyBioMed package (.zip)
  2. unzip
  3. cd PyBioMed-1.0
  4. python install or sudo python install

Recommended installation

There is a simplest configuration on Ubuntu 14.04 (Just click mouse to install):

  1. use the ubuntu software center to search for 'Synaptic Package Manager' and install it. Use 'Synaptic Package Manager' to search for 'openbabel, libopenbabel4, python-openbabel, libopenbabel-dev' and then install them. Search for 'python-rdkit, librdkit1, rdkit-data' and install them. This will make sure the right installation of Pybel and RDKit.
  2. Download, cd PyBioMed-1.0, python install or sudo python install.


  1. The online version of the documentation (alternatively, on
  2. Quick start examples (alternatively, on
  3. Application examples (pipelines) (alternatively on


If you have questions or suggestions, please contact:, and

Please see the file LICENSE for details about the "New BSD" license which covers this software and its associated data and documents.

Copyright (C) 2015-2020 CBDD Group