machine learning, molecular descriptor
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README.md


Introduction

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.

Installation

Install Pybel and RDKit

To install Pybel: http://openbabel.org/docs/current/UseTheLibrary/PythonInstall.html
To install RDKit: http://www.rdkit.org/docs/Install.html

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: https://github.com/gadsbyfly/PyBioMed/blob/master/PyBioMed/download/PyBioMed-1.0.zip.
The install process of PyBioMed is very easy:

On Windows:

(1): download the PyBioMed-1.0.zip

(2): extract or uncompress the PyBioMed-1.0.zip file

(3): cd PyBioMed-1.0

(4): python setup.py install

On Linux:

(1): download the PyBioMed package (.zip)

(2): unzip PyBioMed-1.0.zip

(3): cd PyBioMed-1.0

(4): python setup.py install or sudo python setup.py 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 PyBioMed-1.0.zip, 'cd PyBioMed-1.0', 'python setup.py install or sudo python setup.py install'.

Documentation

(1)The online version of the documentation is available here:
http://projects.scbdd.com/pybiomed/index.html
or http://pybiomed.readthedocs.io/en/latest/
(2)Quick start examples: http://projects.scbdd.com/pybiomed/User_guide.html
or http://pybiomed.readthedocs.io/en/latest/User_guide.html
(3)Application examples(pipelines): http://projects.scbdd.com/pybiomed/application.html
or http://pybiomed.readthedocs.io/en/latest/application.html

Contact

If you have questions or suggestions, please contact: gadsby@163.com, biomed@csu.edu.cn and oriental-cds@163.com

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

Copyright (C) 2015-2017 CBDD Group