# PyBioMed

**Repository Path**: monash_li/PyBioMed

## Basic Information

- **Project Name**: PyBioMed
- **Description**: No description available
- **Primary Language**: Python
- **License**: BSD-3-Clause
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-05-06
- **Last Updated**: 2022-05-10

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

[![Build Status](https://travis-ci.org/gadsbyfly/PyBioMed.svg?branch=master)](https://travis-ci.org/gadsbyfly/PyBioMed)
![](https://img.shields.io/pypi/l/Django.svg) ![](https://img.shields.io/badge/dependencies-rdkit%2C%20pybel-green.svg)
![](https://img.shields.io/badge/platforms-linux%2C%20windows-brightgreen.svg)

## 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 [GitHub](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](http://projects.scbdd.com/pybiomed/index.html) (alternatively, on [readthedocs.io](http://pybiomed.readthedocs.io/en/latest/))
2. [Quick start examples](http://projects.scbdd.com/pybiomed/User_guide.html) (alternatively, on [readthedocs.io](http://pybiomed.readthedocs.io/en/latest/User_guide.html))
3. [Application examples (pipelines)](http://projects.scbdd.com/pybiomed/application.html) (alternatively on [readthedocs.io](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.


# <center> Copyright (C) 2015-2020 CBDD Group </center>