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Installation

Required Software

  • Python 2.7, 3.6 or later. We recommend using Anaconda, which provides the conda package and environment manager as well as many useful packages.
  • NumPy 1.10 or later
  • SciPy - we recommend that you use the latest version, but all versions should be supported.
  • Biopython - we recommend that you use the latest version, but all versions should be supported.

When compiling from source, on Linux for example, you will need a C compiler (e.g. gcc) and Python developer libraries (i.e. python.h). If you don't have Python developer libraries installed on your machine, use your package manager to install python-dev package.

In addition, matplotlib is required for using plotting functions. ProDy, prody-apps, and evol-apps can be operated without this package.

Quick Install

If you have pip installed, type the following:

pip install -U ProDy

If you don't have pip, please download an installation file and follow the instructions.

If you have conda installed, you can also type the following instead:

conda install ProDy

Download & Install

After installing the required packages, you will need to download a suitable ProDy source or installation file from http://python.org/pypi/ProDy. For changes and list of new features see changes.

Linux

Download ProDy-{x}.{y}.{z}.tar.gz. Extract tarball contents and run setup.py as follows:

$ tar -xzf ProDy-x.y.z.tar.gz
$ cd ProDy-x.y.z
$ python setup.py build
$ python setup.py install

If you need root access for installation, try sudo python setup.py install. If you don't have root access, please consult alternate and custom installation schemes in Installing Python Modules.

Mac OS

For installing ProDy, please follow the Linux installation instructions.

Windows

Remove previously installed ProDy release from Uninstall a program in Control Panel.

Download ProDy-1.{x}.{y}.win32-py2.{z}.exe and run to install ProDy.

To be able use prody-apps and evol-apps in command prompt (cmd.exe), append Python and scripts folders (e.g. C:\\Python27 and C:\\Python27\\Scripts) to PATH environment variable.

Recommended Software

  • Scipy, when installed, replaces linear algebra module of Numpy. Scipy linear algebra module is more flexible and can be faster.
  • IPython is a must have for interactive ProDy sessions.
  • PyReadline for colorful IPython sessions on Windows.
  • MDAnalysis or MDTraj for reading molecular dynamics trajectories.

Included in ProDy

Following software is included in the ProDy installation packages:

  • pyparsing is used to define the atom selection grammar.
  • Biopython KDTree package and pairwise2 module are used for distance based atom selections and pairwise sequence alignment, respectively.
  • argparse is used to implement applications and provided for compatibility with Python 2.6.

Source Code

Source code is available at https://github.com/prody/ProDy.