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Installation

Required Software

  • `Python`_ 3.10 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. :program:`gcc`) and Python developer libraries (i.e. :file:`python.h`). If you don't have Python developer libraries installed on your machine, use your package manager to install :file:`python-dev` package.

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

Quick Install

We officially recommend installing through conda:

conda install -c conda-forge prody

Installing From Source (not recommended)

Linux

Download :file:`ProDy-{x}.{y}.{z}.tar.gz`. Extract tarball contents and run :file:`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.

Recommended Software

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.
  • Scipy, when installed, replaces linear algebra module of Numpy. Scipy linear algebra module is more flexible and can be faster.

Source Code

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