.. _getprody:

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. 

.. _Anaconda: https://www.anaconda.com/products/individual

* `NumPy`_ 1.10 or later

* `SciPy` - we recommend that you use the latest version, but all versions should be supported.

.. _SciPy: https://sourceforge.net/projects/scipy/

* `Biopython` - we recommend that you use the latest version, but all versions should be supported.

.. _Biopython: http://biopython.org/wiki/Download/

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
-------------

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 :ref:`changes`.

**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`_.

.. _Installing Python Modules: http://docs.python.org/install/index.html

**Mac OS**


For installing ProDy, please follow the Linux installation instructions.

**Windows**

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

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

To be able use :ref:`prody-apps` and :ref:`evol-apps` in command prompt
(:program:`cmd.exe`), append Python and scripts folders (e.g.
:file:`C:\\Python27` and :file:`C:\\Python27\\Scripts`) to :envvar:`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.


.. _PyReadline: http://ipython.org/pyreadline.html

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.

.. _argparse: http://code.google.com/p/argparse/


Source Code
-----------

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