Installation¶
Required Software¶
- Python 2.7, 3.5 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 Applications, and Evol Applications 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 Release Notes.
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 Applications and Evol Applications 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 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.