Python 2.7, 3.2 or later
Windows: Note that, NumPy and ProDy supports only 32-bit Python on Windows.
Python 2.6 and 3.1 can be used to install and run ProDy. However, note that ProDy tests are performed using Python 2.7 and 3.2, so these are the recommended versions.
NumPy 1.5+ (for Windows, select an installer built using a suitable version of NumPy)
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.
If you have Easy Install installed, type the following:
easy_install -U ProDy
If you don’t have Easy Install, please download an installation file and follow the instructions.
Download a suitable ProDy installation file from http://python.org/pypi/ProDy or here:
| File | Type | Py Version | Size | Downloads |
|---|---|---|---|---|
| ProDy-1.4.2.tar.gz | Source | 907KB | 224 | |
| ProDy-1.4.2.win32-py2.6-numpy1.5.exe | MS Windows installer | 2.6 | 1209KB | 152 |
| ProDy-1.4.2.win32-py2.6.exe | MS Windows installer | 2.6 | 1209KB | 139 |
| ProDy-1.4.2.win32-py2.7-numpy1.5.exe | MS Windows installer | 2.7 | 1209KB | 163 |
| ProDy-1.4.2.win32-py2.7.exe | MS Windows installer | 2.7 | 1209KB | 158 |
| ProDy-1.4.2.win32-py3.1-numpy1.5.exe | MS Windows installer | 3.1 | 1210KB | 138 |
| ProDy-1.4.2.win32-py3.1.exe | MS Windows installer | 3.1 | 1210KB | 135 |
| ProDy-1.4.2.win32-py3.2.exe | MS Windows installer | 3.2 | 1210KB | 136 |
| ProDy-1.4.2.win32-py3.3.exe | MS Windows installer | 3.3 | 1205KB | 157 |
| ProDy-1.4.2.zip | Source | 1060KB | 218 |
For details of ProDy releases see Changes and ProDy Download Statistics.
Windows installers are built using MinGW.
After installing the required packages, you will need to do one of the following:
Remove all previously installed ProDy files. You can find location of installation files as follows:
$ python -c "import prody; print(prody.__path__)"
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.
For installing ProDy, please follow the Linux installation instructions.
Remove previously installed ProDy release from Uninstall a program in Control Panel.
Download ProDy-0.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.
You can test your ProDy installation using the following command:
$ prody test
Note that prody script/command must be reachable from your working directory. For more information on testing, see Testing ProDy.
NMWiz is a VMD plugin for comparative visual analysis of protein dynamics modeled using theory or inferred from experimental structural ensembles. See NMWiz for available updates and installation instructions.
Following software is included in the ProDy installation packages:
Source code can be found at https://bitbucket.org/abakan/prody.