INSTALL

--- Requirements ---

AlGDock is a third-party python extension.
The required programs and extensions should be installed and tested prior to AlGDock. It is recommended to use a scientific distribution of python, including:

Enthought Canopy Python (tested with version 2.7.6)
https://www.enthought.com/products/epd/

or

Anaconda Scientific Python
https://store.continuum.io/cshop/anaconda/

After installing a scientific python distribution, the following extensions are also required:

Scientific Python (tested with version 2.9.2)
http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

Molecular Modeling ToolKit (MMTK) (tested with version 2.7.9)
http://dirac.cnrs-orleans.fr/MMTK

pymbar (tested with version 2.0beta)
https://github.com/choderalab/pymbar

Finally, AlGDock requires the following external programs:
Not Another Molecular Dynamics (NAMD), tested with version 2.9
http://www.ks.uiuc.edu/Research/namd/

--- Installation ---

To install AlGDock, first modify AlGDock/_external_paths.py to point to the locations of the relevant programs. In AlGDock/_external_paths.py, search_paths['MMTK'] should point to the source directory that contains the Include subdirectory.

Then run the commands:
python setup.py build
python setup.py install

--- Testing ---

In the AlGDock/Example/ subdirectory, you may test the program with:

test_python.py

or

test_terminal.sh

It should generate output in the dock and cool subdirectories. The dock and cool subdirectories should be removed before testing.