PyRosetta

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

Chaudhury, S., Lyskov, S., Gray, J.J. (2010) PyRosetta: a script-based interface for implementing custom molecular modeling algorithms using Rosetta. Bioinformatics

As a python package Pyrosetta can be used as an extension by ePMV. This features is currently under development, and getting PyRosettta working inside the python host environment can be relatively difficult and unstable (host software freezing for instance). Moreover, PyRosetta support python2.5 for 32bit modes and python2.6 for 64bits modes. That means that using PyRosetta in an host application support python2.6 in 32bits mode is impossible. As a result PyRosetta is likely to be available only for blender (Mac and Linux).

getting PyRosetta

You can get PyRosetta, after registration, from here. PyRosetta doesn't require any installation but require to setup some environment variable. The package provides the script allowing to easily set up theses environment variable (i.e. SetPyRosettaEnvironment.sh). Check the installation instruction for more details. Once PyRosetta is functional, we need to make available for ePMV and the host software, which will require that the host is aware of the environment variable. The next section will guide you in order to set this for the your os.

setting the environnment

linux

On Linux using the SetPyRosettaEnvironment.sh before running blender should be enough.

Mac

On Mac you will need to modify the SetPyRosettaEnvironment.sh script.The modification permit to set the environment variable available for all Mac application (not only the unix one):

#!/bin/sh

# This script intended to set Pyrosetta environment variables so user can execute 'import rosetta' from

# any file system location. Use 'source SetPyRosettaEnvironment.sh' before starting to work with PyRosetta.

PYROSETTA=${BASH_SOURCE[0]%/*}

export PYROSETTA

export PYTHONPATH=$PYROSETTA:$PYTHONPATH

export DYLD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta:$DYLD_LIBRARY_PATH

export LD_LIBRARY_PATH=$PYROSETTA/rosetta:$LD_LIBRARY_PATH

export PYROSETTA_DATABASE=$PYROSETTA/minirosetta_database

#add this lines

launchctl setenv PYROSETTA $PYROSETTA

launchctl setenv DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH

launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH

launchctl setenv PYROSETTA_DATABASE $PYROSETTA_DATABASE

Windows

Currently unsupported

Tests

Once all variablers are setup, PyRosetta should be available inside the host application python environment.