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.

PyRosetta was created at Johns Hopkins University by Jeffrey J. Gray, Sergey Lyskov, and the PyRosetta Team.

• PyRosetta Main Site
• PyRosetta Tutorial Workshop

• Module Name: PyRosetta (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • PYROSETTA_HOME
• Example files in $PYROSETTA_HOME/demo
• Reference data in /pdb/pdb

Many aspects of PyRosetta require an X11 connection. Please use a Graphical Session on HPC OnDemand

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load PyRosetta
[user@cn3144 ~]$ python
Python 3.12.8 | packaged by conda-forge | (main, Dec  5 2024, 14:24:40) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyrosetta
>>> pyrosetta.init()

... your code here ...

quit()
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -r $PYROSETTA_HOME/demo .
[user@cn3144 ~]$ cd demo
[user@cn3144 ~]$ cp -r $PYROSETTA_HOME/test .
[user@cn3144 ~]$ mkdir .test.output
[user@cn3144 ~]$ python D010_Pose_structure.py

... pyrosetta output here ...

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. PyRosetta.sh). For example:

#!/bin/bash
module load PyRosetta
python your_python_code.py

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PyRosetta.sh