Question about Rosetta Commons license requirements for analysis step

[ChloeQuignot]

Hi AlphaPulldown team,

First of all, thank you for developing this useful tool!

I had a quick question regarding licensing and usage. The pipeline is distributed under the GPL-3.0 license, and I noticed that the workflow uses PyRosetta for the interface energy calculations. Since PyRosetta is distributed under the Rosetta Commons license (https://www.pyrosetta.org/home/licensing-pyrosetta), I was wondering whether this dependency should be mentioned more explicitly in the documentation, especially for users who may need to obtain an appropriate PyRosetta license.

Related to this, do you think it might be feasible to make the PyRosetta step optional in a future version of the pipeline (even if that means skipping the interface energy calculation)? I imagine some users might still benefit from running AlphaPulldown without that component.

Thanks again for all your work on this project,
Chloe

[DimaMolod]

Hi @ChloeQuignot

PyRosetta used to be part of the pipeline, but we’ve fully deprecated that step due to ambiguous results. The workflow no longer relies on PyRosetta for interface energy calculations, so there’s no licensing requirement on the user side and nothing extra they need to obtain. We should probably make that clearer in the docs, so thanks for raising this up.

The interface metrics are now computed using our own open-source scoring code, so the entire pipeline runs under GPL-3.0 without any Rosetta Commons components.

Really appreciate your careful reading and feedback,
Dima