How can I execute this command in pyrosetta?

[404-xianjin]

antibody_designer.linuxgccrelease -s my_ab.pdb -seq_design_cdrs L1 L2 H3 \ -graft_design_cdrs L1 L2 -light_chain kappa -design_H3_stem -inner_kt 2.0 \ -outer_kt 2.0 -seq_design_profile_samples 5 -nstruct 5 -out:prefix tutD5_ <AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H3" mintype="relax" inner_kt="2.0" outer_kt="2.0"/> https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb This example should be executed in rosetta, what I want to know is how to execute this command in pyrosetta. Thanks

Below is the test.py script for my current environment

@ajasja @momeara @jueseph @pjsteiner @danielvarela

[roccomoretti]

The AntibodyDesignMover tag below can be loaded with the XmlObjects functionality, as done in Tut A1. Sequence Design. -- Alternatively, what that does is effectively instantiate the rosettta.protocols.antibody.AntibodyDesignMover and then call a number of configuration setters on that object to set things up properly. (use the help() functionality of Python, or the API documentation to get more info on what functions are available.

The command line antibody_design application is an exceedingly thin wrapper around the AntibodyDesignMover. The only trick might be converting the command line options. But for antibody_design, you might not need to do that. You could potentially just add the options to the pyrosetta.init() call. However, you'll get more flexibility by setting things in the XML tag, using the AntibodyDesignMover documentation as a guide.

[404-xianjin]

I want to use -nstruct 20 -out:prefix this parameter, but I don't know how to write this. rabd = XmlObjects. static_get_mover('<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" light_chain="kappa"/>') I read the parameter option of AntibodyDesignMover, there is no -nstruct and -out: prefix options. In addition, the document mentions the folder "expected_outputs/rabd/tutA2_score.sc", which directory is it in? Where is his absolute path? Thanks @roccomoretti I'm new to this major, and I don't quite understand this document. Thank you for your help.

[ajasja]

@404-xianjin In Pyrosetta you have to do the looping and saving of files yourself. So I would write a for loop and save the poses manually.