How to call SnugDock from PyRosetta

This topic has 1 reply, 2 voices, and was last updated 8 years, 6 months ago by Anonymous.

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- June 21, 2016 at 2:28 pm #2450
  Anonymous
  Hi,
  
  First of all, kudos on all the work that goes into PyRosetta – it makes it quite easy to quickly put together custom protocols.
  
  Quick question – How can I create a SnugDock object in PyRosetta? I am using release 2016.18.58680, and I’ve compiled pyrosetta under Ubuntu 12.04 (the compilation seems fine as I can call lots of rosetta protocols and they work as expected). It doesn’t look like pyrosetta is aware of any of the SnugDock code. Here’s a code snippet:
  
  from rosetta import *
  
  from rosetta.protocols.antibody import *
  
  from rosetta.protocols.antibody.design import *
  
  from rosetta.protocols.antibody.snugdock import *
  
  rosetta.init()
  
  pose = pose_from_file(“mymab.pdb”)
  
  ab_info = AntibodyInfo(pose)
  
  # line below works well, and I can access its functions
  
  modeler = GeneralAntibodyModeler(ab_info)
  
  # line below doesn’t work. Tabbing in ipython for rosetta.protocols.antibody.snugdock doesn’t return anything, while it does for rosetta.protocols.antibody.design
  
  snugler = SnugDock()
  
  Is there any way I can ensure that SnugDock files are considered when compiling pyrosetta?
  
  Thanks,
  
  Andrew
- July 1, 2016 at 3:42 pm #11714
  Anonymous
  Hey Andrew,
  
  There was a namespacing issue with SnugDock in the C++ code. This was fixed yesterday — it should be available in the next weekly release of Rosetta. Please let me know if you have any further issues.
  
  One note on SnugDock (I have never run it through PyRosetta, so there may be further issues), remodeling the CDR H2/H3 loops can be slow, so it may be best to initialize with “init(extra_options=’-loops:refine_outer_cycles 2 -loops:max_inner_cycles 20′)”.
  
  Best,
  
  Jeliazko
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