Dear All,
Is there a way to isolate or select the different structure layers from the pose according to their SASA (surface accessable surface area) in PyRosetta?
I have a python script that can do this from a .pdb file, but is there a way to do it from a PyRosetta pose?
I read that there are movers called LayerSelector and SelectBySASA both in Rosetta for Rosetta Script, is there their equivilent in PyRosetta?
Thank you
Category:
Post Situation:
Pretty much everything object that's availible in Rosetta is availible in PyRosetta.
The LayerSelector residue selector is availible at rosetta.core.select.residue_selector.LayerSelector. Once you've set it up, you would call the apply() method on your Pose, which should return back a Pose-length list of true/false values for the particular layer you've selected.
Alternatively, the LayerSelector is a relatively thin wrapper around the rosetta.core.select.util.SelectResiduesByLayer object , which may give you more control.
The SelectBySASA task operation is in rosetta.protocols.toolbox.task_operations.SelectBySASAOperation -- this is probably not what you want, as it's a TaskOperation, intended for packer setup, rather than something that's intended to be interrogated itself. But if you really wanted it, you could always use it, then interrogate the produced packer task for packing/design behavior and infer the results that way. -- I'd use that as a last resort, though.
If you already have a logic for selection that you want to reuse, and just want to find the SASA of atoms/residues, you can look into the rosetta.core.scorring.calc_per_atom_sasa() and associated functions to get the values that the previously mentioned objects are using. -- Note that this may be a slightly different value than the SASA score you're used to using, due to differences in atomic radii and details of the calculation scheme.
Thank you very much,
I looked into it, but i think it is better to write my own python code, i will export the pose into a .pdb file, run SASA on it, then delete it and use that information to continue.
Thank you