I am using PyRosetta to minimize several complexes and obtain the rosetta calculated energy values. In order to obtain all the rosetta scoring terms, I am using the get_fa_scorefxn function. Whereas I want to retain all the scoring terms, the only option that seems available to see all of them is with the following lines:
scorefxn = get_fa_scorefxn()
pose = pose_from_pdb(<minimized_complex_pdb>)
scorefxn.show(pose)
HOWEVER, the scorefxn.show(pose) prints the terms to the terminal and I am not able to extract the terms within my python code. I tried 'pose.energies().total_energies()[fa_atr]' as is recommended in the pyrosetta documentation appendix A here, but that gives me a type error. I even tried to reassign stdout to a file so scorefxn.show(pose) prints to it, but it doesn't. What is a way around this or am I missing something?
'pose.energies().total_energies()[fa_atr]' is the way to do it. You can also try 'pose.energies().total_energies().get(fa_atr)', though I don't know why that would work when the former doesn't.
When you say it give you a type error, what's the exact error message you get? Is it complaining about the fa_atr? That should be the score type value from rosetta.core.scoring -- If you're accidentally pulling it from somewhere else, it might not work well.
Here are the commands I am entering and the error messages I am getting:
Trial 1: pose.energies().total_energies()['fa_atr']
Error Message: *** NameError: name 'fa_atr' is not defined
Trial 2: pose.energies().total_energies()['fa_atr']
Error Message: *** TypeError: __getitem__(): incompatible function arguments. The following argument types are supported:
Error Message (continued): 1. (self: pyrosetta.rosetta.core.scoring.EMapVector, st: pyrosetta.rosetta.core.scoring.ScoreType) -> float
Error Message (continued): Invoked with: <pyrosetta.rosetta.core.scoring.EMapVector object at 0x7f78ebe06f10>, 'fa_atr'
Trial 3:
fa_atr = rosetta.core.scoring
pose.energies().total_energies().get(fa_atr)
Error Message:
*** TypeError: get(): incompatible function arguments. The following argument types are supported:
1. (self: pyrosetta.rosetta.core.scoring.EMapVector, st: pyrosetta.rosetta.core.scoring.ScoreType) -> float
Invoked with: <pyrosetta.rosetta.core.scoring.EMapVector object at 0x7f78ebe06f80>, <module 'pyrosetta.rosetta.core.scoring' (built-in)>
So maybe i should define fa_atr differently?
Its not a string, it's an enum. Basically a named number. Its a specific type and reduces passing around raw strings.
First do this:
from pyrosetta.rosetta.core.scoring import *
Then just pass fa_atr instead of with the string.