generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

[Anonymous]

So I’m trying to load this ligand_protein complex PDB into PyRosetta by temporarily creating a ResidueTypeSet

from pyrosetta import *

init()

params_path = Vector1()

nonstandard_residue_type = generate_nonstandard_residue_set(params_path)

I got this error message:

 

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

 

I’m using this temporary method becuase I followed this procedure step by step to try to permanently modify the chemical database:

http://www.pyrosetta.org/obtaining-and-preparing-ligand-pdb-files

 

I made sure that I BOTH placd the new cefotaxime.params file into the correct directory but also added the path to the cefotaxime.params file to the residue_types.txt file. 

 

But when I loaded the PDB file a pose, pyrosetta still did not recognize the cef (cefotaxime) residue type. 

 

Any help tp solve either issue is really appreciated !!

 

[Anonymous]

The behavior of generate_nonstandard_residue_set() has changed slightly between versions. It used to be that it added the non-standard type to the standard, global ResidueTypeSet. This caused problems with data consistency, and polluted the general ResidueTypeSet namespace.

Now, non-standard ResidueTypes are associated with the pose they’re used in, rather than just floating around generally. As such, generate_nonstandard_residue_set() now takes a Pose object as part of its code signature (see `help(generate_nonstandard_residue_set)` for more details.) 

What you should do is create an empty pose, add the non-standard ResidueType to it with generate_nonstandard_residue_set(), and then call pose_from_file() on that empty Pose.

 

from pyrosetta import *

init()



params_path = Vector1()

pose = Pose()

generate_nonstandard_residue_set(pose, params_path)

pose_from_file(pose, "Cefotaxime.pdb")

 

generate_nonstandard_residue_set() will still return a ResidueTypeSet object, but it’s now one which is associated with the passed Pose. 

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