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generate_nonstandard_residue_set Exception

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generate_nonstandard_residue_set Exception

generate_nonstandard_residue_set is giving me an error I don't understand. Can anyone tell what I'm doing wrong here?

In [2]: %paste
from rosetta import *
from pyrosetta import *
params_paths = utility.vector1_string()

In [3]: nonstandard_residue_set = generate_nonstandard_residue_set( params_paths )

Exception Traceback (most recent call last)
<ipython-input-6-77bee461beee> in <module>()
----> 1 nonstandard_residue_set = generate_nonstandard_residue_set(params_paths)

pyrosetta/__init__.pyc in generate_nonstandard_residue_set(params_list)
299 # ChemicalManager.get_instance().mm_atom_type_set("fa_standard"),
300 # ChemicalManager.get_instance().orbital_type_set("fa_standard"),)
--> 301 res_set.read_files_for_custom_residue_types(Vector1(params_list))
302 return res_set

pyrosetta/__init__.pyc in Vector1(list_in)
247 else:
248 raise Exception('Vector1: attemting to create vector of unknow type ' +
--> 249 'or mixed type vector init_list = ' + str(list_in))
251 v = t()

Exception: Vector1: attemting to create vector of unknow type or mixed type vector init_list = vector1_std_string[GUA.params]

Post Situation: 
Tue, 2017-06-13 18:28

The PyRosetta team is taking a look at it.

Thu, 2017-06-15 10:36

Cobbling together their responses:


It looks like generate_nonstandard_residue_set is expecting Python list as input - and code give it vector1 so thats why it fail...

 in example...`v` need to be Python list of string not a vector1 object.

Also: for future ref: there is not need to create utility.vector1_string() by hand, instead pyrosetta.Vector1(['GUA.params', 'GUA.params']) could be called...


If you can't figure out what that means, I'll get Sergey to come answer directly.

Thu, 2017-06-15 12:57

This worked:
nonstandard_residue_set = generate_nonstandard_residue_set(["GUA.params"])

Wow, that was easy.

I think this must be out of date:

Thanks guys!

Fri, 2017-06-16 12:23