generate_nonstandard_residue_set Exception

[Anonymous]

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 *
init()
params_paths = utility.vector1_string()
params_paths.extend([“GUA.params”])

In [3]: nonstandard_residue_set = generate_nonstandard_residue_set( params_paths )

---

Exception Traceback (most recent call last)
in ()
—-> 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
303

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))
250
251 v = t()

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

[Anonymous]

The PyRosetta team is taking a look at it.

[Anonymous]

The PyRosetta team is taking a look at it.

[Anonymous]

The PyRosetta team is taking a look at it.

[Anonymous]

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() could be called…

“

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

[Anonymous]

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() could be called…

“

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

[Anonymous]

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() could be called…

“

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

[Anonymous]

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

Wow, that was easy.

I think this must be out of date:
http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf

Thanks guys!

[Anonymous]

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

Wow, that was easy.

I think this must be out of date:
http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf

Thanks guys!

[Anonymous]

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

Wow, that was easy.

I think this must be out of date:
http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf

Thanks guys!

[Author]

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