In [1]:

    

import logging
reload(logging)
logging.basicConfig(level=logging.INFO)


    

In [2]:

    

import rosetta
rosetta.init()
import rosetta.core.import_pose


    

    




INFO:rosetta:Found rosetta database at: /work/fordas/python_local/rosetta/database
INFO:rosetta:Version: 1afb81950d464d6243055cb6a566fd124985cd5f
INFO:rosetta:core.init: Rosetta version  from
INFO:rosetta:core.init: command: pyrosetta -ex1 -ex2aro -database /work/fordas/python_local/rosetta/database
INFO:rosetta:core.init: 'RNG device' seed mode, using '/dev/urandom', seed=73467636 seed_offset=0 real_seed=73467636
INFO:rosetta:core.init.random: RandomGenerator:init: Normal mode, seed=73467636 RG_type=mt19937

In [3]:

    

test_pdb = !curl http://www.rcsb.org/pdb/files/1UBQ.pdb 2> /dev/null | grep ^ATOM


    

In [4]:

    

test_pose = rosetta.core.pose.Pose()
rosetta.core.import_pose.pose_from_pdbstring( test_pose, "\n".join(test_pdb) )


    

    




INFO:rosetta:core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 736 residue types
INFO:rosetta:core.pack.task: Packer task: initialize from command line()

In [5]:

    

from notebook_pv.extractors import PoseModelExtractor
from notebook_pv.widgets import MoleculeDisplayWidget


    

    




:0: FutureWarning: IPython widgets are experimental and may change in the future.

In [6]:

    

test_pose_model = PoseModelExtractor().extract_pose_model(test_pose)


    

In [7]:

    

display_widget = MoleculeDisplayWidget( structure = test_pose_model )


    

In [8]:

    

display_widget


    

In [ ]: