def controlMut():
from pyrosetta.toolbox import generate_resfile_from_pdb, generate_resfile_from_pose
# generate_resfile_from_pdb('2AVX_pyrrolysine.pdb', 'my.resfile')
# ^ causes error EXCN_Base::what()
# likely due to uncleaned file?
#
# what if we clean first ...
from pyrosetta.toolbox import cleanATOM
cleanATOM('2AVX_pyrrolysine.pdb')
generate_resfile_from_pdb('2AVX_pyrrolysine.clean.pdb','my2.resfile')
# ^ doesnt work either causes error: ERROR: Unrecognized residue: LG1
# The following does work.
generate_resfile_from_pose(pose, 'my.resfile')
task_pack = standard_packer_task(pose)
task_pack.restrict_to_repacking()
task_pack.temporarily_fix_everything()
task_pack.temporarily_set_pack_residue(49, True)
print(task_pack)
pack_mover = PackRotamersMover(scorefxn, task_pack)
pack_mover.apply(pose)
import tempfile
# Design
# work around for windows permission problem
YY8_resfile1 = tempfile.mkstemp()[1]
YY8_resfile2 = tempfile.mkstemp()[1]
generate_resfile_from_pdb("../test/data/workshops/1YY8.clean.pdb",
YY8_resfile1)
generate_resfile_from_pose(pose, YY8_resfile2)
task_design = core.pack.task.TaskFactory.create_packer_task(pose)
core.pack.task.parse_resfile(pose, task_design, YY8_resfile2)
mutate_residue(pose, 49, 'E')
#os.remove(YY8_resfile1)
#os.remove(YY8_resfile2)