def exercise_yes_sidechains(prefix="tst_one_resid_rotation_yes_sidechains"):
pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None)
model = mmtbx.model.manager(
model_input = pdb_inp)
with open("%s_start.pdb" % prefix, 'w') as f:
f.write(model.model_as_pdb())
ci = cablam_idealization(model = model, params=master_phil.extract().cablam_idealization, log=sys.stdout)
pdb_txt = model.model_as_pdb()
def exercise_no_sidechains(prefix="tst_single_outliers_sur_no_sidechains"):
pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
s = model.selection("name N or name CA or name C or name O")
model = model.select(s)
with open("%s_start.pdb" % prefix, 'w') as f:
f.write(model.model_as_pdb())
ci = cablam_idealization(model=model,
params=master_phil.extract().cablam_idealization,
log=sys.stdout)
with open("%s_end.pdb" % prefix, 'w') as f:
f.write(model.model_as_pdb())