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())