def exercise_1(): pdb_inp = iotbx.pdb.input(lines=flex.std_string(pdb_str_1.splitlines()), source_info=None) model = mmtbx.model.manager(model_input=pdb_inp) model.process(make_restraints=True) grm = model.get_restraints_manager().geometry pdb_hierarchy = model.get_hierarchy() sites_cart = model.get_sites_cart() # c-beta restraints are added by default!!! assert len(grm.get_c_beta_torsion_proxies()) == 4 #test global selection and removing c-beta restraints tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR") tst_iselection = tst_boolsel.iselection() #test global selection grm2 = grm.select(iselection=tst_iselection) assert len(grm2.get_c_beta_torsion_proxies()) == 2 grm2 = grm.select(selection=tst_boolsel) assert len(grm2.get_c_beta_torsion_proxies()) == 2 #remove a selection grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection) assert len(grm.get_c_beta_torsion_proxies()) == 2 #add a selection grm.remove_c_beta_torsion_restraints_in_place() assert len(grm.get_c_beta_torsion_proxies()) == 0 c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies( pdb_hierarchy, selection=tst_iselection, sigma=2.5) assert len(c_beta_torsion_proxies) == 2
def exercise_4(): """ Testing UNK to be equivalent to ALA """ pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_7).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size() == 10 assert c_beta_skip == {} # pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_7.replace( "UNK", "ALA")).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size() == 10 assert c_beta_skip == {}
def exercise_1(): processed_pdb_file = pdb_interpretation.process( mon_lib_srv = server.server(), ener_lib = server.ener_lib(), raw_records = flex.std_string(pdb_str_1.splitlines()), strict_conflict_handling = True, force_symmetry = True, log = None) grm = processed_pdb_file.geometry_restraints_manager() pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy sites_cart = pdb_hierarchy.atoms().extract_xyz() # c-beta restraints are added by default!!! assert len(grm.get_c_beta_torsion_proxies()) == 4 #test global selection and removing c-beta restraints tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR") tst_iselection = tst_boolsel.iselection() #test global selection grm2 = grm.select(iselection=tst_iselection) assert len(grm2.get_c_beta_torsion_proxies()) == 2 grm2 = grm.select(selection=tst_boolsel) assert len(grm2.get_c_beta_torsion_proxies()) == 2 #remove a selection grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection) assert len(grm.get_c_beta_torsion_proxies()) == 2 #add a selection grm.remove_c_beta_torsion_restraints_in_place() assert len(grm.get_c_beta_torsion_proxies()) == 0 c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies( pdb_hierarchy, selection=tst_iselection, sigma=2.5) assert len(c_beta_torsion_proxies) == 2
def exercise_3(): """ Testing d-peptide """ pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_5).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", [])) == 1 assert len(c_beta_skip.get("-ve", [])) == 0 pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_6).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", [])) == 0 assert len(c_beta_skip.get("-ve", [])) == 1
def exercise_4(): """ Testing UNK to be equivalent to ALA """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_7).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size()==10 assert c_beta_skip == {} # pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_7.replace("UNK","ALA")).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size()==10 assert c_beta_skip == {}
def exercise_2(): """ Testing with ACs """ pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_2).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2 pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_3).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 4 pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str_4).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2
def exercise_3(): """ Testing d-peptide """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_5).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", []))==1 assert len(c_beta_skip.get("-ve", []))==0 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_6).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", []))==0 assert len(c_beta_skip.get("-ve", []))==1
def exercise_2(): """ Testing with ACs """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_2).construct_hierarchy() c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_3).construct_hierarchy() c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 4 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_4).construct_hierarchy() c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2