def run_test1(): ''' Test if iselection for ligand PG5 (chain A resseq 201) is correct. ''' pdb_fname = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/pdbs/one_chain_ligand_water.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(pdb_fname) model = mmtbx.model.manager(model_input = pdb_inp) model.set_log(null_out()) params = iotbx.phil.parse( input_string=master_params_str, process_includes=True).extract() # do not place H atoms for this test #params.validate_ligands.place_hydrogens = False vl_manager = validate_ligands.manager( model = model, fmodel = None, params = params.validate_ligands, log = null_out()) vl_manager.run() tst_get_ligands(vl_manager = vl_manager) tst_get_overlaps(vl_manager = vl_manager)
def run_test2(): ''' Test - occupancy determination for ligands - adp determination for ligands and neighbors Tests are combined to decrease computing time (restraints manager is slow). ''' pdb_fname = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/pdbs/two_chains_ligand_water.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(pdb_fname) model = mmtbx.model.manager(model_input = pdb_inp) model.set_log(null_out()) params = iotbx.phil.parse( input_string=master_params_str, process_includes=True).extract() vl_manager = validate_ligands.manager( model = model, fmodel = None, params = params.validate_ligands, log = null_out) vl_manager.run() tst_get_occupancies(vl_manager = vl_manager) tst_get_adps(vl_manager = vl_manager)
def tst_02(): # Test for remove_clashes import mmtbx.model from mmtbx.clashes import remove_clashes import iotbx.pdb import sys pdb_inp = iotbx.pdb.input(lines=pdb_poor.splitlines(), source_info='None') model = mmtbx.model.manager(model_input=pdb_inp, ) model.set_log(log=null_out()) print "\n", "-" * 79 print " Summary of input model statistics " print "-" * 79 model.get_restraints_manager() geometry = model.geometry_statistics() geometry.show(log=sys.stdout) rc = remove_clashes(model=model) print "\n", "-" * 79 print "Starting residues: %d " % ( rc.model.get_hierarchy().overall_counts().n_residues) print "Side-chains removed: %d Residues removed: %d" % ( rc.side_chains_removed, rc.residues_removed) print "Final residues: %d " % ( rc.new_model.get_hierarchy().overall_counts().n_residues) rc.new_model.set_log(log=null_out()) rc.new_model.get_restraints_manager() new_geometry = rc.new_model.geometry_statistics() new_geometry.show(log=sys.stdout) assert rc.side_chains_removed == 1 assert rc.residues_removed == 0
def run_test2(): ''' Test - occupancy determination for ligands - adp determination for ligands and neighbors Tests are combined to decrease computing time (restraints manager is slow). ''' pdb_inp = iotbx.pdb.input(lines=pdb_str_2.split("\n"), source_info=None) model = mmtbx.model.manager(model_input=pdb_inp) model.set_log(null_out()) params = iotbx.phil.parse(input_string=master_params_str, process_includes=True).extract() vl_manager = validate_ligands.manager(model=model, fmodel=None, params=params.validate_ligands, log=null_out) vl_manager.run() tst_get_occupancies(vl_manager=vl_manager) tst_get_adps(vl_manager=vl_manager)
def run_test1(): ''' Test if iselection for ligand PG5 (chain A resseq 201) is correct. ''' pdb_inp = iotbx.pdb.input(lines=pdb_str_1.split("\n"), source_info=None) model = mmtbx.model.manager(model_input=pdb_inp) model.set_log(null_out()) params = iotbx.phil.parse(input_string=master_params_str, process_includes=True).extract() # do not place H atoms for this test #params.validate_ligands.place_hydrogens = False vl_manager = validate_ligands.manager(model=model, fmodel=None, params=params.validate_ligands, log=null_out()) vl_manager.run() tst_get_ligands(vl_manager=vl_manager) tst_get_overlaps(vl_manager=vl_manager)