from __future__ import absolute_import, division, print_function import time from mmtbx.validation import validate_ligands from mmtbx.validation.validate_ligands import master_params_str import mmtbx.model import iotbx.pdb from libtbx.utils import null_out import libtbx.load_env from libtbx.test_utils import approx_equal import os.path from six.moves import zip def tst_get_adps(vl_manager): ''' Test getting ADPs of ligands and surrounding atoms ''' n_iso_answer = (0,0,0,0,0) n_aniso_answer = (9,9,5,5,6) #print(vl_manager) for id_tuple, ligand_dict in vl_manager.items(): #print(ligand_dict) for altloc, lr in ligand_dict.items(): adps = lr.get_adps() id_str = lr.id_str if (id_str.strip() == 'A BEN 2 A'): assert(adps.n_iso == 0) assert(adps.n_aniso == 9) assert(adps.n_above_100 == 0) assert approx_equal([adps.b_min, adps.b_max, adps.b_mean], [4.7, 8.1, 6.0], eps=0.1) assert(approx_equal( [adps.b_min_within, adps.b_max_within, adps.b_mean_within], [6.1,12.9,7.8], eps=0.1)) if (id_str.strip() == 'A BEN 2 B'): assert(adps.n_iso == 0) assert(adps.n_aniso == 9) assert(adps.n_above_100 == 0) assert approx_equal([adps.b_min, adps.b_max, adps.b_mean], [5.1, 8.2, 6.4], eps=0.1) assert(approx_equal( [adps.b_min_within, adps.b_max_within, adps.b_mean_within], [6.1,12.9,7.8], eps=0.1)) if (id_str.strip() == 'A SO4 3'): assert(adps.n_iso == 5) assert(adps.n_aniso == 0) assert(adps.n_above_100 == 0) assert approx_equal([adps.b_min, adps.b_max, adps.b_mean], [7.4,13.1,10.2], eps=0.1) assert(approx_equal( [adps.b_min_within, adps.b_max_within, adps.b_mean_within], [6.3, 11.1, 7.8], eps=0.1)) if (id_str.strip() == 'A SO4 4'): assert(adps.n_iso == 0) assert(adps.n_aniso == 5) assert(adps.b_min_within is None) assert(adps.n_above_100 == 0) assert approx_equal([adps.b_min, adps.b_max, adps.b_mean], [10.3,14.6,12.3], eps=0.1) if (id_str.strip() == 'A GOL 5'): assert(adps.n_iso == 6) assert(adps.n_aniso == 0) assert(adps.b_min_within is None) assert(adps.n_above_100 == 3) assert approx_equal([adps.b_min, adps.b_max, adps.b_mean], [58.7,114.9,96.9], eps=0.1) 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, stop_for_unknowns=False) model.process(make_restraints=True) 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 tst_get_ligands(vl_manager): ''' Test finding ligand ''' assert (len(vl_manager) == 1) # test iselection for id_tuple, ligand_dict in vl_manager.items(): assert (id_tuple == ('', 'A', ' 201')) lr = ligand_dict[''] assert (list(lr.isel) == [84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95]) def tst_get_overlaps(vl_manager): ''' Test nonbonded overlaps ''' for id_tuple, ligand_dict in vl_manager.items(): for altloc, lr in ligand_dict.items(): clashes_result = lr.get_overlaps() assert(clashes_result.n_clashes == 5) assert approx_equal(clashes_result.clashscore, 31.6, eps=1.0) # anaconda #(['pdb=" HE3 MET A 107 "', 'pdb=" H81 PG5 A 201 "'], 17, 54, 2.0370952358689647, 2.44, '', None), #(['pdb=" CE MET A 107 "', 'pdb=" C8 PG5 A 201 "'], 15, 34, 2.946989989803154, 3.4, '', None), #(['pdb=" CE MET A 107 "', 'pdb=" H83 PG5 A 201 "'], 15, 56, 2.4839921497460486, 2.92, '', None) # # MAC #(['pdb=" CE MET A 107 "', 'pdb=" C8 PG5 A 201 "'], 16, 35, 2.946989989803154, 3.4, '', None), #(['pdb=" HE3 MET A 107 "', 'pdb=" H83 PG5 A 201 "'], 18, 57, 2.026073542594147, 2.44, '', None), #(['pdb=" CE MET A 107 "', 'pdb=" H81 PG5 A 201 "'], 16, 55, 2.4973179613337146, 2.92, '', None) # # Readyset gives different names to H atoms. def tst_get_occupancies(vl_manager): ''' Test occupancy determination ''' assert (len(vl_manager) == 4) id_tuple_answer = [('', 'A', ' 2'), ('', 'A', ' 3'), ('', 'A', ' 4'), ('', 'A', ' 5')] ligand_dict_length_answer = [2, 1, 1, 1] occupancy_answer = [] # TODO six zip me for id_tuple, id_tuple_answer, length_answer in zip(vl_manager.keys(), id_tuple_answer, ligand_dict_length_answer): ligand_dict = vl_manager[id_tuple] assert (id_tuple == id_tuple_answer) assert (len(ligand_dict) == length_answer) for altloc, lr in ligand_dict.items(): occs = lr.get_occupancies() id_str = lr.id_str if (id_str.strip() == 'A BEN 2 A'): assert(occs.occ_mean == 0.56) if (id_str.strip() == 'A BEN 2 B'): assert(occs.occ_mean == 0.44) if (id_str.strip() == 'A SO4 3'): assert(occs.occ_mean == 0.65) if (id_str.strip() == 'A SO4 4'): assert(occs.occ_mean == 0.48) if (id_str.strip() == 'A GOL 5'): assert(occs.occ_mean == 0.67) 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 run(): run_test1() run_test2() if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f" % (time.time()-t0))