from __future__ import absolute_import, division, print_function import time import mmtbx.model import iotbx.pdb from libtbx.utils import null_out from six.moves import zip #----------------------------------------------------------------------------- # This test checks the parameterization of H/D atoms in models containing # both H and D atoms #----------------------------------------------------------------------------- def exercise(pdb_str): params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.use_neutron_distances = True pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(pdb_interpretation_params=params, make_restraints=True) pdb_hierarchy = model.get_hierarchy() sites_cart = model.get_sites_cart() atoms = pdb_hierarchy.atoms() model.setup_riding_h_manager() riding_h_manager = model.get_riding_h_manager() h_parameterization = riding_h_manager.h_parameterization diagnostics = riding_h_manager.diagnostics( sites_cart = sites_cart, threshold = 0.05) h_distances = diagnostics.h_distances number_h = model.get_hd_selection().count(True) number_h_para = len(h_parameterization) - h_parameterization.count(None) if (pdb_str != pdb_str_02): assert (number_h_para == number_h), 'Not all H atoms are parameterized' # For each H atom, check if distance between computed H and that in input model is # not too large for ih in h_distances: labels = atoms[ih].fetch_labels() assert (h_distances[ih] < 0.1), \ 'distance too large: %s atom: %s (%s) residue: %s ' \ % (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip()) #for type1, type2 in zip(type_list, type_list_known): # assert (type1 == type2) pdb_str_00 = """\ CRYST1 14.815 23.523 21.068 90.00 90.00 90.00 P 1 SCALE1 0.067499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.042512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.047465 0.00000 ATOM 1 N ARG A 161 5.235 16.231 12.444 1.00 7.68 N ATOM 2 CA ARG A 161 6.309 16.550 13.364 1.00 9.47 C ATOM 3 C ARG A 161 7.140 17.751 12.856 1.00 10.84 C ATOM 4 O ARG A 161 7.669 18.523 13.658 1.00 11.74 O ATOM 5 CB ARG A 161 7.186 15.310 13.584 1.00 13.82 C ATOM 6 CG ARG A 161 6.357 14.097 14.068 1.00 16.56 C ATOM 7 CD ARG A 161 7.166 13.049 14.764 1.00 11.41 C ATOM 8 NE ARG A 161 6.350 11.919 15.227 1.00 18.74 N ATOM 9 CZ ARG A 161 6.279 10.732 14.648 1.00 12.24 C ATOM 10 NH1 ARG A 161 6.967 10.428 13.537 1.00 11.51 N ATOM 11 NH2 ARG A 161 5.503 9.814 15.194 1.00 16.77 N ATOM 12 DE ARG A 161 5.791 12.059 16.068 1.00 22.49 D ATOM 13 DH11 ARG A 161 7.580 11.112 13.087 1.00 13.81 D ATOM 14 DH21 ARG A 161 5.000 10.019 16.043 1.00 20.13 D ATOM 15 HA ARG A 161 5.875 16.826 14.327 1.00 11.37 H ATOM 16 HB2 ARG A 161 7.666 15.039 12.643 1.00 16.58 H ATOM 17 HB3 ARG A 161 7.940 15.534 14.339 1.00 16.58 H ATOM 18 HG2 ARG A 161 5.598 14.449 14.766 1.00 19.87 H ATOM 19 HG3 ARG A 161 5.878 13.631 13.205 1.00 19.87 H ATOM 20 HD2 ARG A 161 7.917 12.663 14.076 1.00 13.70 H ATOM 21 HD3 ARG A 161 7.651 13.492 15.635 1.00 13.70 H ATOM 22 HH12AARG A 161 6.870 9.515 13.114 0.26 13.81 H ATOM 23 HH22AARG A 161 5.423 8.890 14.766 0.54 20.13 H ATOM 24 DH12BARG A 161 6.870 9.515 13.114 0.74 13.81 D ATOM 25 DH22BARG A 161 5.423 8.890 14.766 0.46 20.13 D TER ATOM 26 N GLY B 2 12.057 9.922 8.317 1.00 27.73 N ATOM 27 CA GLY B 2 11.194 10.314 7.218 1.00 26.03 C ATOM 28 C GLY B 2 9.719 10.240 7.559 1.00 24.25 C ATOM 29 O GLY B 2 9.041 11.263 7.653 1.00 20.41 O ATOM 30 N ILE B 3 9.220 9.022 7.744 1.00 27.73 N ATOM 31 CA ILE B 3 7.818 8.811 8.076 1.00 26.03 C ATOM 32 C ILE B 3 7.565 9.227 9.520 1.00 24.25 C ATOM 33 O ILE B 3 8.276 8.806 10.431 1.00 20.41 O ATOM 34 CB ILE B 3 7.404 7.345 7.845 1.00 27.04 C ATOM 35 CG1 ILE B 3 7.452 7.006 6.354 1.00 28.51 C ATOM 36 CG2 ILE B 3 6.009 7.089 8.398 1.00 26.88 C ATOM 37 CD1 ILE B 3 7.628 5.530 6.070 1.00 28.93 C ATOM 38 DA ILE B 3 7.203 9.439 7.432 1.00 26.09 D ATOM 39 DB ILE B 3 8.109 6.700 8.370 1.00 25.53 D ATOM 40 DD11 ILE B 3 8.556 5.190 6.530 1.00 27.61 D ATOM 41 DG12 ILE B 3 6.516 7.323 5.893 1.00 27.88 D ATOM 42 D AILE B 3 9.763 8.161 7.671 0.96 27.94 D ATOM 43 DD12AILE B 3 7.670 5.378 4.992 0.43 28.45 D ATOM 44 DD13AILE B 3 6.783 4.984 6.490 0.86 28.24 D ATOM 45 DG13AILE B 3 8.288 7.536 5.896 0.69 28.21 D ATOM 46 DG21AILE B 3 5.354 7.909 8.103 0.96 27.70 D ATOM 47 DG22AILE B 3 6.062 7.027 9.485 0.78 27.54 D ATOM 48 DG23AILE B 3 5.635 6.149 7.993 0.81 27.54 D ATOM 49 H BILE B 3 9.763 8.161 7.671 0.04 27.94 H ATOM 50 HG13BILE B 3 8.288 7.536 5.896 0.31 28.21 H ATOM 51 HG21BILE B 3 5.354 7.909 8.103 0.04 27.70 H ATOM 52 HG22BILE B 3 6.062 7.027 9.485 0.22 27.54 H ATOM 53 HG23BILE B 3 5.635 6.149 7.993 0.19 27.54 H ATOM 54 HD12BILE B 3 7.670 5.378 4.992 0.57 28.45 H ATOM 55 HD13BILE B 3 6.783 4.984 6.490 0.14 28.24 H TER """ pdb_str_01 = """ CRYST1 14.630 14.210 14.547 90.00 90.00 90.00 P 1 SCALE1 0.068353 0.000000 0.000000 0.00000 SCALE2 0.000000 0.070373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.068743 0.00000 ATOM 1387 N ILE A 63 21.154 -27.868 -37.969 1.00 22.34 N ATOM 1388 CA ILE A 63 21.399 -26.570 -38.585 1.00 21.95 C ATOM 1389 C ILE A 63 20.231 -25.648 -38.320 1.00 23.15 C ATOM 1390 O ILE A 63 19.079 -25.992 -38.576 1.00 24.15 O ATOM 1391 CB ILE A 63 21.593 -26.710 -40.099 1.00 23.08 C ATOM 1392 CG1 ILE A 63 22.822 -27.578 -40.395 1.00 23.79 C ATOM 1393 CG2 ILE A 63 21.745 -25.345 -40.744 1.00 23.03 C ATOM 1394 CD1 ILE A 63 22.871 -28.137 -41.811 1.00 25.99 C ATOM 1397 DA AILE A 63 22.287 -26.154 -38.157 0.44 22.47 D ATOM 1398 HA BILE A 63 22.287 -26.154 -38.157 0.56 22.47 H ATOM 1399 DB AILE A 63 20.719 -27.170 -40.493 0.99 23.45 D ATOM 1400 HB BILE A 63 20.719 -27.170 -40.493 0.01 23.45 H ATOM 1401 DG12AILE A 63 23.709 -26.976 -40.253 0.54 23.93 D ATOM 1402 HG12BILE A 63 23.709 -26.976 -40.253 0.46 23.93 H ATOM 1403 DG13AILE A 63 22.850 -28.402 -39.700 0.65 23.97 D ATOM 1404 HG13BILE A 63 22.850 -28.402 -39.700 0.35 23.97 H ATOM 1405 HG21 ILE A 63 21.066 -24.629 -40.306 1.00 22.80 H ATOM 1406 DG22AILE A 63 21.541 -25.426 -41.799 0.51 22.86 D ATOM 1407 HG22BILE A 63 21.541 -25.426 -41.799 0.49 22.86 H ATOM 1408 DG23 ILE A 63 22.758 -25.015 -40.597 1.00 23.40 D ATOM 1409 DD11AILE A 63 21.935 -28.641 -42.033 0.67 24.71 D ATOM 1410 HD11BILE A 63 21.935 -28.641 -42.033 0.33 24.71 H ATOM 1411 DD12AILE A 63 23.680 -28.839 -41.891 0.44 24.81 D ATOM 1412 HD12BILE A 63 23.680 -28.839 -41.891 0.56 24.81 H ATOM 1413 DD13AILE A 63 23.024 -27.344 -42.516 0.90 24.27 D ATOM 1414 HD13BILE A 63 23.024 -27.344 -42.516 0.10 24.27 H """ pdb_str_02 = """ CRYST1 15.636 16.098 18.562 90.00 90.00 90.00 P 1 SCALE1 0.063955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.062120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.053874 0.00000 ATOM 517 N GLU A 30 4.726 39.084 1.924 1.00 18.34 N ATOM 519 C GLU A 30 6.556 40.664 2.421 1.00 20.67 C ATOM 533 D GLU A 31 5.082 40.344 3.856 1.00 21.59 D ATOM 534 N AGLU A 31 5.986 40.754 3.619 0.29 20.27 N ATOM 535 CA AGLU A 31 6.623 41.467 4.722 0.29 21.76 C ATOM 536 C AGLU A 31 7.429 40.530 5.617 0.29 20.64 C ATOM 548 N CGLU A 31 5.986 40.753 3.620 0.71 20.17 N ATOM 549 CA CGLU A 31 6.621 41.462 4.726 0.71 21.77 C ATOM 550 C CGLU A 31 7.488 40.540 5.574 0.71 20.61 C """ pdb_list = [pdb_str_00, pdb_str_01, pdb_str_02] pdb_list_name = ['pdb_str_00', 'pdb_str_01', 'pdb_str_02'] #type_list_known = ['2tetra', '2tetra', 'alg1b', '3neigbs', '3neigbs', # '3neigbs', 'alg1b', '2tetra', '2tetra', '2tetra', '2tetra', 'alg1b', # '3neigbs', '2tetra', '2tetra', '3neigbs', '2tetra', '2tetra', # 'flat_2neigbs', 'alg1b', '3neigbs', '2tetra', '2tetra', 'alg1b', # '2tetra', '2tetra', 'alg1b', '2tetra', '2tetra', 'alg1b', '3neigbs', # 'prop', 'prop', 'prop', 'prop', 'prop', 'prop', '3neigbs', 'prop', # 'prop', 'prop', 'prop', 'prop', 'prop', '3neigbs', '2tetra', '2tetra', # 'alg1b', '2tetra', '2tetra', 'alg1b', 'flat_2neigbs'] def run(): for pdb_str, str_name in zip(pdb_list,pdb_list_name): exercise(pdb_str=pdb_str) if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))