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 hydrogen atoms for planar X-H2 groups # Aim is to test if ideal dihedral angles are correct for any configuration #----------------------------------------------------------------------------- def exercise(pdb_str): 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(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) 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) # There are 90 H atoms in pdb_string, check if all of them are recognized assert (number_h_para == number_h), 'Not all H atoms are parameterized' for ih in h_distances: labels = atoms[ih].fetch_labels() assert (h_distances[ih] < 0.01), \ 'distance too large: %s atom: %s (%s) residue: %s ' \ % (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip()) pdb_str_00 = """ CRYST1 13.889 13.738 13.126 90.00 90.00 90.00 P 1 SCALE1 0.071999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.072791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076185 0.00000 ATOM 1 N ASN A 1 5.264 6.323 6.229 1.00 10.00 N ATOM 2 CA ASN A 1 6.108 7.341 6.843 1.00 10.00 C ATOM 3 C ASN A 1 5.944 8.680 6.132 1.00 10.00 C ATOM 4 O ASN A 1 5.516 8.733 4.979 1.00 10.00 O ATOM 5 CB ASN A 1 7.575 6.907 6.817 1.00 10.00 C ATOM 6 CG ASN A 1 7.857 5.750 7.754 1.00 10.00 C ATOM 7 OD1 ASN A 1 7.361 5.713 8.880 1.00 10.00 O ATOM 8 ND2 ASN A 1 8.659 4.797 7.294 1.00 10.00 N ATOM 9 HA ASN A 1 5.844 7.457 7.769 1.00 10.00 H ATOM 10 HB2 ASN A 1 7.806 6.628 5.917 1.00 10.00 H ATOM 11 HB3 ASN A 1 8.131 7.655 7.086 1.00 10.00 H ATOM 12 HD21 ASN A 1 8.849 4.119 7.787 1.00 10.00 H ATOM 13 HD22 ASN A 1 8.988 4.857 6.501 1.00 10.00 H """ pdb_str_01 = """ CRYST1 13.889 13.738 13.126 90.00 90.00 90.00 P 1 SCALE1 0.071999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.072791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076185 0.00000 ATOM 1 N ASN A 1 5.264 6.323 6.229 1.00 10.00 N ATOM 2 CA ASN A 1 6.108 7.341 6.843 1.00 10.00 C ATOM 3 C ASN A 1 5.944 8.680 6.132 1.00 10.00 C ATOM 4 O ASN A 1 5.516 8.733 4.979 1.00 10.00 O ATOM 5 CB ASN A 1 7.575 6.907 6.817 1.00 10.00 C ATOM 6 CG ASN A 1 7.857 5.750 7.754 1.00 10.00 C ATOM 7 OD1 ASN A 1 7.361 5.713 8.880 1.00 10.00 O ATOM 8 ND2 ASN A 1 8.659 4.797 7.294 1.00 10.00 N ATOM 9 HA ASN A 1 5.844 7.457 7.769 1.00 10.00 H ATOM 10 HB2 ASN A 1 7.806 6.628 5.917 1.00 10.00 H ATOM 11 HB3 ASN A 1 8.131 7.655 7.086 1.00 10.00 H ATOM 12 HD21 ASN A 1 8.988 4.857 6.501 1.00 10.00 H ATOM 13 HD22 ASN A 1 8.849 4.119 7.787 1.00 10.00 H """ pdb_str_02 = """ CRYST1 14.446 16.451 11.913 90.00 90.00 90.00 P 1 SCALE1 0.069223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.060787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.083942 0.00000 ATOM 1 N ARG A 50 6.725 11.631 6.607 1.00 10.00 N ATOM 2 CA ARG A 50 7.490 10.491 6.117 1.00 10.00 C ATOM 3 C ARG A 50 8.914 10.908 5.763 1.00 10.00 C ATOM 4 O ARG A 50 9.701 11.267 6.639 1.00 10.00 O ATOM 5 CB ARG A 50 6.806 9.870 4.897 1.00 10.00 C ATOM 6 CG ARG A 50 5.402 9.344 5.166 1.00 10.00 C ATOM 7 CD ARG A 50 5.419 8.122 6.072 1.00 10.00 C ATOM 8 NE ARG A 50 6.111 6.992 5.457 1.00 10.00 N ATOM 9 CZ ARG A 50 6.529 5.916 6.119 1.00 10.00 C ATOM 10 NH1 ARG A 50 6.327 5.812 7.427 1.00 10.00 N ATOM 11 NH2 ARG A 50 7.150 4.940 5.472 1.00 10.00 N ATOM 12 HA ARG A 50 7.540 9.818 6.814 1.00 10.00 H ATOM 13 HB2 ARG A 50 6.740 10.543 4.202 1.00 10.00 H ATOM 14 HB3 ARG A 50 7.345 9.127 4.582 1.00 10.00 H ATOM 15 HG2 ARG A 50 4.880 10.036 5.600 1.00 10.00 H ATOM 16 HG3 ARG A 50 4.990 9.092 4.325 1.00 10.00 H ATOM 17 HD2 ARG A 50 5.872 8.343 6.900 1.00 10.00 H ATOM 18 HD3 ARG A 50 4.505 7.851 6.254 1.00 10.00 H ATOM 19 HE ARG A 50 6.259 7.024 4.611 1.00 10.00 H ATOM 20 HH11 ARG A 50 5.925 6.440 7.855 1.00 10.00 H ATOM 21 HH12 ARG A 50 6.600 5.114 7.847 1.00 10.00 H ATOM 22 HH21 ARG A 50 7.283 5.003 4.624 1.00 10.00 H ATOM 23 HH22 ARG A 50 7.420 4.245 5.899 1.00 10.00 H """ pdb_str_03 = """ CRYST1 14.446 16.451 11.913 90.00 90.00 90.00 P 1 SCALE1 0.069223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.060787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.083942 0.00000 ATOM 1 N ARG A 50 6.725 11.631 6.607 1.00 10.00 N ATOM 2 CA ARG A 50 7.490 10.491 6.117 1.00 10.00 C ATOM 3 C ARG A 50 8.914 10.908 5.763 1.00 10.00 C ATOM 4 O ARG A 50 9.701 11.267 6.639 1.00 10.00 O ATOM 5 CB ARG A 50 6.806 9.870 4.897 1.00 10.00 C ATOM 6 CG ARG A 50 5.402 9.344 5.166 1.00 10.00 C ATOM 7 CD ARG A 50 5.419 8.122 6.072 1.00 10.00 C ATOM 8 NE ARG A 50 6.111 6.992 5.457 1.00 10.00 N ATOM 9 CZ ARG A 50 6.529 5.916 6.119 1.00 10.00 C ATOM 10 NH1 ARG A 50 6.327 5.812 7.427 1.00 10.00 N ATOM 11 NH2 ARG A 50 7.150 4.940 5.472 1.00 10.00 N ATOM 12 HA ARG A 50 7.540 9.818 6.814 1.00 10.00 H ATOM 13 HB2 ARG A 50 6.740 10.543 4.202 1.00 10.00 H ATOM 14 HB3 ARG A 50 7.345 9.127 4.582 1.00 10.00 H ATOM 15 HG2 ARG A 50 4.880 10.036 5.600 1.00 10.00 H ATOM 16 HG3 ARG A 50 4.990 9.092 4.325 1.00 10.00 H ATOM 17 HD2 ARG A 50 5.872 8.343 6.900 1.00 10.00 H ATOM 18 HD3 ARG A 50 4.505 7.851 6.254 1.00 10.00 H ATOM 19 HE ARG A 50 6.259 7.024 4.611 1.00 10.00 H ATOM 21 HH11 ARG A 50 6.600 5.114 7.847 1.00 10.00 H ATOM 20 HH12 ARG A 50 5.925 6.440 7.855 1.00 10.00 H ATOM 23 HH21 ARG A 50 7.420 4.245 5.899 1.00 10.00 H ATOM 22 HH22 ARG A 50 7.283 5.003 4.624 1.00 10.00 H """ pdb_str_04 = """ CRYST1 14.547 13.375 15.374 90.00 90.00 90.00 P 1 SCALE1 0.068743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.074766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.065045 0.00000 ATOM 1 N GLN A 70 6.510 6.937 4.976 1.00 10.00 N ATOM 2 CA GLN A 70 6.727 6.312 6.275 1.00 10.00 C ATOM 3 C GLN A 70 5.406 6.141 7.018 1.00 10.00 C ATOM 4 O GLN A 70 4.992 5.022 7.317 1.00 10.00 O ATOM 5 CB GLN A 70 7.700 7.144 7.113 1.00 10.00 C ATOM 6 CG GLN A 70 8.079 6.506 8.440 1.00 10.00 C ATOM 7 CD GLN A 70 9.104 7.319 9.206 1.00 10.00 C ATOM 8 OE1 GLN A 70 9.517 8.392 8.767 1.00 10.00 O ATOM 9 NE2 GLN A 70 9.521 6.810 10.360 1.00 10.00 N ATOM 10 HA GLN A 70 7.116 5.433 6.144 1.00 10.00 H ATOM 11 HB2 GLN A 70 8.516 7.275 6.605 1.00 10.00 H ATOM 12 HB3 GLN A 70 7.292 8.003 7.304 1.00 10.00 H ATOM 13 HG2 GLN A 70 7.287 6.427 8.993 1.00 10.00 H ATOM 14 HG3 GLN A 70 8.456 5.628 8.273 1.00 10.00 H ATOM 15 HE21 GLN A 70 9.210 6.057 10.635 1.00 10.00 H ATOM 16 HE22 GLN A 70 10.103 7.233 10.832 1.00 10.00 H """ pdb_str_05 = """ CRYST1 14.547 13.375 15.374 90.00 90.00 90.00 P 1 SCALE1 0.068743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.074766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.065045 0.00000 ATOM 1 N GLN A 70 6.510 6.937 4.976 1.00 10.00 N ATOM 2 CA GLN A 70 6.727 6.312 6.275 1.00 10.00 C ATOM 3 C GLN A 70 5.406 6.141 7.018 1.00 10.00 C ATOM 4 O GLN A 70 4.992 5.022 7.317 1.00 10.00 O ATOM 5 CB GLN A 70 7.700 7.144 7.113 1.00 10.00 C ATOM 6 CG GLN A 70 8.079 6.506 8.440 1.00 10.00 C ATOM 7 CD GLN A 70 9.104 7.319 9.206 1.00 10.00 C ATOM 8 OE1 GLN A 70 9.517 8.392 8.767 1.00 10.00 O ATOM 9 NE2 GLN A 70 9.521 6.810 10.360 1.00 10.00 N ATOM 10 HA GLN A 70 7.116 5.433 6.144 1.00 10.00 H ATOM 11 HB2 GLN A 70 8.516 7.275 6.605 1.00 10.00 H ATOM 12 HB3 GLN A 70 7.292 8.003 7.304 1.00 10.00 H ATOM 13 HG2 GLN A 70 7.287 6.427 8.993 1.00 10.00 H ATOM 14 HG3 GLN A 70 8.456 5.628 8.273 1.00 10.00 H ATOM 16 HE21 GLN A 70 10.103 7.233 10.832 1.00 10.00 H ATOM 15 HE22 GLN A 70 9.210 6.057 10.635 1.00 10.00 H """ pdb_list = [pdb_str_00, pdb_str_01, pdb_str_02, pdb_str_03, pdb_str_04, pdb_str_05] pdb_list_name = ['pdb_str_00', 'pdb_str_01', 'pdb_str_02', 'pdb_str_03', 'pdb_str_04', 'pdb_str_05'] def run(): for pdb_str, str_name in zip(pdb_list,pdb_list_name): #print 'pdb_string:', str_name, 'use_ideal_bonds_angles =', True exercise(pdb_str=pdb_str) if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))