from __future__ import absolute_import, division, print_function import time import iotbx.pdb import mmtbx.model from cctbx.array_family import flex from libtbx.utils import null_out from libtbx.test_utils import approx_equal from six.moves import zip from six.moves import range #----------------------------------------------------------------------------- # This finite difference test checks transformation of riding H gradients # for all amino acids, one by one #----------------------------------------------------------------------------- # def exercise(pdb_str, eps): 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) geometry_restraints = model.restraints_manager.geometry xray_structure = model.get_xray_structure() model.setup_riding_h_manager() riding_h_manager = model.get_riding_h_manager() riding_h_manager.idealize_riding_h_positions(xray_structure = xray_structure) sites_cart = xray_structure.sites_cart() g_analytical = geometry_restraints.energies_sites( sites_cart = sites_cart, compute_gradients = True).gradients hd_selection = xray_structure.hd_selection() g_analytical_reduced = riding_h_manager.gradients_reduced_cpp( gradients = g_analytical, sites_cart = sites_cart, hd_selection = hd_selection) # ex = [eps,0,0] ey = [0,eps,0] ez = [0,0,eps] g_fd = flex.vec3_double() for i_site in range(sites_cart.size()): g_fd_i = [] for e in [ex,ey,ez]: ts = [] for sign in [-1,1]: sites_cart_ = sites_cart.deep_copy() xray_structure_ = xray_structure.deep_copy_scatterers() sites_cart_[i_site] = [ sites_cart_[i_site][j]+e[j]*sign for j in range(3)] xray_structure_.set_sites_cart(sites_cart_) # after shift, recalculate H position riding_h_manager.idealize_riding_h_positions( xray_structure=xray_structure_) sites_cart_ = xray_structure_.sites_cart() ts.append(geometry_restraints.energies_sites( sites_cart = sites_cart_, compute_gradients = False).target) g_fd_i.append((ts[1]-ts[0])/(2*eps)) g_fd.append(g_fd_i) g_fd_reduced = g_fd.select(~hd_selection) for g1, g2 in zip(g_analytical_reduced, g_fd_reduced): assert approx_equal(g1,g2, 1.e-4) #Alanine pdb_str_01 = """ CRYST1 11.863 12.347 12.550 90.00 90.00 90.00 P 1 SCALE1 0.084296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.080991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.079681 0.00000 ATOM 1 N ALA B 84 7.017 5.016 7.287 1.00 10.00 N ATOM 2 CA ALA B 84 5.784 5.706 7.445 1.00 10.00 C ATOM 3 C ALA B 84 5.129 5.694 6.011 1.00 10.00 C ATOM 4 O ALA B 84 5.714 5.812 4.900 1.00 10.00 O ATOM 5 CB ALA B 84 6.261 7.426 7.444 1.00 10.00 C ATOM 6 HA ALA B 84 5.269 5.787 7.982 1.00 10.00 H ATOM 7 HB1 ALA B 84 5.337 8.016 7.304 1.00 10.00 H ATOM 8 HB2 ALA B 84 6.549 7.313 8.459 1.00 10.00 H ATOM 9 HB3 ALA B 84 6.616 7.667 6.795 1.00 10.00 H """ # Arginine: 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 6.642 11.452 6.691 1.00 10.00 N ATOM 2 CA ARG A 50 7.570 10.240 6.682 1.00 10.00 C ATOM 3 C ARG A 50 9.005 10.280 6.707 1.00 10.00 C ATOM 4 O ARG A 50 9.602 11.108 6.810 1.00 10.00 O ATOM 5 CB ARG A 50 6.962 9.371 5.075 1.00 10.00 C ATOM 6 CG ARG A 50 5.382 9.275 4.806 1.00 10.00 C ATOM 7 CD ARG A 50 4.830 7.928 6.084 1.00 10.00 C ATOM 8 NE ARG A 50 5.434 6.841 5.374 1.00 10.00 N ATOM 9 CZ ARG A 50 6.450 6.116 6.035 1.00 10.00 C ATOM 10 NH1 ARG A 50 7.392 6.694 6.803 1.00 10.00 N ATOM 11 NH2 ARG A 50 6.898 5.026 5.305 1.00 10.00 N ATOM 12 HA ARG A 50 6.817 9.405 7.203 1.00 10.00 H ATOM 13 HB2 ARG A 50 7.451 9.961 4.409 1.00 10.00 H ATOM 14 HB3 ARG A 50 7.391 8.588 5.297 1.00 10.00 H ATOM 15 HG2 ARG A 50 5.016 10.089 5.174 1.00 10.00 H ATOM 16 HG3 ARG A 50 5.385 9.031 4.141 1.00 10.00 H ATOM 17 HD2 ARG A 50 5.268 8.147 6.643 1.00 10.00 H ATOM 18 HD3 ARG A 50 3.909 8.226 5.899 1.00 10.00 H ATOM 19 HE ARG A 50 5.208 6.478 4.962 1.00 10.00 H ATOM 20 HH11 ARG A 50 6.970 7.301 7.302 1.00 10.00 H ATOM 21 HH12 ARG A 50 7.866 6.356 7.069 1.00 10.00 H ATOM 22 HH21 ARG A 50 6.604 4.626 5.005 1.00 10.00 H ATOM 23 HH22 ARG A 50 7.522 4.396 5.734 1.00 10.00 H """ #Asparagine pdb_str_03 = """ 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 35 5.108 6.598 6.668 1.00 10.00 N ATOM 2 CA ASN A 35 6.071 7.634 7.159 1.00 10.00 C ATOM 3 C ASN A 35 6.113 8.702 6.163 1.00 10.00 C ATOM 4 O ASN A 35 5.556 8.558 4.817 1.00 10.00 O ATOM 5 CB ASN A 35 7.439 6.520 6.538 1.00 10.00 C ATOM 6 CG ASN A 35 7.597 5.465 7.487 1.00 10.00 C ATOM 7 OD1 ASN A 35 6.743 4.980 8.032 1.00 10.00 O ATOM 8 ND2 ASN A 35 8.841 4.827 7.318 1.00 10.00 N ATOM 9 HA ASN A 35 6.387 7.612 7.973 1.00 10.00 H ATOM 10 HB2 ASN A 35 7.452 6.464 5.548 1.00 10.00 H ATOM 11 HB3 ASN A 35 8.153 7.444 6.485 1.00 10.00 H ATOM 12 HD21 ASN A 35 9.022 4.464 7.804 1.00 10.00 H ATOM 13 HD22 ASN A 35 9.521 5.284 7.192 1.00 10.00 H """ # Aspartic Acid pdb_str_04 = """ CRYST1 14.178 13.514 11.978 90.00 90.00 90.00 P 1 SCALE1 0.070532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.073997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.083486 0.00000 ATOM 1 N ASP A 121 4.844 6.380 4.967 1.00 10.00 N ATOM 2 CA ASP A 121 6.237 6.469 5.750 1.00 10.00 C ATOM 3 C ASP A 121 5.959 7.525 7.138 1.00 10.00 C ATOM 4 O ASP A 121 5.683 8.452 6.797 1.00 10.00 O ATOM 5 CB ASP A 121 7.582 6.234 5.277 1.00 10.00 C ATOM 6 CG ASP A 121 8.550 6.163 6.136 1.00 10.00 C ATOM 7 OD1 ASP A 121 9.035 5.174 6.337 1.00 10.00 O ATOM 8 OD2 ASP A 121 9.115 7.253 6.644 1.00 10.00 O ATOM 9 HA ASP A 121 6.173 5.442 6.266 1.00 10.00 H ATOM 10 HB2 ASP A 121 7.509 5.748 4.630 1.00 10.00 H ATOM 11 HB3 ASP A 121 7.714 7.340 4.588 1.00 10.00 H """ # Cysteine pdb_str_05 = """ CRYST1 12.081 11.399 14.639 90.00 90.00 90.00 P 1 SCALE1 0.082775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.087727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.068311 0.00000 ATOM 1 N CYS A 96 4.823 5.221 7.409 1.00 10.00 N ATOM 2 CA CYS A 96 6.273 5.028 7.456 1.00 10.00 C ATOM 3 C CYS A 96 6.932 5.026 9.008 1.00 10.00 C ATOM 4 O CYS A 96 7.163 5.942 9.454 1.00 10.00 O ATOM 5 CB CYS A 96 6.905 6.223 6.813 1.00 10.00 C ATOM 6 SG CYS A 96 6.265 6.407 5.142 1.00 10.00 S ATOM 7 HA CYS A 96 6.714 4.104 6.960 1.00 10.00 H ATOM 8 HB2 CYS A 96 6.849 7.034 6.999 1.00 10.00 H ATOM 9 HB3 CYS A 96 8.130 6.106 6.575 1.00 10.00 H ATOM 10 HG CYS A 96 6.882 7.238 4.630 1.00 10.00 H """ # Glutamine pdb_str_06 = """ 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 6.344 7.129 5.035 1.00 10.00 N ATOM 2 CA GLN A 70 6.644 6.208 6.336 1.00 10.00 C ATOM 3 C GLN A 70 5.352 6.178 6.970 1.00 10.00 C ATOM 4 O GLN A 70 5.126 4.898 7.373 1.00 10.00 O ATOM 5 CB GLN A 70 7.877 6.998 7.230 1.00 10.00 C ATOM 6 CG GLN A 70 7.974 6.681 8.575 1.00 10.00 C ATOM 7 CD GLN A 70 9.249 7.237 9.063 1.00 10.00 C ATOM 8 OE1 GLN A 70 9.559 8.209 8.935 1.00 10.00 O ATOM 9 NE2 GLN A 70 9.506 6.762 10.402 1.00 10.00 N ATOM 10 HA GLN A 70 7.249 5.584 6.195 1.00 10.00 H ATOM 11 HB2 GLN A 70 8.663 7.126 6.476 1.00 10.00 H ATOM 12 HB3 GLN A 70 7.331 8.179 7.116 1.00 10.00 H ATOM 13 HG2 GLN A 70 7.234 6.385 8.986 1.00 10.00 H ATOM 14 HG3 GLN A 70 8.549 5.809 8.279 1.00 10.00 H ATOM 15 HE21 GLN A 70 9.114 6.119 10.657 1.00 10.00 H ATOM 16 HE22 GLN A 70 10.235 7.102 10.671 1.00 10.00 H """ # Glutamic Acid pdb_str_07 = """ CRYST1 15.127 14.767 13.161 90.00 90.00 90.00 P 1 SCALE1 0.066107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.067719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.075982 0.00000 ATOM 1 N GLU A 24 9.022 8.042 4.852 1.00 10.00 N ATOM 2 CA GLU A 24 8.611 8.384 6.596 1.00 10.00 C ATOM 3 C GLU A 24 9.851 8.805 7.028 1.00 10.00 C ATOM 4 O GLU A 24 10.208 9.672 7.827 1.00 10.00 O ATOM 5 CB GLU A 24 8.163 7.285 7.084 1.00 10.00 C ATOM 6 CG GLU A 24 6.610 6.769 6.720 1.00 10.00 C ATOM 7 CD GLU A 24 6.069 5.633 7.216 1.00 10.00 C ATOM 8 OE1 GLU A 24 5.180 5.275 7.007 1.00 10.00 O ATOM 9 OE2 GLU A 24 6.826 5.071 8.182 1.00 10.00 O ATOM 10 HA GLU A 24 8.239 8.942 6.618 1.00 10.00 H ATOM 11 HB2 GLU A 24 8.834 6.577 7.107 1.00 10.00 H ATOM 12 HB3 GLU A 24 8.074 7.246 7.880 1.00 10.00 H ATOM 13 HG2 GLU A 24 5.925 7.518 6.600 1.00 10.00 H ATOM 14 HG3 GLU A 24 6.944 6.683 5.520 1.00 10.00 H """ # Glycine pdb_str_08 = """ CRYST1 13.147 11.167 10.709 90.00 90.00 90.00 P 1 SCALE1 0.076063 0.000000 0.000000 0.00000 SCALE2 0.000000 0.089550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.093379 0.00000 ATOM 1 N GLY B 93 8.304 6.036 5.544 1.00 10.00 N ATOM 2 CA GLY B 93 7.319 4.905 5.595 1.00 10.00 C ATOM 3 C GLY B 93 5.882 5.364 4.847 1.00 10.00 C ATOM 4 O GLY B 93 5.143 5.776 5.738 1.00 10.00 O ATOM 5 HA2 GLY B 93 7.870 4.339 5.372 1.00 10.00 H ATOM 6 HA3 GLY B 93 7.123 4.618 6.529 1.00 10.00 H """ # Histidine pdb_str_09 = """ CRYST1 12.286 14.857 15.512 90.00 90.00 90.00 P 1 SCALE1 0.081393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.067308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.064466 0.00000 ATOM 1 N HIS A 34 7.292 7.714 9.065 1.00 10.00 N ATOM 2 CA HIS A 34 6.363 8.592 8.255 1.00 10.00 C ATOM 3 C HIS A 34 6.024 9.792 9.401 1.00 10.00 C ATOM 4 O HIS A 34 6.246 9.507 10.701 1.00 10.00 O ATOM 5 CB HIS A 34 4.951 8.082 8.105 1.00 10.00 C ATOM 6 CG HIS A 34 5.323 6.839 7.073 1.00 10.00 C ATOM 7 ND1 HIS A 34 5.021 7.108 5.763 1.00 10.00 N ATOM 8 CD2 HIS A 34 5.317 5.623 7.295 1.00 10.00 C ATOM 9 CE1 HIS A 34 5.333 5.771 5.081 1.00 10.00 C ATOM 10 NE2 HIS A 34 5.601 4.927 6.077 1.00 10.00 N ATOM 11 HA HIS A 34 6.539 9.000 7.667 1.00 10.00 H ATOM 12 HB2 HIS A 34 4.722 7.760 8.940 1.00 10.00 H ATOM 13 HB3 HIS A 34 4.532 8.544 7.770 1.00 10.00 H ATOM 14 HD2 HIS A 34 5.433 5.063 7.987 1.00 10.00 H ATOM 15 HE1 HIS A 34 5.162 5.891 3.986 1.00 10.00 H """ # Isoleucine pdb_str_10 = """ CRYST1 14.040 13.236 13.685 90.00 90.00 90.00 P 1 SCALE1 0.071225 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.073073 0.00000 ATOM 1 N ILE B 81 6.774 6.654 8.528 1.00 10.00 N ATOM 2 CA ILE B 81 6.248 6.915 7.265 1.00 10.00 C ATOM 3 C ILE B 81 5.064 5.915 6.912 1.00 10.00 C ATOM 4 O ILE B 81 4.891 4.882 7.591 1.00 10.00 O ATOM 5 CB ILE B 81 7.374 7.060 6.201 1.00 10.00 C ATOM 6 CG1 ILE B 81 7.928 5.644 6.013 1.00 10.00 C ATOM 7 CG2 ILE B 81 8.450 8.146 6.766 1.00 10.00 C ATOM 8 CD1 ILE B 81 9.014 5.797 4.814 1.00 10.00 C ATOM 9 HA ILE B 81 5.805 7.933 7.605 1.00 10.00 H ATOM 10 HB ILE B 81 6.968 7.172 5.320 1.00 10.00 H ATOM 11 HG12 ILE B 81 8.488 5.662 7.117 1.00 10.00 H ATOM 12 HG13 ILE B 81 7.287 4.921 5.901 1.00 10.00 H ATOM 13 HG21 ILE B 81 8.841 8.468 5.740 1.00 10.00 H ATOM 14 HG22 ILE B 81 7.916 9.169 6.877 1.00 10.00 H ATOM 15 HG23 ILE B 81 8.650 8.115 7.619 1.00 10.00 H ATOM 16 HD11 ILE B 81 9.263 4.839 4.994 1.00 10.00 H ATOM 17 HD12 ILE B 81 8.679 5.953 4.216 1.00 10.00 H ATOM 18 HD13 ILE B 81 9.551 6.406 5.137 1.00 10.00 H """ # Leucine pdb_str_11 = """ CRYST1 13.550 15.138 12.702 90.00 90.00 90.00 P 1 SCALE1 0.073801 0.000000 0.000000 0.00000 SCALE2 0.000000 0.066059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.078728 0.00000 ATOM 1 N LEU B 94 6.273 6.593 4.935 1.00 10.00 N ATOM 2 CA LEU B 94 7.641 7.224 5.628 1.00 10.00 C ATOM 3 C LEU B 94 8.422 6.084 6.113 1.00 10.00 C ATOM 4 O LEU B 94 8.638 5.157 5.672 1.00 10.00 O ATOM 5 CB LEU B 94 7.066 8.117 6.861 1.00 10.00 C ATOM 6 CG LEU B 94 6.206 9.526 6.450 1.00 10.00 C ATOM 7 CD1 LEU B 94 5.918 10.237 7.727 1.00 10.00 C ATOM 8 CD2 LEU B 94 4.891 9.251 5.577 1.00 10.00 C ATOM 9 HA LEU B 94 7.928 7.858 4.837 1.00 10.00 H ATOM 10 HB2 LEU B 94 6.600 7.347 7.185 1.00 10.00 H ATOM 11 HB3 LEU B 94 7.833 8.235 7.219 1.00 10.00 H ATOM 12 HG LEU B 94 7.048 9.715 5.954 1.00 10.00 H ATOM 13 HD11 LEU B 94 5.564 11.132 7.460 1.00 10.00 H ATOM 14 HD12 LEU B 94 5.689 9.764 8.196 1.00 10.00 H ATOM 15 HD13 LEU B 94 6.901 10.482 8.316 1.00 10.00 H ATOM 16 HD21 LEU B 94 4.622 9.894 5.701 1.00 10.00 H ATOM 17 HD22 LEU B 94 5.223 8.782 4.700 1.00 10.00 H ATOM 18 HD23 LEU B 94 4.327 8.453 6.346 1.00 10.00 H """ # Lysine pdb_str_12 = """ CRYST1 14.470 17.497 11.416 90.00 90.00 90.00 P 1 SCALE1 0.069109 0.000000 0.000000 0.00000 SCALE2 0.000000 0.057153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.087596 0.00000 ATOM 1 N LYS A 76 4.981 10.159 4.860 1.00 10.00 N ATOM 2 CA LYS A 76 5.876 10.071 6.050 1.00 10.00 C ATOM 3 C LYS A 76 6.304 11.829 6.325 1.00 10.00 C ATOM 4 O LYS A 76 5.161 12.466 6.576 1.00 10.00 O ATOM 5 CB LYS A 76 7.337 9.388 5.906 1.00 10.00 C ATOM 6 CG LYS A 76 7.118 7.831 5.788 1.00 10.00 C ATOM 7 CD LYS A 76 8.453 7.428 5.736 1.00 10.00 C ATOM 8 CE LYS A 76 8.134 5.835 5.433 1.00 10.00 C ATOM 9 NZ LYS A 76 9.426 4.919 5.392 1.00 10.00 N ATOM 10 HA LYS A 76 5.397 10.002 6.803 1.00 10.00 H ATOM 11 HB2 LYS A 76 7.655 9.920 5.112 1.00 10.00 H ATOM 12 HB3 LYS A 76 7.624 9.427 6.543 1.00 10.00 H ATOM 13 HG2 LYS A 76 6.592 7.548 6.676 1.00 10.00 H ATOM 14 HG3 LYS A 76 6.469 7.536 5.090 1.00 10.00 H ATOM 15 HD2 LYS A 76 8.768 7.405 4.630 1.00 10.00 H ATOM 16 HD3 LYS A 76 9.025 7.220 6.546 1.00 10.00 H ATOM 17 HE2 LYS A 76 7.580 5.564 6.304 1.00 10.00 H ATOM 18 HE3 LYS A 76 7.440 5.632 4.831 1.00 10.00 H ATOM 19 HZ1 LYS A 76 9.379 4.186 5.442 1.00 10.00 H ATOM 20 HZ2 LYS A 76 9.725 5.254 4.549 1.00 10.00 H ATOM 21 HZ3 LYS A 76 9.965 5.006 6.093 1.00 10.00 H """ # Methionine pdb_str_13 = """ CRYST1 13.775 12.351 15.645 90.00 90.00 90.00 P 1 SCALE1 0.072595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.080965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.063918 0.00000 ATOM 1 N MET B 37 7.603 5.375 6.446 1.00 10.00 N ATOM 2 CA MET B 37 6.723 6.349 6.607 1.00 10.00 C ATOM 3 C MET B 37 6.323 7.146 5.241 1.00 10.00 C ATOM 4 O MET B 37 5.062 7.131 4.970 1.00 10.00 O ATOM 5 CB MET B 37 6.932 7.378 7.483 1.00 10.00 C ATOM 6 CG MET B 37 7.258 6.900 9.095 1.00 10.00 C ATOM 7 SD MET B 37 8.785 5.488 9.096 1.00 10.00 S ATOM 8 CE MET B 37 8.590 5.149 10.517 1.00 10.00 C ATOM 9 HA MET B 37 5.885 6.031 6.839 1.00 10.00 H ATOM 10 HB2 MET B 37 7.862 7.670 7.351 1.00 10.00 H ATOM 11 HB3 MET B 37 6.364 7.936 7.854 1.00 10.00 H ATOM 12 HG2 MET B 37 7.509 7.571 9.764 1.00 10.00 H ATOM 13 HG3 MET B 37 6.614 6.240 9.246 1.00 10.00 H ATOM 14 HE1 MET B 37 9.624 4.355 10.601 1.00 10.00 H ATOM 15 HE2 MET B 37 9.070 5.811 11.280 1.00 10.00 H ATOM 16 HE3 MET B 37 8.003 4.499 11.109 1.00 10.00 H """ # Phenylanaline pdb_str_14 = """ CRYST1 11.802 16.578 13.976 90.00 90.00 90.00 P 1 SCALE1 0.084731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.060321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.071551 0.00000 ATOM 1 N PHE A 63 6.412 9.770 7.572 1.00 10.00 N ATOM 2 CA PHE A 63 6.289 9.157 6.198 1.00 10.00 C ATOM 3 C PHE A 63 6.292 10.223 5.110 1.00 10.00 C ATOM 4 O PHE A 63 6.451 11.437 5.241 1.00 10.00 O ATOM 5 CB PHE A 63 5.580 8.319 6.063 1.00 10.00 C ATOM 6 CG PHE A 63 5.743 6.958 6.849 1.00 10.00 C ATOM 7 CD1 PHE A 63 6.569 6.117 6.768 1.00 10.00 C ATOM 8 CD2 PHE A 63 5.050 7.055 8.045 1.00 10.00 C ATOM 9 CE1 PHE A 63 6.802 5.054 7.620 1.00 10.00 C ATOM 10 CE2 PHE A 63 5.331 6.153 8.840 1.00 10.00 C ATOM 11 CZ PHE A 63 6.270 5.103 8.840 1.00 10.00 C ATOM 12 HA PHE A 63 7.224 9.004 5.959 1.00 10.00 H ATOM 13 HB2 PHE A 63 4.619 8.277 5.936 1.00 10.00 H ATOM 14 HB3 PHE A 63 5.713 7.612 5.105 1.00 10.00 H ATOM 15 HD1 PHE A 63 7.301 6.004 5.919 1.00 10.00 H ATOM 16 HD2 PHE A 63 4.436 7.641 8.314 1.00 10.00 H ATOM 17 HE1 PHE A 63 7.224 4.307 7.397 1.00 10.00 H ATOM 18 HE2 PHE A 63 4.727 6.172 9.862 1.00 10.00 H ATOM 19 HZ PHE A 63 6.045 4.444 9.418 1.00 10.00 H """ # Proline pdb_str_15 = """ CRYST1 12.293 14.006 12.486 90.00 90.00 90.00 P 1 SCALE1 0.081347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.071398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.080090 0.00000 ATOM 1 N PRO A 4 4.920 7.325 6.411 1.00 10.00 N ATOM 2 CA PRO A 4 6.162 6.834 5.666 1.00 10.00 C ATOM 3 C PRO A 4 6.405 5.341 5.894 1.00 10.00 C ATOM 4 O PRO A 4 7.098 4.853 4.957 1.00 10.00 O ATOM 5 CB PRO A 4 7.380 7.894 6.618 1.00 10.00 C ATOM 6 CG PRO A 4 6.640 8.868 7.204 1.00 10.00 C ATOM 7 CD PRO A 4 5.415 8.476 7.560 1.00 10.00 C ATOM 8 HA PRO A 4 6.250 7.067 4.776 1.00 10.00 H ATOM 9 HB2 PRO A 4 7.921 7.337 7.346 1.00 10.00 H ATOM 10 HB3 PRO A 4 8.016 8.080 5.830 1.00 10.00 H ATOM 11 HG2 PRO A 4 7.167 9.579 7.723 1.00 10.00 H ATOM 12 HG3 PRO A 4 6.492 9.649 6.528 1.00 10.00 H ATOM 13 HD2 PRO A 4 5.306 8.082 8.255 1.00 10.00 H ATOM 14 HD3 PRO A 4 4.496 9.094 7.222 1.00 10.00 H """ # Serine pdb_str_16 = """ CRYST1 12.893 12.708 12.721 90.00 90.00 90.00 P 1 SCALE1 0.077561 0.000000 0.000000 0.00000 SCALE2 0.000000 0.078691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.078610 0.00000 ATOM 1 N SER A 73 5.347 5.750 5.075 1.00 10.00 N ATOM 2 CA SER A 73 5.894 5.594 6.421 1.00 10.00 C ATOM 3 C SER A 73 5.946 7.282 6.996 1.00 10.00 C ATOM 4 O SER A 73 5.026 7.627 7.452 1.00 10.00 O ATOM 5 CB SER A 73 7.501 5.019 6.235 1.00 10.00 C ATOM 6 OG SER A 73 8.063 4.929 7.844 1.00 10.00 O ATOM 7 HA SER A 73 5.300 5.295 7.021 1.00 10.00 H ATOM 8 HB2 SER A 73 7.399 4.067 6.115 1.00 10.00 H ATOM 9 HB3 SER A 73 8.072 5.776 5.734 1.00 10.00 H ATOM 10 HG SER A 73 8.499 4.647 7.768 1.00 10.00 H """ # Threonine pdb_str_17 = """ CRYST1 11.909 12.199 14.459 90.00 90.00 90.00 P 1 SCALE1 0.083970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.081974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.069161 0.00000 ATOM 1 N THR A 68 6.967 7.035 7.598 1.00 10.00 N ATOM 2 CA THR A 68 5.580 6.835 7.409 1.00 10.00 C ATOM 3 C THR A 68 4.981 6.180 8.674 1.00 10.00 C ATOM 4 O THR A 68 6.079 5.829 9.469 1.00 10.00 O ATOM 5 CB THR A 68 5.071 6.452 6.355 1.00 10.00 C ATOM 6 OG1 THR A 68 5.819 5.087 6.249 1.00 10.00 O ATOM 7 CG2 THR A 68 5.178 7.219 5.045 1.00 10.00 C ATOM 8 HA THR A 68 4.978 7.946 7.649 1.00 10.00 H ATOM 9 HB THR A 68 3.853 6.156 6.182 1.00 10.00 H ATOM 10 HG1 THR A 68 6.272 5.006 6.437 1.00 10.00 H ATOM 11 HG21 THR A 68 5.183 6.722 4.241 1.00 10.00 H ATOM 12 HG22 THR A 68 4.943 8.119 5.225 1.00 10.00 H ATOM 13 HG23 THR A 68 6.305 7.117 4.778 1.00 10.00 H """ # Triptophane pdb_str_18 = """ CRYST1 12.502 12.982 18.312 90.00 90.00 90.00 P 1 SCALE1 0.079987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.077030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.054609 0.00000 ATOM 1 N TRP A 49 7.019 6.036 6.855 1.00 10.00 N ATOM 2 CA TRP A 49 6.009 5.654 7.261 1.00 10.00 C ATOM 3 C TRP A 49 5.132 5.145 5.877 1.00 10.00 C ATOM 4 O TRP A 49 5.267 5.983 5.027 1.00 10.00 O ATOM 5 CB TRP A 49 5.058 6.563 8.316 1.00 10.00 C ATOM 6 CG TRP A 49 6.065 6.967 9.207 1.00 10.00 C ATOM 7 CD1 TRP A 49 6.863 7.994 9.455 1.00 10.00 C ATOM 8 CD2 TRP A 49 5.959 6.505 10.743 1.00 10.00 C ATOM 9 NE1 TRP A 49 7.435 8.004 10.831 1.00 10.00 N ATOM 10 CE2 TRP A 49 6.803 7.200 11.335 1.00 10.00 C ATOM 11 CE3 TRP A 49 5.119 5.187 11.318 1.00 10.00 C ATOM 12 CZ2 TRP A 49 7.129 6.620 12.976 1.00 10.00 C ATOM 13 CZ3 TRP A 49 5.299 5.155 12.457 1.00 10.00 C ATOM 14 CH2 TRP A 49 6.374 5.658 13.211 1.00 10.00 C ATOM 15 HA TRP A 49 6.139 4.842 7.608 1.00 10.00 H ATOM 16 HB2 TRP A 49 5.070 7.319 7.481 1.00 10.00 H ATOM 17 HB3 TRP A 49 4.305 6.336 8.251 1.00 10.00 H ATOM 18 HD1 TRP A 49 7.226 8.582 8.796 1.00 10.00 H ATOM 19 HE1 TRP A 49 8.120 8.555 10.929 1.00 10.00 H ATOM 20 HE3 TRP A 49 4.311 5.074 10.564 1.00 10.00 H ATOM 21 HZ2 TRP A 49 7.806 7.092 13.214 1.00 10.00 H ATOM 22 HZ3 TRP A 49 4.914 4.129 12.933 1.00 10.00 H ATOM 23 HH2 TRP A 49 6.353 5.513 14.064 1.00 10.00 H """ # Tyrosine pdb_str_19 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.057 7.968 5.049 1.00 10.00 N ATOM 2 CA TYR A 139 10.657 7.531 6.379 1.00 10.00 C ATOM 3 C TYR A 139 12.203 7.725 6.416 1.00 10.00 C ATOM 4 O TYR A 139 12.999 8.272 7.373 1.00 10.00 O ATOM 5 CB TYR A 139 10.644 6.145 6.711 1.00 10.00 C ATOM 6 CG TYR A 139 9.159 5.899 6.690 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.503 5.230 5.513 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.317 6.046 8.121 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.876 4.938 5.643 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.209 5.706 8.077 1.00 10.00 C ATOM 11 CZ TYR A 139 6.420 5.365 6.855 1.00 10.00 C ATOM 12 OH TYR A 139 5.027 4.949 7.088 1.00 10.00 O ATOM 13 HA TYR A 139 10.303 8.174 6.785 1.00 10.00 H ATOM 14 HB2 TYR A 139 10.989 5.647 5.882 1.00 10.00 H ATOM 15 HB3 TYR A 139 10.828 5.883 7.586 1.00 10.00 H ATOM 16 HD1 TYR A 139 8.618 5.356 4.741 1.00 10.00 H ATOM 17 HD2 TYR A 139 8.841 6.121 8.546 1.00 10.00 H ATOM 18 HE1 TYR A 139 6.432 5.030 4.892 1.00 10.00 H ATOM 19 HE2 TYR A 139 6.780 5.619 9.066 1.00 10.00 H ATOM 20 HH TYR A 139 4.693 5.141 7.840 1.00 10.00 H """ # Valine pdb_str_20 = """ CRYST1 12.396 13.122 13.130 90.00 90.00 90.00 P 1 SCALE1 0.080671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.076208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076161 0.00000 ATOM 1 N VAL B 78 4.820 5.520 7.634 1.00 10.00 N ATOM 2 CA VAL B 78 6.105 5.869 7.138 1.00 10.00 C ATOM 3 C VAL B 78 6.717 7.176 8.084 1.00 10.00 C ATOM 4 O VAL B 78 5.750 8.012 8.022 1.00 10.00 O ATOM 5 CB VAL B 78 6.029 6.374 5.701 1.00 10.00 C ATOM 6 CG1 VAL B 78 5.673 4.961 4.874 1.00 10.00 C ATOM 7 CG2 VAL B 78 7.349 6.810 5.233 1.00 10.00 C ATOM 8 HA VAL B 78 7.125 5.144 7.411 1.00 10.00 H ATOM 9 HB VAL B 78 5.404 6.962 5.498 1.00 10.00 H ATOM 10 HG11 VAL B 78 5.583 5.210 4.024 1.00 10.00 H ATOM 11 HG12 VAL B 78 6.062 4.120 5.126 1.00 10.00 H ATOM 12 HG13 VAL B 78 4.907 4.924 5.317 1.00 10.00 H ATOM 13 HG21 VAL B 78 7.299 7.038 4.409 1.00 10.00 H ATOM 14 HG22 VAL B 78 7.542 7.634 5.823 1.00 10.00 H ATOM 15 HG23 VAL B 78 7.889 5.963 5.346 1.00 10.00 H """ pdb_list = [pdb_str_01, pdb_str_02, pdb_str_03, pdb_str_04, pdb_str_05, pdb_str_06, pdb_str_07, pdb_str_08, pdb_str_09, pdb_str_10, pdb_str_11, pdb_str_12, pdb_str_13, pdb_str_14, pdb_str_15, pdb_str_16, pdb_str_17, pdb_str_18, pdb_str_19, pdb_str_20] # pdb_list_name = ['pdb_str_01', 'pdb_str_02', 'pdb_str_03', 'pdb_str_04', 'pdb_str_05', 'pdb_str_06', 'pdb_str_07', 'pdb_str_08', 'pdb_str_09', 'pdb_str_10', 'pdb_str_11', 'pdb_str_12', 'pdb_str_13', 'pdb_str_14', 'pdb_str_15', 'pdb_str_16', 'pdb_str_17', 'pdb_str_18', 'pdb_str_19', 'pdb_str_20'] #pdb_list = [pdb_str_02] #pdb_list_name = ['pdb_str_02'] def run(): #for use_ideal_bonds_angles in [True, False]: for pdb_str, str_name in zip(pdb_list,pdb_list_name): #print 'pdb_string:', str_name, 'idealize =', idealize exercise(pdb_str=pdb_str, eps=1.e-4) if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time:", round(time.time()-t0, 2), "seconds")