from __future__ import absolute_import, division, print_function import mmtbx.model import libtbx.load_env from libtbx.utils import format_cpu_times from libtbx.test_utils import approx_equal import iotbx.pdb from six.moves import range # 1yjp pdb_str = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O """ pdb_str_h = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 0 H1 GLY A 1 -9.510 5.337 6.223 1.00 16.77 H new ATOM 0 H2 GLY A 1 -9.322 3.948 6.605 1.00 16.77 H new ATOM 0 H3 GLY A 1 -8.169 4.790 6.336 1.00 16.77 H new ATOM 0 HA2 GLY A 1 -9.934 3.875 4.420 1.00 16.57 H new ATOM 0 HA3 GLY A 1 -8.879 4.974 4.082 1.00 16.57 H new ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 0 H ASN A 2 -8.047 3.272 2.473 1.00 15.02 H new ATOM 0 HA ASN A 2 -6.733 1.174 3.217 1.00 14.10 H new ATOM 0 HB2 ASN A 2 -6.122 2.739 0.949 1.00 15.38 H new ATOM 0 HB3 ASN A 2 -5.601 1.285 1.164 1.00 15.38 H new ATOM 0 HD21 ASN A 2 -8.947 1.914 -0.529 1.00 11.72 H new ATOM 0 HD22 ASN A 2 -7.860 2.919 -0.363 1.00 11.72 H new ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 0 H ASN A 3 -4.602 0.748 3.841 1.00 12.26 H new ATOM 0 HA ASN A 3 -3.100 2.869 4.573 1.00 11.74 H new ATOM 0 HB2 ASN A 3 -4.044 1.744 6.479 1.00 12.15 H new ATOM 0 HB3 ASN A 3 -3.366 0.414 6.029 1.00 12.15 H new ATOM 0 HD21 ASN A 3 -0.555 0.864 7.759 1.00 13.48 H new ATOM 0 HD22 ASN A 3 -1.514 -0.093 7.140 1.00 13.48 H new ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N ATOM 0 H GLN A 4 -1.149 3.076 3.622 1.00 10.29 H new ATOM 0 HA GLN A 4 0.474 0.933 3.341 1.00 10.53 H new ATOM 0 HB2 GLN A 4 -0.098 1.834 1.188 1.00 9.80 H new ATOM 0 HB3 GLN A 4 0.726 3.104 1.561 1.00 9.80 H new ATOM 0 HG2 GLN A 4 2.622 1.523 1.904 1.00 10.25 H new ATOM 0 HG3 GLN A 4 1.763 0.514 1.080 1.00 10.25 H new ATOM 0 HE21 GLN A 4 2.571 0.327 -0.983 1.00 9.05 H new ATOM 0 HE22 GLN A 4 3.085 1.436 -1.834 1.00 9.05 H new ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 0 H GLN A 5 2.017 0.978 4.974 1.00 10.38 H new ATOM 0 HA GLN A 5 3.309 3.316 5.477 1.00 11.39 H new ATOM 0 HB2 GLN A 5 2.951 1.240 7.349 1.00 11.96 H new ATOM 0 HB3 GLN A 5 3.844 2.489 7.623 1.00 11.96 H new ATOM 0 HG2 GLN A 5 2.050 3.889 7.743 1.00 10.81 H new ATOM 0 HG3 GLN A 5 1.119 2.892 6.989 1.00 10.81 H new ATOM 0 HE21 GLN A 5 1.953 3.942 9.959 1.00 12.30 H new ATOM 0 HE22 GLN A 5 1.276 2.925 10.811 1.00 12.30 H new ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 0 H ASN A 6 5.395 3.511 4.947 1.00 11.99 H new ATOM 0 HA ASN A 6 6.892 1.355 4.162 1.00 12.30 H new ATOM 0 HB2 ASN A 6 7.129 3.972 3.143 1.00 12.13 H new ATOM 0 HB3 ASN A 6 7.914 2.730 2.620 1.00 12.13 H new ATOM 0 HD21 ASN A 6 4.545 3.635 1.128 1.00 10.07 H new ATOM 0 HD22 ASN A 6 5.342 4.524 2.018 1.00 10.07 H new ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O ATOM 0 H TYR A 7 8.106 0.981 6.066 1.00 14.70 H new ATOM 0 HA TYR A 7 8.843 2.985 7.664 1.00 15.18 H new ATOM 0 HB2 TYR A 7 9.349 0.216 7.999 1.00 15.35 H new ATOM 0 HB3 TYR A 7 9.666 1.277 9.097 1.00 15.35 H new ATOM 0 HD1 TYR A 7 7.051 -0.513 7.619 1.00 15.68 H new ATOM 0 HD2 TYR A 7 7.783 2.394 10.280 1.00 14.80 H new ATOM 0 HE1 TYR A 7 4.901 -0.719 8.422 1.00 13.46 H new ATOM 0 HE2 TYR A 7 5.618 2.183 11.122 1.00 14.33 H new ATOM 0 HH TYR A 7 3.629 1.138 10.911 1.00 14.39 H new """ pdb_str_base = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N """ pdb_str_water = """\ HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O """ def exercise_adopting_coord_restraints(): inp_1 = iotbx.pdb.input(lines=pdb_str_h, source_info=None) h_model = mmtbx.model.manager(model_input = inp_1) h_model.process(make_restraints=True) inp_2 = iotbx.pdb.input(lines=pdb_str, source_info=None) model = mmtbx.model.manager(model_input = inp_2) model.process(make_restraints=True) # case 1: big model adopting small model. h_model.set_reference_coordinate_restraints(ref_model = model) # print h_model.restraints_as_geo() rcp = h_model.get_restraints_manager().geometry.reference_coordinate_proxies assert len(rcp) == 59 # Note iseqs, hydrogens are skipped answer = [ [(0,) , (-9.009, 4.612, 6.102), 25.0], [(1,) , (-9.052, 4.207, 4.651), 25.0], [(2,) , (-8.015, 3.14, 4.419), 25.0], [(3,) , (-7.523, 2.521, 5.381), 25.0], [(9,) , (-7.656, 2.923, 3.155), 25.0], [(10,), (-6.522, 2.038, 2.831), 25.0]] # for p in rcp: # print p.i_seqs, p.ref_sites, p.weight for i in range(6): assert rcp[i].i_seqs == answer[i][0], "%s %s" % (rcp[i].i_seqs, answer[i][0]) assert approx_equal(rcp[i].ref_sites, answer[i][1]) assert approx_equal(rcp[i].weight, answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2]) # case 2: small model adopting big model. model.set_reference_coordinate_restraints(ref_model=h_model) rcp = model.get_restraints_manager().geometry.reference_coordinate_proxies assert len(rcp) == 59 # Note iseqs, hydrogens are skipped answer = [ [(0,), (-9.009, 4.612, 6.102), 25.0], [(1,), (-9.052, 4.207, 4.651), 25.0], [(2,), (-8.015, 3.14, 4.419), 25.0], [(3,), (-7.523, 2.521, 5.381), 25.0], [(4,), (-7.656, 2.923, 3.155), 25.0], [(5,), (-6.522, 2.038, 2.831), 25.0]] for i in range(6): assert rcp[i].i_seqs == answer[i][0] assert approx_equal(rcp[i].ref_sites, answer[i][1]) assert approx_equal(rcp[i].weight, answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2]) def exercise_adopting_coord_restraints_water(): inp_1 = iotbx.pdb.input(lines=pdb_str_base, source_info=None) nowat_model = mmtbx.model.manager(model_input = inp_1) nowat_model.process(make_restraints=True) # Changing coordinates a little to make sure right ones are used for # reference restraints for a in nowat_model.get_hierarchy().atoms(): a.xyz = (a.xyz[0]+1, a.xyz[1], a.xyz[2]) nowat_model.set_sites_cart_from_hierarchy() inp_2 = iotbx.pdb.input(lines=pdb_str_base+pdb_str_water, source_info=None) wat_model = mmtbx.model.manager(model_input = inp_2) wat_model.process(make_restraints=True) nowat_model.set_reference_coordinate_restraints( ref_model = wat_model) rcp = nowat_model.get_restraints_manager().geometry.reference_coordinate_proxies assert len(rcp) == 20, len(rcp) answer = [[(0,) , (-9.009, 4.612, 6.102), 25.0], [(1,) , (-9.052, 4.207, 4.651), 25.0], [(2,) , (-8.015, 3.14, 4.419), 25.0], [(3,) , (-7.523, 2.521, 5.381), 25.0], [(4,) , (-7.656, 2.923, 3.155), 25.0], [(5,) , (-6.522, 2.038, 2.831), 25.0], [(6,) , (-5.241, 2.537, 3.427), 25.0], [(7,) , (-4.978, 3.742, 3.426), 25.0], [(8,) , (-6.346, 1.881, 1.341), 25.0], [(9,) , (-7.584, 1.342, 0.692), 25.0], [(10,), (-8.025, 0.227, 1.016), 25.0], [(11,), (-8.204, 2.155, -0.169), 25.0], [(12,), (-4.438, 1.59, 3.905), 25.0], [(13,), (-3.193, 1.904, 4.589), 25.0], [(14,), (-1.955, 1.332, 3.895), 25.0], [(15,), (-1.872, 0.119, 3.648), 25.0], [(16,), (-3.259, 1.378, 6.042), 25.0], [(17,), (-2.006, 1.739, 6.861), 25.0], [(18,), (-1.702, 2.925, 7.072), 25.0], [(19,), (-1.271, 0.715, 7.306), 25.0]] for i in range(20): assert rcp[i].i_seqs == answer[i][0] assert approx_equal(rcp[i].ref_sites, answer[i][1]) assert approx_equal(rcp[i].weight, answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2]) # print nowat_model.model_as_pdb() wat_model.set_reference_coordinate_restraints(ref_model=nowat_model) rcp = wat_model.get_restraints_manager().geometry.reference_coordinate_proxies assert len(rcp) == 20, len(rcp) # Note different x coord here answer = [[(0,) , (-8.009, 4.612, 6.102), 25.0], [(1,) , (-8.052, 4.207, 4.651), 25.0], [(2,) , (-7.015, 3.14, 4.419), 25.0], [(3,) , (-6.523, 2.521, 5.381), 25.0], [(4,) , (-6.656, 2.923, 3.155), 25.0], [(5,) , (-5.522, 2.038, 2.831), 25.0], [(6,) , (-4.241, 2.537, 3.427), 25.0], [(7,) , (-3.978, 3.742, 3.426), 25.0], [(8,) , (-5.346, 1.881, 1.341), 25.0], [(9,) , (-6.584, 1.342, 0.692), 25.0], [(10,), (-7.025, 0.227, 1.016), 25.0], [(11,), (-7.204, 2.155, -0.169), 25.0], [(12,), (-3.438, 1.59, 3.905), 25.0], [(13,), (-2.193, 1.904, 4.589), 25.0], [(14,), (-0.955, 1.332, 3.895), 25.0], [(15,), (-0.872, 0.119, 3.648), 25.0], [(16,), (-2.259, 1.378, 6.042), 25.0], [(17,), (-1.006, 1.739, 6.861), 25.0], [(18,), (-0.702, 2.925, 7.072), 25.0], [(19,), (-0.271, 0.715, 7.306), 25.0]] for i in range(20): assert rcp[i].i_seqs == answer[i][0] assert approx_equal(rcp[i].ref_sites, answer[i][1]) assert approx_equal(rcp[i].weight, answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2]) # for p in rcp: # print p.i_seqs, p.ref_sites, p.weight def run(): if (not libtbx.env.has_module("reduce")): print("Reduce not installed.") return exercise_adopting_coord_restraints() exercise_adopting_coord_restraints_water() print(format_cpu_times()) if (__name__ == "__main__"): run()