from __future__ import absolute_import, division, print_function import iotbx.ncs as ncs import iotbx.pdb from iotbx.ncs import ncs_group_master_phil import iotbx.phil pdb_str_1 = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 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 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 23 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 24 CA AGLN A 4 0.384 1.888 3.199 0.50 10.53 C ATOM 25 CB AGLN A 4 0.656 2.148 1.711 0.50 9.80 C ATOM 26 CG AGLN A 4 1.944 1.458 1.213 0.50 10.25 C ATOM 27 CD AGLN A 4 2.504 2.044 -0.089 0.50 12.43 C ATOM 28 OE1AGLN A 4 2.744 3.268 -0.190 0.50 14.62 O ATOM 29 NE2AGLN A 4 2.750 1.161 -1.091 0.50 9.05 N ATOM 30 CA BGLN A 4 0.484 1.888 3.199 0.50 10.53 C ATOM 31 CB BGLN A 4 0.756 2.148 1.711 0.50 9.80 C ATOM 32 CG BGLN A 4 -0.021 1.186 0.788 0.50 10.25 C ATOM 33 CD BGLN A 4 0.170 1.463 -0.708 0.50 12.43 C ATOM 34 OE1BGLN A 4 0.485 2.604 -1.113 0.50 14.62 O ATOM 35 NE2BGLN A 4 0.013 0.404 -1.543 0.50 9.05 N ATOM 36 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 37 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 38 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 39 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 40 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 41 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 42 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 43 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 44 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 45 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 46 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 47 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 48 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 49 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 50 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 51 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 52 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 53 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 54 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 55 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 56 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 57 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 58 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 59 CD1 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 60 CD2 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 61 CE1 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 62 CE2 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 63 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 64 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 65 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O TER HETATM 66 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 67 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 68 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 69 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 70 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 71 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 72 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O ATOM 1 N GLY B 1 9.009 7.045 -6.102 1.00 16.77 N ATOM 2 CA GLY B 1 9.052 6.640 -4.651 1.00 16.57 C ATOM 3 C GLY B 1 8.015 5.573 -4.419 1.00 16.16 C ATOM 4 O GLY B 1 7.523 4.954 -5.381 1.00 16.78 O ATOM 5 N ASN B 2 7.656 5.356 -3.155 1.00 15.02 N ATOM 6 CA ASN B 2 6.522 4.471 -2.831 1.00 14.10 C ATOM 7 C ASN B 2 5.241 4.970 -3.427 1.00 13.13 C ATOM 8 O ASN B 2 4.978 6.175 -3.426 1.00 11.91 O ATOM 9 CB ASN B 2 6.346 4.314 -1.341 1.00 15.38 C ATOM 10 CG ASN B 2 7.584 3.775 -0.692 1.00 14.08 C ATOM 11 OD1 ASN B 2 8.025 2.660 -1.016 1.00 17.46 O ATOM 12 ND2 ASN B 2 8.204 4.588 0.169 1.00 11.72 N ATOM 13 N ASN B 3 4.438 4.023 -3.905 1.00 12.26 N ATOM 14 CA ASN B 3 3.193 4.337 -4.589 1.00 11.74 C ATOM 15 C ASN B 3 1.955 3.765 -3.895 1.00 11.10 C ATOM 16 O ASN B 3 1.872 2.552 -3.648 1.00 10.42 O ATOM 17 CB ASN B 3 3.259 3.811 -6.042 1.00 12.15 C ATOM 18 CG ASN B 3 2.006 4.172 -6.861 1.00 12.82 C ATOM 19 OD1 ASN B 3 1.702 5.358 -7.072 1.00 15.05 O ATOM 20 ND2 ASN B 3 1.271 3.148 -7.306 1.00 13.48 N ATOM 21 N GLN B 4 1.005 4.661 -3.598 1.00 10.29 N ATOM 22 C GLN B 4 -1.435 5.039 -4.088 1.00 10.24 C ATOM 23 O GLN B 4 -1.547 6.276 -4.115 1.00 8.86 O ATOM 24 CA AGLN B 4 -0.384 4.321 -3.199 0.50 10.53 C ATOM 25 CB AGLN B 4 -0.656 4.581 -1.711 0.50 9.80 C ATOM 26 CG AGLN B 4 -1.944 3.891 -1.213 0.50 10.25 C ATOM 27 CD AGLN B 4 -2.504 4.477 0.089 0.50 12.43 C ATOM 28 OE1AGLN B 4 -2.744 5.701 0.190 0.50 14.62 O ATOM 29 NE2AGLN B 4 -2.750 3.594 1.091 0.50 9.05 N ATOM 30 CA BGLN B 4 -0.484 4.321 -3.199 0.50 10.53 C ATOM 31 CB BGLN B 4 -0.756 4.581 -1.711 0.50 9.80 C ATOM 32 CG BGLN B 4 0.021 3.619 -0.788 0.50 10.25 C ATOM 33 CD BGLN B 4 -0.170 3.896 0.708 0.50 12.43 C ATOM 34 OE1BGLN B 4 -0.485 5.037 1.113 0.50 14.62 O ATOM 35 NE2BGLN B 4 -0.013 2.837 1.543 0.50 9.05 N ATOM 36 N GLN B 5 -2.154 4.254 -4.871 1.00 10.38 N ATOM 37 CA GLN B 5 -3.270 4.794 -5.640 1.00 11.39 C ATOM 38 C GLN B 5 -4.594 4.201 -5.172 1.00 11.52 C ATOM 39 O GLN B 5 -4.768 2.979 -5.054 1.00 12.05 O ATOM 40 CB GLN B 5 -3.056 4.616 -7.147 1.00 11.96 C ATOM 41 CG GLN B 5 -1.829 5.383 -7.647 1.00 10.81 C ATOM 42 CD GLN B 5 -1.344 4.847 -8.954 1.00 13.10 C ATOM 43 OE1 GLN B 5 -0.774 3.758 -9.002 1.00 10.65 O ATOM 44 NE2 GLN B 5 -1.549 5.620 -10.039 1.00 12.30 N ATOM 45 N ASN B 6 -5.514 5.097 -4.856 1.00 11.99 N ATOM 46 CA ASN B 6 -6.831 4.743 -4.318 1.00 12.30 C ATOM 47 C ASN B 6 -7.854 5.194 -5.324 1.00 13.40 C ATOM 48 O ASN B 6 -8.219 6.376 -5.374 1.00 13.92 O ATOM 49 CB ASN B 6 -7.065 5.449 -2.993 1.00 12.13 C ATOM 50 CG ASN B 6 -5.961 5.168 -2.003 1.00 12.77 C ATOM 51 OD1 ASN B 6 -5.798 4.037 -1.551 1.00 14.27 O ATOM 52 ND2 ASN B 6 -5.195 6.180 -1.679 1.00 10.07 N ATOM 53 N TYR B 7 -8.292 4.250 -6.147 1.00 14.70 N ATOM 54 CA TYR B 7 -9.159 4.577 -7.299 1.00 15.18 C ATOM 55 C TYR B 7 -10.603 4.764 -6.885 1.00 15.91 C ATOM 56 O TYR B 7 -11.041 4.244 -5.855 1.00 15.76 O ATOM 57 CB TYR B 7 -9.061 3.498 -8.369 1.00 15.35 C ATOM 58 CG TYR B 7 -7.665 3.362 -8.902 1.00 14.45 C ATOM 59 CD1 TYR B 7 -7.210 4.189 -9.920 1.00 14.80 C ATOM 60 CD2 TYR B 7 -6.771 2.454 -8.327 1.00 15.68 C ATOM 61 CE1 TYR B 7 -5.904 4.082 -10.416 1.00 14.33 C ATOM 62 CE2 TYR B 7 -5.480 2.339 -8.796 1.00 13.46 C ATOM 63 CZ TYR B 7 -5.047 3.162 -9.831 1.00 15.09 C ATOM 64 OH TYR B 7 -3.766 3.022 -10.291 1.00 14.39 O ATOM 65 OXT TYR B 7 -11.358 5.432 -7.612 1.00 17.49 O TER HETATM 66 O HOH B 8 6.471 7.660 -7.124 1.00 22.62 O HETATM 67 O HOH B 9 -10.431 4.291 -3.216 1.00 19.71 O HETATM 68 O HOH B 10 11.286 4.189 1.468 1.00 17.08 O HETATM 69 O HOH B 11 -11.808 6.612 -9.970 1.00 23.99 O HETATM 70 O HOH B 12 -13.605 3.760 -9.198 1.00 26.17 O HETATM 71 O HOH B 13 2.749 5.862 -10.024 1.00 39.15 O HETATM 72 O HOH B 14 1.500 3.115 -10.967 1.00 43.49 O END """ def exercise_1(): """ Pure NCS search with AC and water that should be dropped """ h = iotbx.pdb.input(lines=pdb_str_1, source_info=None).construct_hierarchy() ncs_inp = ncs.input(hierarchy = h) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert ncs_groups[0].master_iselection.size() == 50, ncs_groups[0].master_iselection.size() assert ncs_groups[0].master_iselection.size() == ncs_groups[0].copies[0].iselection.size() def exercise_2(): """ Same as 1, but include water """ search_params = ncs.input.get_default_params() search_params.ncs_search.exclude_selection = "element H or element D" h = iotbx.pdb.input(lines=pdb_str_1, source_info=None).construct_hierarchy() ncs_inp = ncs.input( hierarchy = h, params=search_params.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert ncs_groups[0].master_iselection.size() == 57, ncs_groups[0].master_iselection.size() assert ncs_groups[0].master_iselection.size() == ncs_groups[0].copies[0].iselection.size() def exercise_3(): """ Same as 2, but also provide groups and don't check them allowing AC to be included """ phil_str=""" ncs_group { reference = chain A selection = chain B } """ search_params = ncs.input.get_default_params() search_params.ncs_search.exclude_selection = "element H or element D" search_params.ncs_search.validate_user_supplied_groups = False phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(phil_str)).extract() h = iotbx.pdb.input(lines=pdb_str_1, source_info=None).construct_hierarchy() ncs_inp = ncs.input( hierarchy = h, params=search_params.ncs_search, ncs_phil_groups=phil_groups.ncs_group) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert ncs_groups[0].master_iselection.size() == 72, ncs_groups[0].master_iselection.size() assert ncs_groups[0].master_iselection.size() == ncs_groups[0].copies[0].iselection.size() assert h.atoms_size() == 72*2, h.atoms_size() # covers whole model if (__name__ == "__main__"): exercise_1() exercise_2() exercise_3() print("OK")