from __future__ import division import iotbx.pdb from libtbx.test_utils import approx_equal import mmtbx.refinement.rigid_body m1_in_str = """\ CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 4 ATOM 1 N ASP L -1 49.347 -62.804 60.380 1.00 34.60 N ATOM 2 CA ASP L -1 47.975 -63.194 59.946 1.00 33.86 C ATOM 3 C ASP L -1 47.122 -63.665 61.114 1.00 34.02 C ATOM 4 O ASP L -1 47.573 -64.451 61.947 1.00 32.23 O ATOM 9 N VAL L -2 45.889 -63.176 61.175 1.00 31.94 N ATOM 10 CA VAL L -2 44.978 -63.576 62.233 1.00 29.81 C ATOM 20 CB GLN L 0 45.127 -68.170 63.455 1.00 29.74 C ATOM 21 CG GLN L 0 44.676 -69.611 63.591 1.00 39.72 C ATOM 22 CD GLN L 0 45.288 -70.292 64.807 1.00 51.31 C ATOM 25 N MET L 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 26 CA CMET L 4 40.497 -68.318 62.576 0.30 22.89 C ATOM 27 C CMET L 4 40.326 -69.824 62.795 0.30 21.48 C ATOM 28 O CMET L 4 40.633 -70.625 61.911 0.30 23.73 O ATOM 25 N TYR L 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 26 CA DTYR L 4 40.497 -68.318 62.576 0.70 22.89 C ATOM 27 C DTYR L 4 40.326 -69.824 62.795 0.70 21.48 C ATOM 28 O DTYR L 4 40.633 -70.625 61.911 0.70 23.73 O ATOM 186 N GLN L 27 43.266 -62.813 67.460 1.00 23.64 N ATOM 187 CA GLN L 27 43.289 -61.405 67.832 1.00 24.84 C ATOM 197 C SER L 27A 39.920 -58.676 67.377 1.00 22.05 C ATOM 198 O SER L 27A 40.712 -58.050 66.678 1.00 19.83 O ATOM 202 CA LEU L 27B 38.173 -58.446 65.720 1.00 20.41 C ATOM 203 C LEU L 27B 37.484 -57.089 65.854 1.00 21.13 C ATOM 235 N ASN L 28 36.659 -48.175 64.751 1.00 23.50 N ATOM 236 CA ASN L 28 35.418 -47.408 64.733 1.00 19.92 C TER ATOM 1702 N GLY H 1 19.054 -57.059 39.111 1.00 41.20 N ATOM 1703 CA GLY H 1 20.002 -57.281 40.238 1.00 41.19 C ATOM 1704 C GLY H 1 21.452 -57.171 39.802 1.00 40.03 C ATOM 1959 N ASN H 35A 36.815 -57.860 44.928 1.00 15.79 N ATOM 1960 CA ASN H 35A 37.803 -58.882 45.265 1.00 16.70 C ATOM 1967 N TRP H 36 39.095 -60.772 44.593 1.00 17.23 N ATOM 1968 CA TRP H 36 39.440 -62.016 43.926 1.00 19.02 C TER ATOM 3383 O HOH S 215 45.158 -61.466 59.209 1.00 21.71 O ATOM 3384 O HOH S 216 26.065 -71.512 48.872 1.00 18.56 O ATOM 3385 O HOH S 217 26.885 -90.624 56.632 0.92 16.47 O ATOM 3386 O HOH S 218 22.026 -89.723 46.422 1.04 19.34 O TER HETATM 3387 O WAT L 219 33.576 -94.407 39.044 1.08 30.66 HETATM 3388 O WAT L 220 39.377 -73.892 61.395 1.40 42.96 HETATM 3389 O AWAT L 221 21.907 -98.365 40.731 0.40 16.45 HETATM 3390 O BWAT L 221 28.591 -95.257 59.711 0.60 20.75 TER ATOM 1001 AU AU 500 14.333 3.856 26.301 1.00 7.97 Au TER ATOM 3342 N VAL 226 20.817 -97.348 23.861 1.00 34.12 N ATOM 3349 N PRO 227 19.065-100.553 23.842 1.00 41.92 N ATOM 3350 CA PRO 227 19.109-101.900 24.416 1.00 46.30 C ATOM 3351 C PRO 227 20.202-102.722 23.753 1.00 50.65 C ATOM 3356 N ARG 228 20.811-103.620 24.514 1.00 56.77 N TER ATOM 25 N MET X 4 41.894 -68.026 62.256 1.00 24.27 N TER ATOM 1001 AU AU K 502 11.333 3.856 26.301 1.00 7.97 ATOM 1001 AU AU K 100 14.333 0.856 26.301 1.00 7.97 Au ATOM 1001 AU AU K 900 14.333 3.856 21.301 1.00 7.97 Au END """ m1_out_str = """\ CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 4 ATOM 1 N ASP L -1 49.347 -62.804 60.380 1.00 34.60 N ATOM 2 CA ASP L -1 47.975 -63.194 59.946 1.00 33.86 C ATOM 3 C ASP L -1 47.122 -63.665 61.114 1.00 34.02 C ATOM 4 O ASP L -1 47.573 -64.451 61.947 1.00 32.23 O ATOM 9 N VAL L -2 45.889 -63.176 61.175 1.00 31.94 N ATOM 10 CA VAL L -2 44.978 -63.576 62.233 1.00 29.81 C ATOM 20 CB GLN L 0 45.127 -68.170 63.455 1.00 29.74 C ATOM 21 CG GLN L 0 44.676 -69.611 63.591 1.00 39.72 C ATOM 22 CD GLN L 0 45.288 -70.292 64.807 1.00 51.31 C ATOM 25 N MET L 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 26 CA CMET L 4 40.497 -68.318 62.576 0.30 22.89 C ATOM 27 C CMET L 4 40.326 -69.824 62.795 0.30 21.48 C ATOM 28 O CMET L 4 40.633 -70.625 61.911 0.30 23.73 O ATOM 25 N TYR L 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 26 CA DTYR L 4 40.497 -68.318 62.576 0.70 22.89 C ATOM 27 C DTYR L 4 40.326 -69.824 62.795 0.70 21.48 C ATOM 28 O DTYR L 4 40.633 -70.625 61.911 0.70 23.73 O ATOM 186 N GLN L 27 43.266 -62.813 67.460 1.00 23.64 N ATOM 187 CA GLN L 27 43.289 -61.405 67.832 1.00 24.84 C ATOM 197 C SER L 27A 39.920 -58.676 67.377 1.00 22.05 C ATOM 198 O SER L 27A 40.712 -58.050 66.678 1.00 19.83 O ATOM 202 CA LEU L 27B 38.173 -58.446 65.720 1.00 20.41 C ATOM 203 C LEU L 27B 37.484 -57.089 65.854 1.00 21.13 C ATOM 235 N ASN L 28 36.659 -48.175 64.751 1.00 23.50 N ATOM 236 CA ASN L 28 35.418 -47.408 64.733 1.00 19.92 C TER ATOM 1702 N GLY H 1 19.054 -57.059 39.111 1.00 41.20 N ATOM 1703 CA GLY H 1 20.002 -57.281 40.238 1.00 41.19 C ATOM 1704 C GLY H 1 21.452 -57.171 39.802 1.00 40.03 C ATOM 1959 N ASN H 35A 36.815 -57.860 44.928 1.00 15.79 N ATOM 1960 CA ASN H 35A 37.803 -58.882 45.265 1.00 16.70 C ATOM 1967 N TRP H 36 39.095 -60.772 44.593 1.00 17.23 N ATOM 1968 CA TRP H 36 39.440 -62.016 43.926 1.00 19.02 C TER ATOM 3342 N VAL 226 20.817 -97.348 23.861 1.00 34.12 N ATOM 3349 N PRO 227 19.065-100.553 23.842 1.00 41.92 N ATOM 3350 CA PRO 227 19.109-101.900 24.416 1.00 46.30 C ATOM 3351 C PRO 227 20.202-102.722 23.753 1.00 50.65 C ATOM 3356 N ARG 228 20.811-103.620 24.514 1.00 56.77 N TER END """ m2_in_str = """\ CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 4 ATOM 1 O5' DC A 1 29.670 19.013 -2.305 1.00 11.26 O ATOM 2 C5' DC A 1 30.109 19.727 -1.144 1.00 2.03 C ATOM 3 C4' DC A 1 30.024 19.014 0.202 1.00 4.76 C ATOM 4 O4' DC A 1 28.912 18.160 0.419 1.00 7.08 O ATOM 5 C3' DC A 1 31.204 18.275 0.705 1.00 9.25 C ATOM 6 O3' DC A 1 31.448 18.682 2.066 1.00 11.24 O ATOM 20 P DG A 2 32.339 20.004 2.406 1.00 11.95 P ATOM 45 P DC A 3 28.538 23.069 6.214 1.00 19.73 P ATOM 46 OP1 DC A 3 29.232 24.056 7.091 1.00 19.15 O ATOM 47 OP2 DC A 3 29.008 21.652 6.240 1.00 19.23 O ATOM 48 O5' DC A 3 26.905 23.120 6.436 1.00 16.82 O TER ATOM 139 O5' DC B 7 13.405 26.346 3.336 1.00 15.19 O ATOM 140 C5' DC B 7 13.472 24.969 2.944 1.00 4.19 C ATOM 158 P DG B 8 11.130 21.728 3.702 1.00 12.13 P ATOM 159 OP1 DG B 8 10.341 22.682 2.901 1.00 14.52 O ATOM 186 O5' DC B 9 16.676 16.828 1.638 1.00 13.48 O ATOM 187 C5' DC B 9 17.151 15.620 2.196 1.00 3.67 C ATOM 188 C4' DC B 9 17.855 15.745 3.510 1.00 2.48 C TER HETATM 277 O HOH A 13 32.050 21.145 7.029 1.00 28.46 O HETATM 278 O HOH A 14 29.068 18.914 5.393 1.00 44.50 O HETATM 279 O HOH A 15 29.984 22.375 10.338 1.00 42.18 O END """ m2_out_str = """\ CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 4 ATOM 1 O5' DC A 1 29.670 19.013 -2.305 1.00 11.26 O ATOM 2 C5' DC A 1 30.109 19.727 -1.144 1.00 2.03 C ATOM 3 C4' DC A 1 30.024 19.014 0.202 1.00 4.76 C ATOM 4 O4' DC A 1 28.912 18.160 0.419 1.00 7.08 O ATOM 5 C3' DC A 1 31.204 18.275 0.705 1.00 9.25 C ATOM 6 O3' DC A 1 31.448 18.682 2.066 1.00 11.24 O ATOM 20 P DG A 2 32.339 20.004 2.406 1.00 11.95 P ATOM 45 P DC A 3 28.538 23.069 6.214 1.00 19.73 P ATOM 46 OP1 DC A 3 29.232 24.056 7.091 1.00 19.15 O ATOM 47 OP2 DC A 3 29.008 21.652 6.240 1.00 19.23 O ATOM 48 O5' DC A 3 26.905 23.120 6.436 1.00 16.82 O TER ATOM 139 O5' DC B 7 13.405 26.346 3.336 1.00 15.19 O ATOM 140 C5' DC B 7 13.472 24.969 2.944 1.00 4.19 C ATOM 158 P DG B 8 11.130 21.728 3.702 1.00 12.13 P ATOM 159 OP1 DG B 8 10.341 22.682 2.901 1.00 14.52 O ATOM 186 O5' DC B 9 16.676 16.828 1.638 1.00 13.48 O ATOM 187 C5' DC B 9 17.151 15.620 2.196 1.00 3.67 C ATOM 188 C4' DC B 9 17.855 15.745 3.510 1.00 2.48 C TER END """ m3_in_str = """\ CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 4 ATOM 1 N ASP L -1 49.347 -62.804 60.380 1.00 34.60 N ATOM 2 CA ASP L -1 47.975 -63.194 59.946 1.00 33.86 C ATOM 3 C ASP L -1 47.122 -63.665 61.114 1.00 34.02 C ATOM 4 O ASP L -1 47.573 -64.451 61.947 1.00 32.23 O ATOM 9 N VAL L -2 45.889 -63.176 61.175 1.00 31.94 N ATOM 10 CA VAL L -2 44.978 -63.576 62.233 1.00 29.81 C ATOM 20 CB GLN L 0 45.127 -68.170 63.455 1.00 29.74 C ATOM 21 CG GLN L 0 44.676 -69.611 63.591 1.00 39.72 C ATOM 22 CD GLN L 0 45.288 -70.292 64.807 1.00 51.31 C ATOM 25 N MET L 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 26 CA CMET L 4 40.497 -68.318 62.576 0.30 22.89 C ATOM 27 C CMET L 4 40.326 -69.824 62.795 0.30 21.48 C ATOM 28 O CMET L 4 40.633 -70.625 61.911 0.30 23.73 O TER HETATM 3387 O WAT L 219 33.576 -94.407 39.044 1.08 30.66 HETATM 3388 O WAT L 220 39.377 -73.892 61.395 1.40 42.96 HETATM 3389 O AWAT L 221 21.907 -98.365 40.731 0.40 16.45 HETATM 3390 O BWAT L 221 28.591 -95.257 59.711 0.60 20.75 TER ATOM 1001 AU AU L 500 14.333 3.856 26.301 1.00 7.97 Au TER END """ def exercise_00(): pdb_inp = iotbx.pdb.input(source_info=None, lines=m1_in_str) pdb_hierarchy = pdb_inp.construct_hierarchy() pdb_hierarchy.atoms().reset_i_seq() sel_strings=mmtbx.refinement.rigid_body.rigid_groups_from_pdb_chains( pdb_hierarchy=pdb_hierarchy) answer = [ "(chain 'L' and resid -1 through 28)", "(chain 'H' and resid 1 through 36)", "(chain ' ' and resid 226 through 228)"] for sel_string in sel_strings: assert sel_string in answer assert len(sel_strings) == 3 selection = pdb_hierarchy.atom_selection_cache().selection( string=" or ".join(answer)) xrs_1 = pdb_inp.xray_structure_simple().select(selection = selection) xrs_2 = iotbx.pdb.input(source_info=None, lines=m1_out_str).xray_structure_simple() assert approx_equal( xrs_1.structure_factors(d_min=2).f_calc().data(), xrs_2.structure_factors(d_min=2).f_calc().data()) def exercise_01(): pdb_inp = iotbx.pdb.input(source_info=None, lines=m2_in_str) pdb_hierarchy = pdb_inp.construct_hierarchy() pdb_hierarchy.atoms().reset_i_seq() sel_strings=mmtbx.refinement.rigid_body.rigid_groups_from_pdb_chains( pdb_hierarchy=pdb_hierarchy) answer = [ "(chain 'A' and resid 1 through 3)", "(chain 'B' and resid 7 through 9)"] for sel_string in sel_strings: assert sel_string in answer assert len(sel_strings) == 2 selection = pdb_hierarchy.atom_selection_cache().selection( string=" or ".join(answer)) xrs_1 = pdb_inp.xray_structure_simple().select(selection = selection) xrs_2 = iotbx.pdb.input(source_info=None, lines=m2_out_str).xray_structure_simple() assert approx_equal( xrs_1.structure_factors(d_min=2).f_calc().data(), xrs_2.structure_factors(d_min=2).f_calc().data()) def exercise_02 () : pdb_inp = iotbx.pdb.input(source_info=None, lines=m3_in_str) pdb_hierarchy = pdb_inp.construct_hierarchy() pdb_hierarchy.atoms().reset_i_seq() sel_strings=mmtbx.refinement.rigid_body.rigid_groups_from_pdb_chains( pdb_hierarchy=pdb_hierarchy, group_all_by_chain=True) assert sel_strings == ["(chain 'L' and not (resname HOH or resname WAT))"] if (__name__ == "__main__"): exercise_00() exercise_01() exercise_02() print "OK"