from __future__ import division from libtbx.test_utils import approx_equal import iotbx.ncs import iotbx.pdb pdb_str_1 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER """ pdb_str_2 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 O HOH S 1 109.583 203.076 175.423 1.00 0.00 O TER ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER ATOM 9 O TYR D 4 189.583 273.076 175.423 1.00 0.00 O TER """ pdb_str_3 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 O HOH C 34 189.583 273.076 175.423 1.00 0.00 O ATOM 10 O HOH C 34 188.804 273.006 174.173 1.00 0.00 O ATOM 11 O HOH C 34 188.920 271.622 173.510 1.00 0.00 O ATOM 12 O HOH C 34 189.986 271.004 173.508 1.00 0.00 O TER """ pdb_str_4 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N TYR C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA TYR C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C TYR C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O TYR C 34 189.986 271.004 173.508 1.00 0.00 O TER """ pdb_str_5 = """ ATOM 1 N MET A 1 158.070 173.095 147.115 1.00 50.00 N ATOM 2 CA MET A 1 157.408 172.627 148.359 1.00 50.00 C ATOM 3 CB MET A 1 157.550 171.094 148.516 1.00 50.00 C ATOM 4 CG MET A 1 156.748 170.503 149.691 1.00 50.00 C ATOM 5 SD MET A 1 154.968 170.855 149.612 1.00 50.00 S ATOM 6 CE MET A 1 154.505 169.913 151.091 1.00 50.00 C ATOM 7 C MET A 1 157.958 173.331 149.563 1.00 50.00 C ATOM 8 O MET A 1 157.196 173.814 150.399 1.00 50.00 O TER ATOM 9 N MET B 1 174.781 155.306 150.054 1.00 50.00 N ATOM 10 CA MET B 1 174.332 154.630 151.298 1.00 50.00 C ATOM 11 CB MET B 1 175.016 153.251 151.453 1.00 50.00 C ATOM 12 CG MET B 1 174.481 152.410 152.628 1.00 50.00 C ATOM 13 SD MET B 1 172.693 152.099 152.550 1.00 50.00 S ATOM 14 CE MET B 1 172.601 151.052 154.028 1.00 50.00 C ATOM 15 C MET B 1 174.594 155.484 152.502 1.00 50.00 C ATOM 16 O MET B 1 173.710 155.660 153.339 1.00 50.00 O TER ATOM 17 N MET C 1 148.867 195.697 144.146 1.00 50.00 N ATOM 18 CA MET C 1 148.080 195.499 145.390 1.00 50.00 C ATOM 19 CB MET C 1 147.662 194.018 145.549 1.00 50.00 C ATOM 20 CG MET C 1 146.701 193.755 146.723 1.00 50.00 C ATOM 21 SD MET C 1 145.166 194.723 146.643 1.00 50.00 S ATOM 22 CE MET C 1 144.395 194.012 148.122 1.00 50.00 C ATOM 23 C MET C 1 148.846 195.960 146.594 1.00 50.00 C ATOM 24 O MET C 1 148.308 196.685 147.429 1.00 50.00 O TER ATOM 417 N MET 1 1 274.499 237.478 69.907 1.00 50.00 N ATOM 418 CA MET 1 1 275.223 237.861 71.146 1.00 50.00 C ATOM 419 CB MET 1 1 275.281 239.400 71.298 1.00 50.00 C ATOM 420 CG MET 1 1 276.159 239.886 72.466 1.00 50.00 C ATOM 421 SD MET 1 1 277.878 239.307 72.379 1.00 50.00 S ATOM 422 CE MET 1 1 278.468 240.186 73.852 1.00 50.00 C ATOM 423 C MET 1 1 274.593 237.238 72.356 1.00 50.00 C ATOM 424 O MET 1 1 275.291 236.663 73.190 1.00 50.00 O TER END """ def exercise_00(prefix="iotbx_ncs_exercise_00"): pdb_file_name = "%s.pdb"%prefix ncs_params_str = """ ncs_group { master_selection = chain A copy_selection = chain B copy_selection = chain C } """ def check_result(ncs_inp, test_i): if test_i == 0: l1, l2, l3 = [0,1,2,3], [4,5,6,7], [8,9,10,11] elif test_i == 1: l1, l2, l3 = [1,2,3,4], [5,6,7,8], [9,10,11,12] else: assert 0 ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 ncs_group = ncs_groups[0] assert approx_equal(ncs_group.master_iselection, l1) assert len(ncs_group.copies) == 2 assert approx_equal(ncs_group.copies[0].iselection, l2) assert approx_equal(ncs_group.copies[1].iselection, l3) for test_i, pdb_str in enumerate([pdb_str_1, pdb_str_2]): of = open(pdb_file_name, "w") print >> of, pdb_str of.close() pdb_inp = iotbx.pdb.input(file_name = pdb_file_name) if test_i == 0: # XXX Not implemented. Fix later. # using pdb_inp ncs_inp = iotbx.ncs.input(pdb_inp = pdb_inp) check_result(ncs_inp,test_i) # using file_name ncs_inp = iotbx.ncs.input(file_name = pdb_file_name) check_result(ncs_inp,test_i) # using pdb string ncs_inp = iotbx.ncs.input(pdb_string = pdb_str) check_result(ncs_inp,test_i) # using combination of pdb_inp and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_inp = pdb_inp, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) # using combination of pdb file name and Phil parameter string ncs_inp = iotbx.ncs.input(file_name = pdb_file_name, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) # using combination of pdb string and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_string = pdb_str, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) def exercise_01(prefix="iotbx_ncs_exercise_01"): """ Make sure provided selections take precedence and are correctly respected. """ pdb_file_name = "%s.pdb"%prefix ncs_params_str = """ ncs_group { master_selection = chain C copy_selection = chain A } """ def check_result(ncs_inp, test_i): if test_i == 0: l1, l2 = [8,9,10,11], [0,1,2,3] elif test_i == 1: l1, l2 = [9,10,11,12], [1,2,3,4] else: assert 0 ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 ncs_group = ncs_groups[0] assert approx_equal(ncs_group.master_iselection, l1) assert len(ncs_group.copies) == 1 assert approx_equal(ncs_group.copies[0].iselection, l2) for test_i, pdb_str in enumerate([pdb_str_1, pdb_str_2]): of = open(pdb_file_name, "w") print >> of, pdb_str of.close() pdb_inp = iotbx.pdb.input(file_name = pdb_file_name) # using combination of pdb_inp and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_inp = pdb_inp, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) # using combination of pdb file name and Phil parameter string ncs_inp = iotbx.ncs.input(file_name = pdb_file_name, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) # using combination of pdb string and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_string = pdb_str, ncs_selection_params = ncs_params_str) check_result(ncs_inp,test_i) def exercise_02(prefix="iotbx_ncs_exercise_02"): """ This is expected to fail as requested chains cannot be matched. """ pdb_file_name = "%s.pdb"%prefix ncs_params_str = """ ncs_group { master_selection = chain C copy_selection = chain A } """ for test_i, pdb_str in enumerate([pdb_str_3, pdb_str_4]): of = open(pdb_file_name, "w") print >> of, pdb_str of.close() pdb_inp = iotbx.pdb.input(file_name = pdb_file_name) # using combination of pdb_inp and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_inp = pdb_inp, ncs_selection_params = ncs_params_str) ncs_groups = ncs_inp.get_ncs_restraints_group_list() # using combination of pdb file name and Phil parameter string ncs_inp = iotbx.ncs.input(file_name = pdb_file_name, ncs_selection_params = ncs_params_str) ncs_groups = ncs_inp.get_ncs_restraints_group_list() # using combination of pdb string and Phil parameter string ncs_inp = iotbx.ncs.input(pdb_string = pdb_str, ncs_selection_params = ncs_params_str) ncs_groups = ncs_inp.get_ncs_restraints_group_list() def exercise_03(prefix="iotbx_ncs_exercise_03"): """ Expect one master and 3 copies. """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_5) ncs_inp = iotbx.ncs.input(pdb_inp = pdb_inp) ncs_groups = ncs_inp.get_ncs_restraints_group_list() asc = ncs_inp.hierarchy.atom_selection_cache() sel_master = asc.selection(string = "chain A") sel_copy_1 = asc.selection(string = "chain B") sel_copy_2 = asc.selection(string = "chain C") sel_copy_3 = asc.selection(string = "chain 1") assert len(ncs_groups)==1 ng = ncs_groups[0] # chains are sorted by name (numbers first) assert approx_equal(sel_master.iselection(), ng.master_iselection) assert approx_equal(sel_copy_1.iselection(), ng.copies[1].iselection) assert approx_equal(sel_copy_2.iselection(), ng.copies[2].iselection) assert approx_equal(sel_copy_3.iselection(), ng.copies[0].iselection) if (__name__ == "__main__"): exercise_00() exercise_01() exercise_02() exercise_03()