from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.model import time """ Test multiplication of hierarchy and SS annotations in different combinations of MTRIX and BIOMT records presence. Corner case where MTRIX and BIOMT are identical. We want to silently skip BIOMT multiplication if MTRIX was done, but not skip if MTRIX was not done. """ # pdb id: 7a5v pdb_lines = """ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.309017 -0.951057 0.000000 239.91182 MTRIX2 2 0.951057 0.309017 0.000000 -37.99830 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.809017 -0.587785 0.000000 350.18719 MTRIX2 3 0.587785 -0.809017 0.000000 178.42929 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.309017 -0.951057 0.000000 239.91182 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -37.99830 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 350.18719 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 178.42929 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 ATOM 21 N SER A 10 121.825 143.282 92.198 1.00 49.53 N ATOM 22 CA SER A 10 122.763 143.750 91.142 1.00 53.90 C ATOM 23 C SER A 10 122.515 145.240 90.852 1.00 44.64 C ATOM 24 O SER A 10 123.502 145.971 90.659 1.00 49.23 O ATOM 25 CB SER A 10 122.649 142.922 89.891 1.00 54.86 C ATOM 26 OG SER A 10 121.430 143.193 89.228 1.00 60.17 O ATOM 27 N PHE A 11 121.253 145.670 90.877 1.00 39.99 N ATOM 28 CA PHE A 11 120.852 147.084 90.685 1.00 46.43 C ATOM 29 C PHE A 11 121.347 147.931 91.873 1.00 53.53 C ATOM 30 O PHE A 11 121.866 149.042 91.635 1.00 45.84 O ATOM 31 CB PHE A 11 119.339 147.230 90.531 1.00 45.10 C ATOM 32 CG PHE A 11 118.884 148.665 90.434 1.00 50.94 C ATOM 33 CD1 PHE A 11 119.380 149.498 89.437 1.00 58.07 C ATOM 34 CD2 PHE A 11 118.032 149.212 91.385 1.00 57.16 C ATOM 35 CE1 PHE A 11 118.988 150.831 89.362 1.00 56.76 C ATOM 36 CE2 PHE A 11 117.629 150.541 91.299 1.00 59.88 C ATOM 37 CZ PHE A 11 118.121 151.352 90.299 1.00 55.92 C ATOM 38 N VAL A 12 121.144 147.455 93.110 1.00 43.35 N ATOM 39 CA VAL A 12 121.615 148.167 94.333 1.00 40.73 C ATOM 40 C VAL A 12 123.143 148.194 94.308 1.00 37.70 C ATOM 41 O VAL A 12 123.700 149.281 94.511 1.00 41.01 O ATOM 42 CB VAL A 12 121.073 147.560 95.640 1.00 46.83 C ATOM 43 CG1 VAL A 12 121.686 148.244 96.866 1.00 40.11 C ATOM 44 CG2 VAL A 12 119.551 147.638 95.701 1.00 41.22 C ATOM 45 N LYS A 13 123.785 147.091 93.923 1.00 36.58 N ATOM 46 CA LYS A 13 125.268 147.018 93.854 1.00 41.77 C ATOM 47 C LYS A 13 125.761 148.054 92.839 1.00 42.08 C ATOM 48 O LYS A 13 126.776 148.724 93.128 1.00 38.35 O ATOM 49 CB LYS A 13 125.757 145.612 93.490 1.00 46.55 C ATOM 50 CG LYS A 13 127.268 145.492 93.315 1.00 46.87 C ATOM 51 CD LYS A 13 127.740 144.113 92.898 1.00 58.69 C ATOM 52 CE LYS A 13 129.223 144.071 92.578 1.00 64.30 C ATOM 53 NZ LYS A 13 130.049 143.879 93.793 1.00 72.87 N ATOM 54 N GLU A 14 125.080 148.160 91.694 1.00 42.55 N ATOM 55 CA GLU A 14 125.407 149.148 90.630 1.00 47.24 C ATOM 56 C GLU A 14 125.269 150.559 91.210 1.00 34.67 C ATOM 57 O GLU A 14 126.169 151.376 90.970 1.00 40.45 O ATOM 58 CB GLU A 14 124.498 148.982 89.407 1.00 52.19 C ATOM 59 CG GLU A 14 125.009 147.963 88.402 1.00 82.30 C ATOM 60 CD GLU A 14 124.265 147.939 87.071 1.00104.62 C """ def exercise_biomt_only(): """ Use-case for phenix.pdb.biomt_reconstruction - we want to expand only using biomt """ inp = iotbx.pdb.input(lines=pdb_lines, source_info=None) model = mmtbx.model.manager( model_input = inp, expand_with_mtrix = False) assert model.get_number_of_atoms() == 40, model.get_number_of_atoms() model.expand_with_BIOMT_records() assert model.get_number_of_atoms() == 120, model.get_number_of_atoms() def exercise_mtrix_only(): """ Use-case for phenix.pdb.mtrix_reconstruction - we want to expand only using mtrix """ inp = iotbx.pdb.input(lines=pdb_lines, source_info=None) model = mmtbx.model.manager( model_input = inp) assert model.get_number_of_atoms() == 120, model.get_number_of_atoms() # use-case for phenix.real_space_refine ??? when normally we want to expand by MTRIX first # and by BIOMT second, but not in case when BIOMT == MTRIX... model.expand_with_BIOMT_records() assert model.get_number_of_atoms() == 120, model.get_number_of_atoms() if (__name__ == "__main__"): t0 = time.time() exercise_biomt_only() exercise_mtrix_only() print("Total time: %8.3f"%(time.time() - t0)) print("OK.")