from __future__ import absolute_import, division, print_function from libtbx import easy_run import iotbx.mtz from libtbx.test_utils import approx_equal import time pdb_str = """ CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 MODEL 1 ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 0.00 N ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 0.00 C ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 0.00 C ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 0.00 O ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 0.00 C ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 0.00 C ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 0.00 S ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 0.00 C ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 0.00 N ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 0.00 C ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 0.00 C ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 0.00 O ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 0.00 C ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 0.00 C ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 0.00 C ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 0.00 O ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 0.00 N ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 0.00 N ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 0.00 C ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 0.00 C ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 0.00 O ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 0.00 C ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 0.00 C ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 0.00 C ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 0.00 C ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 0.00 N ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 0.00 C ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 0.00 C ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 0.00 O ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 0.00 C ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 0.00 C ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 0.00 C ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 0.00 C ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 0.00 C ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 0.00 C ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 0.00 C ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 0.00 N ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 0.00 C ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 0.00 C ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 0.00 O ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 0.00 C ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 0.00 C ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 0.00 C TER ENDMDL MODEL 2 ATOM 1 N MET A 1 27.840 24.430 2.614 1.00 0.00 N ATOM 2 CA MET A 1 26.766 25.413 2.842 1.00 0.00 C ATOM 3 C MET A 1 27.413 26.639 3.531 1.00 0.00 C ATOM 4 O MET A 1 28.386 26.463 4.263 1.00 0.00 O ATOM 5 CB MET A 1 25.612 24.880 3.649 1.00 0.00 C ATOM 6 CG MET A 1 25.853 24.860 5.134 1.00 0.00 C ATOM 7 SD MET A 1 24.430 23.959 5.904 1.00 0.00 S ATOM 8 CE MET A 1 24.947 23.984 7.620 1.00 0.00 C ATOM 9 N GLN A 2 26.835 27.770 3.258 1.00 0.00 N ATOM 10 CA GLN A 2 27.350 29.021 3.898 1.00 0.00 C ATOM 11 C GLN A 2 26.600 29.253 5.202 1.00 0.00 C ATOM 12 O GLN A 2 25.365 29.024 5.330 1.00 0.00 O ATOM 13 CB GLN A 2 27.233 30.148 2.905 1.00 0.00 C ATOM 14 CG GLN A 2 27.382 31.546 3.409 1.00 0.00 C ATOM 15 CD GLN A 2 27.286 32.562 2.270 1.00 0.00 C ATOM 16 OE1 GLN A 2 28.283 33.160 1.870 1.00 0.00 O ATOM 17 NE2 GLN A 2 26.062 32.733 1.806 1.00 0.00 N ATOM 18 N ILE A 3 27.349 29.656 6.217 1.00 0.00 N ATOM 19 CA ILE A 3 26.735 30.058 7.497 1.00 0.00 C ATOM 20 C ILE A 3 27.382 31.428 7.862 1.00 0.00 C ATOM 21 O ILE A 3 28.406 31.711 7.264 1.00 0.00 O ATOM 22 CB ILE A 3 26.844 29.050 8.645 1.00 0.00 C ATOM 23 CG1 ILE A 3 28.310 28.748 8.999 1.00 0.00 C ATOM 24 CG2 ILE A 3 25.991 27.771 8.287 1.00 0.00 C ATOM 25 CD1 ILE A 3 28.467 28.087 10.417 1.00 0.00 C ATOM 26 N PHE A 4 26.714 32.097 8.771 1.00 0.00 N ATOM 27 CA PHE A 4 27.272 33.436 9.197 1.00 0.00 C ATOM 28 C PHE A 4 27.651 33.362 10.650 1.00 0.00 C ATOM 29 O PHE A 4 26.850 32.778 11.395 1.00 0.00 O ATOM 30 CB PHE A 4 26.195 34.498 8.946 1.00 0.00 C ATOM 31 CG PHE A 4 25.788 34.609 7.499 1.00 0.00 C ATOM 32 CD1 PHE A 4 24.647 33.966 7.038 1.00 0.00 C ATOM 33 CD2 PHE A 4 26.636 35.346 6.640 1.00 0.00 C ATOM 34 CE1 PHE A 4 24.312 34.031 5.677 1.00 0.00 C ATOM 35 CE2 PHE A 4 26.310 35.392 5.267 1.00 0.00 C ATOM 36 CZ PHE A 4 25.120 34.778 4.853 1.00 0.00 C ATOM 37 N VAL A 5 28.760 33.943 11.096 1.00 0.00 N ATOM 38 CA VAL A 5 29.105 33.965 12.503 1.00 0.00 C ATOM 39 C VAL A 5 29.138 35.461 12.900 1.00 0.00 C ATOM 40 O VAL A 5 30.022 36.103 12.320 1.00 0.00 O ATOM 41 CB VAL A 5 30.463 33.317 12.814 1.00 0.00 C ATOM 42 CG1 VAL A 5 30.711 33.394 14.304 1.00 0.00 C ATOM 43 CG2 VAL A 5 30.457 31.838 12.352 1.00 0.00 C TER ENDMDL END """ #cctbx.diffuse pdb=m.pdb probabilities=0.5,0.5 resolution=4.0 prefix=tst def exercise(): fo = open("tst_diffuse.pdb","w") print(pdb_str, file=fo) fo.close() cmd = " ".join([ "cctbx.diffuse", "pdb=tst_diffuse.pdb", "probabilities=0.5,0.5", "resolution=4.0", "prefix=tst_diffuse"]) if 0: print(cmd) easy_run.call(cmd) mas = iotbx.mtz.object(file_name="tst_diffuse.mtz").as_miller_arrays() assert len(mas) == 1 ma = mas[0] assert ma.data().size() == 937, ma.data().size() assert approx_equal(ma.d_max_min(), (32.728, 4.0), 1.e-3) assert approx_equal((ma.data()/1000.).min_max_mean().as_tuple(), (0.001, 6.118, 0.35456), 1.e-3) assert ma.info().labels == ['I', 'SIGI'] assert approx_equal(ma.unit_cell().parameters(), (50.84,42.77,28.95,90.0,90.0,90.0), 1.e-2) if __name__ == '__main__': t0 = time.time() exercise() print("Time: %5.2f"%(time.time()-t0)) print("OK")