from __future__ import absolute_import, division, print_function import time import mmtbx.model import iotbx.pdb from mmtbx.validation import ramalyze # ------------------------------------------------------------------------------ # Make sure that pdb file with several models produces results for all models # ------------------------------------------------------------------------------ def exercise(): pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) pdb_hierarchy = model.get_hierarchy() r = ramalyze.ramalyze( pdb_hierarchy = pdb_hierarchy, outliers_only = False) assert (len(r.results) == 3), 'Supposed to fail until fixed. Ramalyze results not available for all models.' pdb_str = """ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ATOM 1 N ASN A 1 1.329 0.000 0.000 1.00 1.00 N ATOM 2 CA ASN A 1 2.093 -0.001 -1.242 1.00 64.21 C ATOM 3 C ASN A 1 1.973 -1.345 -1.954 1.00 21.54 C ATOM 4 O ASN A 1 2.071 -1.423 -3.178 1.00 42.13 O ATOM 5 CB ASN A 1 3.565 0.309 -0.960 1.00 52.42 C ATOM 6 CG ASN A 1 4.305 0.774 -2.199 1.00 64.34 C ATOM 7 OD1 ASN A 1 4.331 0.081 -3.217 1.00 14.30 O ATOM 8 ND2 ASN A 1 4.913 1.952 -2.118 1.00 64.45 N ATOM 9 H1 ASN A 1 1.808 0.001 0.855 1.00 15.23 H ATOM 10 HA ASN A 1 1.688 0.769 -1.881 1.00 62.21 H ATOM 11 HB2 ASN A 1 3.625 1.089 -0.215 1.00 4.30 H ATOM 12 HB3 ASN A 1 4.049 -0.580 -0.585 1.00 41.42 H ATOM 13 HD21 ASN A 1 4.851 2.448 -1.276 1.00 0.23 H ATOM 14 HD22 ASN A 1 5.399 2.276 -2.905 1.00 40.32 H ATOM 15 N VAL A 2 1.759 -2.403 -1.177 1.00 2.11 N ATOM 16 CA VAL A 2 1.623 -3.744 -1.732 1.00 65.20 C ATOM 17 C VAL A 2 0.180 -4.031 -2.128 1.00 74.53 C ATOM 18 O VAL A 2 -0.536 -4.748 -1.429 1.00 30.45 O ATOM 19 CB VAL A 2 2.092 -4.816 -0.730 1.00 64.25 C ATOM 20 CG1 VAL A 2 2.069 -6.195 -1.373 1.00 50.44 C ATOM 21 CG2 VAL A 2 3.483 -4.486 -0.209 1.00 13.30 C ATOM 22 H VAL A 2 1.690 -2.278 -0.207 1.00 43.35 H ATOM 23 HA VAL A 2 2.247 -3.806 -2.612 1.00 23.21 H ATOM 24 HB VAL A 2 1.409 -4.822 0.106 1.00 41.00 H ATOM 25 HG11 VAL A 2 2.853 -6.803 -0.948 1.00 21.35 H ATOM 26 HG12 VAL A 2 1.111 -6.660 -1.192 1.00 63.34 H ATOM 27 HG13 VAL A 2 2.227 -6.098 -2.437 1.00 44.14 H ATOM 28 HG21 VAL A 2 3.405 -4.080 0.789 1.00 40.14 H ATOM 29 HG22 VAL A 2 4.082 -5.384 -0.186 1.00 63.31 H ATOM 30 HG23 VAL A 2 3.948 -3.760 -0.859 1.00 1.55 H ATOM 31 N ASP A 3 -0.242 -3.468 -3.255 1.00 10.11 N ATOM 32 CA ASP A 3 -1.601 -3.665 -3.746 1.00 41.42 C ATOM 33 C ASP A 3 -1.619 -4.643 -4.916 1.00 74.14 C ATOM 34 O ASP A 3 -1.696 -4.238 -6.077 1.00 21.55 O ATOM 35 CB ASP A 3 -2.210 -2.328 -4.173 1.00 71.21 C ATOM 36 CG ASP A 3 -2.287 -1.335 -3.030 1.00 22.40 C ATOM 37 OD1 ASP A 3 -1.324 -0.559 -2.852 1.00 33.41 O ATOM 38 OD2 ASP A 3 -3.310 -1.334 -2.314 1.00 4.32 O ATOM 39 H ASP A 3 0.376 -2.907 -3.769 1.00 51.30 H ATOM 40 HA ASP A 3 -2.189 -4.076 -2.940 1.00 22.31 H ATOM 41 HB2 ASP A 3 -1.605 -1.898 -4.958 1.00 61.42 H ATOM 42 HB3 ASP A 3 -3.209 -2.498 -4.546 1.00 71.35 H TER 43 ASP A 3 ENDMDL MODEL 2 ATOM 1 N ASN A 1 1.728 -3.986 -1.323 1.00 51.14 N ATOM 2 CA ASN A 1 2.250 -2.656 -1.616 1.00 71.03 C ATOM 3 C ASN A 1 1.152 -1.749 -2.162 1.00 53.34 C ATOM 4 O ASN A 1 0.899 -1.718 -3.367 1.00 12.41 O ATOM 5 CB ASN A 1 3.399 -2.747 -2.622 1.00 42.32 C ATOM 6 CG ASN A 1 4.579 -3.531 -2.082 1.00 65.14 C ATOM 7 OD1 ASN A 1 5.209 -3.132 -1.102 1.00 55.44 O ATOM 8 ND2 ASN A 1 4.886 -4.654 -2.722 1.00 35.14 N ATOM 9 H1 ASN A 1 1.721 -4.663 -2.032 1.00 31.13 H ATOM 10 HA ASN A 1 2.623 -2.236 -0.694 1.00 54.13 H ATOM 11 HB2 ASN A 1 3.047 -3.236 -3.519 1.00 11.31 H ATOM 12 HB3 ASN A 1 3.734 -1.750 -2.868 1.00 63.43 H ATOM 13 HD21 ASN A 1 4.340 -4.910 -3.495 1.00 24.31 H ATOM 14 HD22 ASN A 1 5.644 -5.181 -2.393 1.00 73.24 H ATOM 15 N VAL A 2 0.502 -1.010 -1.268 1.00 21.51 N ATOM 16 CA VAL A 2 -0.568 -0.101 -1.660 1.00 1.25 C ATOM 17 C VAL A 2 -1.748 -0.863 -2.251 1.00 51.04 C ATOM 18 O VAL A 2 -2.193 -0.573 -3.362 1.00 73.21 O ATOM 19 CB VAL A 2 -0.075 0.937 -2.685 1.00 42.21 C ATOM 20 CG1 VAL A 2 -1.101 2.047 -2.857 1.00 63.03 C ATOM 21 CG2 VAL A 2 1.272 1.505 -2.262 1.00 55.34 C ATOM 22 H VAL A 2 0.749 -1.079 -0.322 1.00 40.21 H ATOM 23 HA VAL A 2 -0.898 0.426 -0.776 1.00 74.01 H ATOM 24 HB VAL A 2 0.050 0.442 -3.637 1.00 31.22 H ATOM 25 HG11 VAL A 2 -0.656 2.993 -2.587 1.00 5.23 H ATOM 26 HG12 VAL A 2 -1.425 2.081 -3.887 1.00 42.51 H ATOM 27 HG13 VAL A 2 -1.950 1.854 -2.218 1.00 60.04 H ATOM 28 HG21 VAL A 2 2.045 0.776 -2.452 1.00 73.22 H ATOM 29 HG22 VAL A 2 1.477 2.403 -2.827 1.00 45.03 H ATOM 30 HG23 VAL A 2 1.249 1.741 -1.209 1.00 33.20 H ATOM 31 N ASP A 3 -2.251 -1.838 -1.502 1.00 61.14 N ATOM 32 CA ASP A 3 -3.382 -2.642 -1.952 1.00 25.01 C ATOM 33 C ASP A 3 -3.129 -3.202 -3.348 1.00 61.32 C ATOM 34 O ASP A 3 -3.762 -2.788 -4.319 1.00 13.41 O ATOM 35 CB ASP A 3 -4.662 -1.806 -1.948 1.00 74.23 C ATOM 36 CG ASP A 3 -5.117 -1.450 -0.547 1.00 13.13 C ATOM 37 OD1 ASP A 3 -4.608 -2.061 0.416 1.00 22.02 O ATOM 38 OD2 ASP A 3 -5.982 -0.559 -0.412 1.00 71.45 O ATOM 39 H ASP A 3 -1.852 -2.021 -0.626 1.00 35.24 H ATOM 40 HA ASP A 3 -3.498 -3.465 -1.263 1.00 62.12 H ATOM 41 HB2 ASP A 3 -4.488 -0.890 -2.494 1.00 34.02 H ATOM 42 HB3 ASP A 3 -5.450 -2.365 -2.432 1.00 51.44 H TER 43 ASP A 3 ENDMDL MODEL 3 ATOM 1 N ASN A 1 0.315 -4.452 -3.331 1.00 42.01 N ATOM 2 CA ASN A 1 0.480 -3.854 -2.011 1.00 52.12 C ATOM 3 C ASN A 1 0.359 -2.335 -2.083 1.00 54.35 C ATOM 4 O ASN A 1 0.991 -1.690 -2.920 1.00 11.31 O ATOM 5 CB ASN A 1 1.836 -4.241 -1.419 1.00 2.14 C ATOM 6 CG ASN A 1 1.801 -4.332 0.095 1.00 41.02 C ATOM 7 OD1 ASN A 1 1.394 -3.390 0.775 1.00 22.22 O ATOM 8 ND2 ASN A 1 2.229 -5.470 0.629 1.00 42.11 N ATOM 9 H1 ASN A 1 1.058 -4.413 -3.969 1.00 51.24 H ATOM 10 HA ASN A 1 -0.304 -4.236 -1.374 1.00 64.13 H ATOM 11 HB2 ASN A 1 2.132 -5.203 -1.811 1.00 23.01 H ATOM 12 HB3 ASN A 1 2.570 -3.501 -1.700 1.00 1.32 H ATOM 13 HD21 ASN A 1 2.539 -6.177 0.025 1.00 24.23 H ATOM 14 HD22 ASN A 1 2.217 -5.556 1.605 1.00 72.10 H ATOM 15 N VAL A 2 -0.458 -1.769 -1.200 1.00 71.03 N ATOM 16 CA VAL A 2 -0.661 -0.326 -1.162 1.00 54.31 C ATOM 17 C VAL A 2 -1.033 0.213 -2.539 1.00 12.52 C ATOM 18 O VAL A 2 -0.225 0.866 -3.200 1.00 73.12 O ATOM 19 CB VAL A 2 0.598 0.405 -0.659 1.00 53.34 C ATOM 20 CG1 VAL A 2 0.336 1.899 -0.539 1.00 60.15 C ATOM 21 CG2 VAL A 2 1.053 -0.173 0.672 1.00 63.12 C ATOM 22 H VAL A 2 -0.935 -2.336 -0.559 1.00 4.15 H ATOM 23 HA VAL A 2 -1.470 -0.120 -0.475 1.00 63.43 H ATOM 24 HB VAL A 2 1.387 0.258 -1.381 1.00 64.43 H ATOM 25 HG11 VAL A 2 1.120 2.443 -1.046 1.00 11.14 H ATOM 26 HG12 VAL A 2 -0.617 2.135 -0.990 1.00 1.10 H ATOM 27 HG13 VAL A 2 0.321 2.179 0.504 1.00 74.33 H ATOM 28 HG21 VAL A 2 0.189 -0.445 1.260 1.00 64.44 H ATOM 29 HG22 VAL A 2 1.659 -1.050 0.495 1.00 23.13 H ATOM 30 HG23 VAL A 2 1.635 0.564 1.205 1.00 14.11 H ATOM 31 N ASP A 3 -2.261 -0.063 -2.964 1.00 42.14 N ATOM 32 CA ASP A 3 -2.741 0.396 -4.263 1.00 34.24 C ATOM 33 C ASP A 3 -4.199 0.839 -4.177 1.00 5.10 C ATOM 34 O ASP A 3 -4.996 0.250 -3.447 1.00 4.24 O ATOM 35 CB ASP A 3 -2.593 -0.713 -5.306 1.00 10.31 C ATOM 36 CG ASP A 3 -1.146 -0.959 -5.687 1.00 75.20 C ATOM 37 OD1 ASP A 3 -0.715 -2.131 -5.652 1.00 42.22 O ATOM 38 OD2 ASP A 3 -0.446 0.019 -6.021 1.00 14.21 O ATOM 39 H ASP A 3 -2.859 -0.588 -2.391 1.00 44.52 H ATOM 40 HA ASP A 3 -2.138 1.240 -4.560 1.00 13.30 H ATOM 41 HB2 ASP A 3 -3.002 -1.630 -4.908 1.00 31.01 H ATOM 42 HB3 ASP A 3 -3.139 -0.436 -6.196 1.00 11.03 H TER 43 ASP A 3 ENDMDL END """ if (__name__ == "__main__"): t0 = time.time() exercise() print("OK. Time: %8.3f"%(time.time()-t0))