from __future__ import absolute_import, division, print_function from mmtbx.validation.molprobity import nqh_minimize from iotbx import pdb from libtbx.utils import null_out import time pdb_str_1 = \ """USER MOD Single : A 49 GLN :FLIP amide:sc= 0.595 F(o=-3.2!,f=0.59) USER MOD Single : A 60 ASN B:FLIP amide:sc= -0.0622 F(o=-0.92,f=-0.062) ATOM 321 N ARG A 42 32.478 30.917 22.269 1.00 5.73 N ATOM 322 CA ARG A 42 31.200 30.329 22.780 1.00 6.97 C ATOM 323 C ARG A 42 30.210 30.509 21.650 1.00 7.15 C ATOM 324 O ARG A 42 29.978 31.726 21.269 1.00 7.33 O ATOM 325 CB ARG A 42 30.847 30.931 24.118 1.00 13.23 C ATOM 326 CG ARG A 42 29.412 30.796 24.598 1.00 21.27 C ATOM 327 CD ARG A 42 29.271 31.314 26.016 1.00 26.14 C ATOM 328 NE ARG A 42 27.875 31.317 26.443 1.00 32.26 N ATOM 329 CZ ARG A 42 27.132 32.423 26.574 1.00 34.32 C ATOM 330 NH1 ARG A 42 27.630 33.656 26.461 1.00 35.30 N ATOM 331 NH2 ARG A 42 25.810 32.299 26.732 1.00 36.39 N ATOM 0 HA ARG A 42 31.236 29.383 22.989 1.00 6.97 H new ATOM 0 HB2 ARG A 42 31.424 30.530 24.787 1.00 13.23 H new ATOM 0 HB3 ARG A 42 31.063 31.876 24.086 1.00 13.23 H new ATOM 0 HG2 ARG A 42 28.821 31.289 24.008 1.00 21.27 H new ATOM 0 HG3 ARG A 42 29.139 29.866 24.560 1.00 21.27 H new ATOM 0 HD2 ARG A 42 29.794 30.762 26.618 1.00 26.14 H new ATOM 0 HD3 ARG A 42 29.630 32.213 26.071 1.00 26.14 H new ATOM 0 HE ARG A 42 27.507 30.561 26.622 1.00 32.26 H new ATOM 0 HH11 ARG A 42 28.467 33.768 26.296 1.00 35.30 H new ATOM 0 HH12 ARG A 42 27.114 34.338 26.553 1.00 35.30 H new ATOM 0 HH21 ARG A 42 25.450 31.518 26.748 1.00 36.39 H new ATOM 0 HH22 ARG A 42 25.320 33.000 26.817 1.00 36.39 H new ATOM 377 N GLN A 49 23.880 26.727 23.851 1.00 8.89 N ATOM 378 CA GLN A 49 25.349 26.872 23.643 1.00 7.18 C ATOM 379 C GLN A 49 25.743 25.586 22.922 1.00 8.23 C ATOM 380 O GLN A 49 25.325 24.489 23.378 1.00 9.70 O ATOM 381 CB GLN A 49 26.070 27.025 24.960 1.00 11.67 C ATOM 382 CG GLN A 49 27.553 27.356 24.695 1.00 15.82 C ATOM 383 CD GLN A 49 28.262 27.576 26.020 1.00 20.21 C ATOM 384 OE1 GLN A 49 27.777 28.585 26.739 1.00 23.23 O flip ATOM 385 NE2 GLN A 49 29.189 26.840 26.335 1.00 20.67 N flip ATOM 0 HA GLN A 49 25.584 27.663 23.134 1.00 7.18 H new ATOM 0 HB2 GLN A 49 25.660 27.730 25.485 1.00 11.67 H new ATOM 0 HB3 GLN A 49 25.998 26.207 25.477 1.00 11.67 H new ATOM 0 HG2 GLN A 49 27.975 26.632 24.207 1.00 15.82 H new ATOM 0 HG3 GLN A 49 27.624 28.150 24.142 1.00 15.82 H new ATOM 0 HE21 GLN A 49 29.437 26.210 25.805 1.00 20.67 H new ATOM 0 HE22 GLN A 49 29.592 26.954 27.086 1.00 20.67 H new ATOM 467 N BASN A 60 19.993 20.884 14.049 1.00 12.38 N ATOM 468 CA BASN A 60 19.065 21.352 12.999 1.00 13.94 C ATOM 469 C BASN A 60 19.442 22.745 12.510 1.00 14.16 C ATOM 470 O BASN A 60 18.571 23.610 12.289 1.00 14.26 O ATOM 471 CB BASN A 60 17.586 21.282 13.461 1.00 19.23 C ATOM 472 CG BASN A 60 16.576 21.258 12.315 1.00 22.65 C ATOM 473 OD1BASN A 60 16.924 20.586 11.216 1.00 25.45 O flip ATOM 474 ND2BASN A 60 15.440 21.819 12.378 1.00 24.09 N flip ATOM 0 H BASN A 60 20.401 20.147 13.878 1.00 12.38 H new ATOM 0 HA BASN A 60 19.150 20.747 12.246 1.00 13.94 H new ATOM 0 HB2BASN A 60 17.464 20.487 14.004 1.00 19.23 H new ATOM 0 HB3BASN A 60 17.398 22.045 14.029 1.00 19.23 H new ATOM 0 HD21BASN A 60 15.213 22.253 13.085 1.00 24.09 H new ATOM 0 HD22BASN A 60 14.897 21.766 11.714 1.00 24.09 H new END """ def run_validation(pdb_file, ignore_hd=True): from mmtbx.validation import restraints import mmtbx.command_line cmdline = mmtbx.command_line.load_model_and_data( args=[pdb_file], master_phil=mmtbx.command_line.generic_simple_input_phil(), process_pdb_file=True, require_data=False, out=null_out()) validation = restraints.combined( pdb_hierarchy=cmdline.pdb_hierarchy, xray_structure=cmdline.xray_structure, geometry_restraints_manager=cmdline.geometry, ignore_hd=ignore_hd) return validation def exercise_nqh_minimize(): open('modelFH.pdb', 'w').write(pdb_str_1) args = ['modelFH.pdb', 'modelFH_reg.pdb', '.'] nqh_minimize.run(args) v1 = run_validation('modelFH.pdb', ignore_hd=True) v2 = run_validation('modelFH_reg.pdb', ignore_hd=True) assert v1.bonds.n_outliers == 3 assert v2.bonds.n_outliers == 0 if (__name__ == "__main__"): t0 = time.time() exercise_nqh_minimize() print("OK. Time: %8.3f"%(time.time()-t0))