from __future__ import absolute_import, division, print_function import time, sys, os from six.moves import cStringIO as StringIO import libtbx.load_env import mmtbx.model import iotbx.pdb from mmtbx.monomer_library import pdb_interpretation def run(): verbose = "--verbose" in sys.argv[1:] exercise_00(verbose=verbose) exercise_01(verbose=verbose) exercise_02(verbose=verbose) exercise_03(verbose=verbose) exercise_04(verbose=verbose) exercise_05(verbose=verbose) def get_model(file_name, log, pdb_str=None): pdb_interpretation_params = iotbx.phil.parse( input_string=pdb_interpretation.grand_master_phil_str, process_includes=True).extract() pdb_interpretation_params.pdb_interpretation.sort_atoms=False if not pdb_str: pdb_inp = iotbx.pdb.input(file_name=file_name) else: pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = False, log=log) model.process(pdb_interpretation_params=pdb_interpretation_params) return model def exercise_00(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/occ_mix1.pdb", test=os.path.isfile) model = get_model(pdb_file, log) model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) assert(model.get_hd_selection().count(True) == 14) atom_names = [x.strip() for x in atoms.extract_name()] assert ('DA' not in atom_names) def exercise_01(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_hd.pdb", test=os.path.isfile) model = get_model(pdb_file, log) model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) assert(model.get_hd_selection().count(True) == 7) def exercise_02(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_lys_arg_ser_tyr_neutron_hd.pdb", test=os.path.isfile) model = get_model(pdb_file, log) model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) assert(model.get_hd_selection().count(True) == 47) def exercise_03(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/NAD_594_HD.pdb", test=os.path.isfile) model = get_model(pdb_file, log) model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) assert(model.get_hd_selection().count(True) == 43) def exercise_04(verbose): if (verbose): log = sys.stdout else: log = StringIO() model = get_model(file_name=None, log = log, pdb_str = pdb_str_1) model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) assert(model.get_hd_selection().count(True) == 15) atom_names = [x.strip() for x in atoms.extract_name()] assert ('D' not in atom_names) assert ('DG' not in atom_names) def exercise_05(verbose): if (verbose): log = sys.stdout else: log = StringIO() model = get_model(file_name=None, log = log, pdb_str = pdb_str_2) #model.get_hierarchy().write_pdb_file(file_name="haha.pdb") model.de_deuterate() assert(len(model.hd_group_selections())==0) ph = model.get_hierarchy() atoms = ph.atoms() assert(atoms.extract_element().count('D') == 0) #print(model.get_hd_selection().count(True)) assert(model.get_hd_selection().count(True) == 35) assert(model.selection('resname DOD').count(True) == 0) #ph.write_pdb_file(file_name="test.pdb") pdb_str_1 = ''' CRYST1 43.705 48.284 96.292 90.00 90.00 90.00 P 1 SCALE1 0.022881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010385 0.00000 ATOM 65 N SER A 4 9.243 -32.509 -36.471 1.00 38.02 N ATOM 66 CA SER A 4 10.063 -33.604 -36.981 1.00 39.55 C ATOM 67 C SER A 4 11.459 -33.153 -37.367 1.00 37.45 C ATOM 68 O SER A 4 11.633 -32.304 -38.239 1.00 38.82 O ATOM 69 CB SER A 4 9.384 -34.279 -38.180 1.00 41.66 C ATOM 70 OG SER A 4 8.375 -35.181 -37.753 1.00 44.91 O ATOM 71 DA SER A 4 10.165 -34.324 -36.187 1.00 38.72 D ATOM 72 D ASER A 4 8.730 -31.950 -37.103 0.62 38.48 D ATOM 73 DB2ASER A 4 10.116 -34.818 -38.774 0.63 41.36 D ATOM 74 DB3ASER A 4 8.918 -33.518 -38.793 0.36 41.73 D ATOM 75 DG ASER A 4 8.699 -36.084 -37.842 0.36 43.61 D ATOM 76 H BSER A 4 8.730 -31.950 -37.103 0.28 38.48 H ATOM 77 HB2BSER A 4 8.918 -33.518 -38.793 0.64 41.73 H ATOM 78 HB3BSER A 4 10.116 -34.818 -38.774 0.37 41.36 H ATOM 79 HG BSER A 4 8.699 -36.084 -37.842 0.64 43.61 H ATOM 80 N SER A 5 26.478 -19.398 45.776 1.00 19.78 N ATOM 81 C SER A 5 27.940 -19.562 43.818 1.00 21.99 C ATOM 82 O SER A 5 29.005 -19.770 43.306 1.00 21.20 O ATOM 83 CA ASER A 5 27.849 -19.441 45.318 0.64 18.99 C ATOM 84 CB ASER A 5 28.611 -20.590 45.987 0.64 21.66 C ATOM 85 OG ASER A 5 28.819 -20.337 47.363 0.64 23.21 O ATOM 86 DG ASER A 5 29.639 -20.155 47.499 0.64 22.10 D ATOM 87 H ASER A 5 26.064 -20.150 45.742 0.06 18.55 H ATOM 88 HA ASER A 5 28.296 -18.610 45.561 0.64 20.89 H ATOM 89 HB2ASER A 5 28.094 -21.408 45.903 0.00 22.17 H ATOM 90 HB3ASER A 5 29.468 -20.686 45.544 0.64 22.38 H ATOM 91 CA BSER A 5 27.851 -19.476 45.322 0.36 19.02 C ATOM 92 CB BSER A 5 28.561 -20.680 45.932 0.36 21.98 C ATOM 93 OG BSER A 5 28.005 -21.879 45.425 0.36 25.40 O ATOM 94 D BSER A 5 26.023 -20.128 45.688 0.94 18.55 D ATOM 95 HA BSER A 5 28.327 -18.675 45.599 0.36 21.03 H ATOM 96 HB2BSER A 5 29.498 -20.638 45.691 0.36 22.55 H ATOM 97 HB3BSER A 5 28.462 -20.665 46.898 0.36 23.83 H ATOM 98 HG BSER A 5 27.486 -22.196 46.000 0.36 22.10 H TER ''' pdb_str_2 = ''' CRYST1 43.705 48.284 96.292 90.00 90.00 90.00 P 1 SCALE1 0.022881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010385 0.00000 ATOM 1 N ASN A 1 25.174 -24.761 -21.940 1.00 16.59 N ATOM 2 CA ASN A 1 25.971 -25.578 -22.850 1.00 17.25 C ATOM 3 C ASN A 1 26.037 -24.941 -24.225 1.00 16.66 C ATOM 4 O ASN A 1 27.077 -24.979 -24.874 1.00 18.42 O ATOM 5 CB ASN A 1 25.498 -27.040 -22.913 1.00 18.30 C ATOM 6 CG ASN A 1 24.187 -27.208 -23.672 1.00 20.42 C ATOM 7 OD1 ASN A 1 23.167 -26.590 -23.335 1.00 20.87 O ATOM 8 ND2 ASN A 1 24.200 -28.069 -24.685 1.00 18.15 N ATOM 9 DA ASN A 1 26.975 -25.581 -22.461 1.00 15.99 D ATOM 10 DD21 ASN A 1 25.030 -28.545 -24.882 1.00 16.07 D ATOM 11 D AASN A 1 24.379 -25.105 -21.517 0.82 16.71 D ATOM 12 DB2AASN A 1 25.358 -27.400 -21.898 0.65 18.82 D ATOM 13 DB3AASN A 1 26.255 -27.641 -23.402 0.56 18.30 D ATOM 14 DD22AASN A 1 23.370 -28.163 -25.192 0.72 16.98 D ATOM 15 H BASN A 1 24.379 -25.105 -21.517 0.18 16.71 H ATOM 16 HB2BASN A 1 26.255 -27.641 -23.402 0.44 18.30 H ATOM 17 HB3BASN A 1 25.358 -27.400 -21.898 0.35 18.82 H ATOM 18 HD22BASN A 1 23.370 -28.163 -25.192 0.28 16.98 H ATOM 19 N ASN A 2 23.615 -22.281 -25.492 1.00 16.59 N ATOM 20 CA ASN A 2 24.412 -23.098 -26.402 1.00 17.25 C ATOM 21 C ASN A 2 24.478 -22.461 -27.777 1.00 16.66 C ATOM 22 O ASN A 2 25.518 -22.499 -28.426 1.00 18.42 O ATOM 23 CB ASN A 2 23.939 -24.560 -26.465 1.00 18.30 C ATOM 24 CG ASN A 2 22.628 -24.728 -27.224 1.00 20.42 C ATOM 25 OD1 ASN A 2 21.608 -24.110 -26.887 1.00 20.87 O ATOM 26 ND2 ASN A 2 22.641 -25.589 -28.237 1.00 18.15 N ATOM 27 DA ASN A 2 25.416 -23.101 -26.013 1.00 15.99 D ATOM 28 HD21 ASN A 2 23.471 -26.065 -28.434 1.00 16.07 H ATOM 29 D AASN A 2 22.820 -22.625 -25.069 0.82 16.71 D ATOM 30 DB2AASN A 2 23.799 -24.920 -25.450 0.65 18.82 D ATOM 31 DB3AASN A 2 24.696 -25.161 -26.954 0.56 18.30 D ATOM 32 DD22AASN A 2 21.811 -25.683 -28.744 0.72 16.98 D ATOM 33 H BASN A 2 22.820 -22.625 -25.069 0.18 16.71 H ATOM 34 HB2BASN A 2 24.696 -25.161 -26.954 0.44 18.30 H ATOM 35 HB3BASN A 2 23.799 -24.920 -25.450 0.35 18.82 H ATOM 36 HD22BASN A 2 21.811 -25.683 -28.744 0.28 16.98 H ATOM 37 N LEU A 3 23.374 -21.865 -28.222 1.00 15.90 N ATOM 38 CA LEU A 3 23.342 -21.224 -29.530 1.00 15.47 C ATOM 39 C LEU A 3 23.637 -19.727 -29.491 1.00 18.18 C ATOM 40 O LEU A 3 24.174 -19.175 -30.462 1.00 20.24 O ATOM 41 CB LEU A 3 22.021 -21.521 -30.238 1.00 15.76 C ATOM 42 CG LEU A 3 21.790 -23.005 -30.533 1.00 19.30 C ATOM 43 CD1 LEU A 3 20.460 -23.197 -31.290 1.00 20.74 C ATOM 44 CD2 LEU A 3 22.957 -23.627 -31.336 1.00 17.02 C ATOM 45 DA LEU A 3 24.132 -21.653 -30.101 1.00 12.76 D ATOM 46 DB3 LEU A 3 21.233 -21.196 -29.610 1.00 17.93 D ATOM 47 D ALEU A 3 22.567 -21.865 -27.663 0.91 16.63 D ATOM 48 DB2ALEU A 3 21.964 -20.976 -31.155 0.67 16.51 D ATOM 49 DG ALEU A 3 21.719 -23.530 -29.581 0.68 18.31 D ATOM 50 DD11ALEU A 3 19.620 -22.925 -30.652 0.74 20.52 D ATOM 51 DD12ALEU A 3 20.364 -24.239 -31.597 0.77 19.78 D ATOM 52 DD13ALEU A 3 20.458 -22.568 -32.171 0.49 20.26 D ATOM 53 DD21ALEU A 3 23.466 -22.855 -31.890 0.40 16.87 D ATOM 54 DD22ALEU A 3 22.563 -24.357 -32.028 0.00 16.68 D ATOM 55 DD23ALEU A 3 23.653 -24.109 -30.673 0.89 14.39 D ATOM 56 H BLEU A 3 22.567 -21.865 -27.663 0.09 16.63 H ATOM 57 HB2BLEU A 3 21.964 -20.976 -31.155 0.33 14.51 H ATOM 58 HG BLEU A 3 21.719 -23.530 -29.581 0.32 18.31 H ATOM 59 HD11BLEU A 3 19.620 -22.925 -30.652 0.26 20.52 H ATOM 60 HD12BLEU A 3 20.364 -24.239 -31.597 0.23 19.78 H ATOM 61 HD13BLEU A 3 20.458 -22.568 -32.171 0.51 20.26 H ATOM 62 HD21BLEU A 3 23.466 -22.855 -31.890 0.60 16.87 H ATOM 63 HD22BLEU A 3 22.563 -24.357 -32.028 0.58 16.68 H ATOM 64 HD23BLEU A 3 23.653 -24.109 -30.673 0.11 14.39 H TER HETATM 100 O DOD B 1 25.202 -21.329 -23.306 1.00 30.00 O HETATM 101 D1 DOD B 1 25.963 -20.763 -23.255 1.00 30.00 D HETATM 102 D2 DOD B 1 24.439 -20.764 -23.305 1.00 30.00 D HETATM 103 O HOH B 2 26.442 -21.454 -25.349 1.00 30.00 O HETATM 104 D1 HOH B 2 27.249 -20.953 -25.339 1.00 30.00 D HETATM 105 O HOH B 3 24.970 -18.184 -24.460 1.00 30.00 O HETATM 106 O HOH B 4 21.573 -23.174 -24.023 1.00 30.00 O HETATM 107 D2 HOH B 4 20.731 -22.736 -24.071 1.00 30.00 D HETATM 108 D1 AHOH B 4 22.045 -22.784 -23.297 1.00 30.00 D HETATM 109 D1 BHOH B 4 22.145 -21.784 -22.297 1.00 30.00 D HETATM 110 D1 HOH B 5 21.772 -27.767 -28.880 1.00 30.00 D HETATM 111 O DOD B 6 17.493 -24.723 -25.229 1.00 20.00 O HETATM 112 D1 DOD B 6 17.492 -25.660 -25.470 1.00 20.00 D HETATM 113 D2 DOD B 6 18.304 -24.255 -25.470 1.00 20.00 D TER 114 HOH B 6 HETATM 1 PG ATP C 1 3.232 -0.948 -8.256 1.00 20.00 A P HETATM 2 O1G ATP C 1 4.490 -0.168 -7.985 1.00 20.00 A O HETATM 3 O2G ATP C 1 2.572 -0.420 -9.500 1.00 20.00 A O HETATM 4 O3G ATP C 1 3.573 -2.392 -8.447 1.00 20.00 A O HETATM 5 PB ATP C 1 2.368 0.364 -5.856 1.00 20.00 A P HETATM 6 O1B ATP C 1 3.702 0.219 -5.162 1.00 20.00 A O HETATM 7 O2B ATP C 1 2.287 1.719 -6.506 1.00 20.00 A O HETATM 8 O3B ATP C 1 2.218 -0.793 -6.996 1.00 20.00 A O HETATM 9 PA ATP C 1 0.926 1.250 -3.494 1.00 20.00 A P HETATM 10 O1A ATP C 1 -0.200 2.200 -3.825 1.00 20.00 A O HETATM 11 O2A ATP C 1 2.197 2.037 -3.253 1.00 20.00 A O HETATM 12 O3A ATP C 1 1.155 0.210 -4.753 1.00 20.00 A O HETATM 13 O5' ATP C 1 0.538 0.381 -2.115 1.00 20.00 A O HETATM 14 C5' ATP C 1 -0.378 0.948 -1.194 1.00 20.00 A C HETATM 15 C4' ATP C 1 -1.094 -0.162 -0.442 1.00 20.00 A C HETATM 16 O4' ATP C 1 -0.263 -0.783 0.344 1.00 20.00 A O HETATM 17 C3' ATP C 1 -2.258 0.478 0.549 1.00 20.00 A C HETATM 18 O3' ATP C 1 -3.508 0.701 -0.219 1.00 20.00 A O HETATM 19 C2' ATP C 1 -2.450 -0.373 1.436 1.00 20.00 A C HETATM 20 O2' ATP C 1 -3.564 -1.296 1.031 1.00 20.00 A O HETATM 21 C1' ATP C 1 -1.075 -1.183 1.553 1.00 20.00 A C HETATM 22 N9 ATP C 1 -0.436 -0.847 2.669 1.00 20.00 A N HETATM 23 C8 ATP C 1 0.891 -0.729 2.488 1.00 20.00 A C HETATM 24 N7 ATP C 1 1.445 -0.426 3.672 1.00 20.00 A N HETATM 25 C5 ATP C 1 0.455 -0.356 4.593 1.00 20.00 A C HETATM 26 C6 ATP C 1 0.464 -0.066 5.953 1.00 20.00 A C HETATM 27 N6 ATP C 1 1.576 0.468 6.779 1.00 20.00 A N HETATM 28 N1 ATP C 1 -0.678 -0.046 6.637 1.00 20.00 A N HETATM 29 C2 ATP C 1 -1.855 -0.311 6.004 1.00 20.00 A C HETATM 30 N3 ATP C 1 -1.865 -0.595 4.675 1.00 20.00 A N HETATM 31 C4 ATP C 1 -0.703 -0.615 3.975 1.00 20.00 A C HETATM 32 H5'1 ATP C 1 0.163 1.581 -0.485 1.00 20.00 A H HETATM 33 H5'2 ATP C 1 -1.105 1.545 -1.731 1.00 20.00 A H HETATM 34 H4' ATP C 1 -1.548 -0.870 -1.145 1.00 20.00 A H HETATM 35 H3' ATP C 1 -1.912 1.393 0.983 1.00 20.00 A H HETATM 36 HO3' ATP C 1 -3.892 1.548 0.031 1.00 20.00 A H HETATM 37 H2' ATP C 1 -2.680 0.114 2.384 1.00 20.00 A H HETATM 38 HO2' ATP C 1 -4.066 -1.553 1.810 1.00 20.00 A H HETATM 39 H1' ATP C 1 -1.273 -2.266 1.534 1.00 20.00 A H HETATM 40 H8 ATP C 1 1.431 -0.922 1.560 1.00 20.00 A H HETATM 41 HN61 ATP C 1 2.477 0.646 6.359 1.00 20.00 A H HETATM 42 HN62 ATP C 1 1.445 0.610 7.769 1.00 20.00 A H HETATM 43 H2 ATP C 1 -2.804 -0.294 6.573 1.00 20.00 A H TER END ''' if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))