from __future__ import division from mmtbx import building from libtbx.utils import null_out from cStringIO import StringIO def exercise_model_utils () : pdb_in = get_1yjp_pdb() residue = pdb_in.hierarchy.only_model().chains()[0].residue_groups()[0].only_atom_group() sele = pdb_in.hierarchy.atom_selection_cache().selection("resname TYR") water_sel = building.get_nearby_water_selection( pdb_hierarchy=pdb_in.hierarchy, xray_structure=pdb_in.input.xray_structure_simple(), selection=sele) assert (list(water_sel.iselection()) == [59, 60, 61, 62, 63]) from mmtbx.monomer_library import idealized_aa from mmtbx.monomer_library import server mon_lib_srv = server.server() ideal_dict = idealized_aa.residue_dict() for resname, hierarchy in ideal_dict.iteritems() : residue = hierarchy.only_model().only_chain().only_residue_group().only_atom_group() result = building.generate_sidechain_clusters(residue, mon_lib_srv) if (len(result) == 0) : assert (residue.resname in ["ALA", "GLY"]) # show_chain_resseq_ranges resids = [ (1,''),(2,''),(2,'A'),(4,''),(5,''),(6,''),(10,'B') ] import iotbx.pdb.hierarchy chain = iotbx.pdb.hierarchy.chain(id='A') for (resseq, icode) in resids : rg = iotbx.pdb.hierarchy.residue_group(resseq="%4d" % resseq, icode=icode) chain.append_residue_group(rg) out = StringIO() building.show_chain_resseq_ranges(chain.residue_groups(), out=out, prefix=" ") assert out.getvalue() == """ chain 'A': 1-2A,4-6,10B\n""", out.getvalue() def exercise_box_rebuild () : pdb_in = get_1yjp_pdb() xrs = pdb_in.input.xray_structure_simple() fc = xrs.structure_factors(d_min=1.5).f_calc() fc_fft = fc.fft_map(resolution_factor=0.25) fc_map = fc_fft.apply_sigma_scaling().real_map_unpadded() sel_cache = pdb_in.hierarchy.atom_selection_cache() sel = sel_cache.selection("resseq 4:5") sites_orig = xrs.sites_cart().deep_copy() xrs.shake_sites_in_place(0.3, selection=sel) pdb_in.hierarchy.atoms().set_xyz(xrs.sites_cart()) sites_shaken = xrs.sites_cart().deep_copy() sites_new = building.run_real_space_annealing( xray_structure=xrs, pdb_hierarchy=pdb_in.hierarchy, selection=sel, target_map=fc_map, rsr_after_anneal=False, d_min=1.5, out=null_out()) pdb_in.hierarchy.atoms().set_xyz(sites_new) rmsd_start = sites_orig.rms_difference(sites_shaken) assert (rmsd_start > 0.1) assert (sites_orig.rms_difference(sites_new) < rmsd_start) assert (sites_orig.select(sel).rms_difference(sites_new.select(sel)) > 0) assert (sites_new.select(sel).rms_difference(sites_shaken.select(sel)) > 0) assert (sites_orig.select(~sel).rms_difference(sites_new.select(~sel)) == 0) box_builder = building.box_build_refine_base( pdb_hierarchy=pdb_in.hierarchy, xray_structure=xrs, processed_pdb_file=None, target_map=fc_map, selection=sel, d_min=1.5, out=null_out()) box_builder.restrain_atoms(box_builder.others_in_box, 0.02) box_builder.geometry_minimization() box_builder.real_space_refine() sites_new = box_builder.update_original_coordinates() assert (sites_orig.rms_difference(sites_new) < 0.3) assert (box_builder.mean_density_at_sites() > 3) def exercise_map_utils () : hierarchy, fmodel = get_1yjp_pdb_and_fmodel() sel_cache = hierarchy.atom_selection_cache() sele = sel_cache.selection("resseq 5 and (name CD or name OE1 or name NE2)") sele_all = sel_cache.selection("resseq 5") fmodel.xray_structure.scale_adp(factor=0.5, selection=sele) fmodel.update_xray_structure(update_f_calc=True) two_fofc_map, fofc_map = building.get_difference_maps(fmodel) map_stats = building.local_density_quality( fofc_map=fofc_map, two_fofc_map=two_fofc_map, atom_selection=sele_all, xray_structure=fmodel.xray_structure) out = StringIO() map_stats.show_atoms_outside_density(out=out, two_fofc_cutoff=3.0) pdb_strs = [ l.split(":")[0] for l in out.getvalue().splitlines() ] assert len(pdb_strs) > 0 # XXX there seems to be a stochastic effect here #assert (pdb_strs == ['pdb=" CA GLN A 5 "', 'pdb=" CB GLN A 5 "', # 'pdb=" CD GLN A 5 "', 'pdb=" NE2 GLN A 5 "']), \ # pdb_strs fc_map = fmodel.map_coefficients(map_type="Fc").fft_map( resolution_factor=0.25).apply_sigma_scaling().real_map_unpadded() assert (map_stats.number_of_atoms_below_fofc_map_level() == 3) assert (map_stats.fraction_of_nearby_grid_points_above_cutoff() > 0.0) stats = building.get_model_map_stats( selection=sele_all, target_map=two_fofc_map, model_map=fc_map, unit_cell=fmodel.xray_structure.unit_cell(), sites_cart=fmodel.xray_structure.sites_cart(), pdb_atoms=hierarchy.atoms()) #print stats.cc, stats.min, stats.mean # XXX numbers are not exact because of R-free flags are generated randomly #assert (stats.cc > 0.7) and (stats.min > 1.5) and (stats.mean > 2.5) def get_1yjp_pdb_and_fmodel () : import mmtbx.utils pdb_in = get_1yjp_pdb() xrs = pdb_in.input.xray_structure_simple() f_calc = abs(xrs.structure_factors(d_min=1.5).f_calc()) f_calc.set_observation_type_xray_amplitude() flags = f_calc.generate_r_free_flags() fmodel = mmtbx.utils.fmodel_simple( xray_structures=[xrs], f_obs=f_calc, r_free_flags=flags, scattering_table="n_gaussian", bulk_solvent_and_scaling=False, skip_twin_detection=True) return pdb_in.hierarchy, fmodel def get_1yjp_pdb() : import iotbx.pdb.hierarchy return iotbx.pdb.hierarchy.input(pdb_string="""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 0.80 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 0.80 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 0.80 9.05 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 0.80 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 0.80 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 0.80 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O TER HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O END """) if (__name__ == "__main__") : exercise_model_utils() exercise_map_utils() exercise_box_rebuild() print "OK"