from __future__ import division from mmtbx import real_space_correlation import mmtbx.utils from iotbx import file_reader import iotbx.pdb.hierarchy from scitbx.array_family import flex import libtbx.load_env from libtbx.test_utils import approx_equal from libtbx.utils import null_out from libtbx import group_args import os def exercise_1(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/1yjp_h.pdb", test=os.path.isfile) mtz_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/reflection_files/1yjp.mtz", test=os.path.isfile) if (None in [pdb_file, mtz_file]) : print "phenix_regression not found, skipping test" return False pdb_in = file_reader.any_file(pdb_file) hierarchy = pdb_in.file_object.hierarchy hierarchy.atoms().reset_i_seq() xrs = pdb_in.file_object.xray_structure_simple() mtz_in = file_reader.any_file(mtz_file) f_obs = mtz_in.file_server.miller_arrays[0] r_free = mtz_in.file_server.miller_arrays[1] r_free = r_free.customized_copy(data=(r_free.data()==1)) fmodel = mmtbx.utils.fmodel_simple( f_obs=f_obs, r_free_flags=r_free, xray_structures=[xrs], scattering_table="n_gaussian") map_stats = real_space_correlation.map_statistics_for_fragment( fragment=hierarchy, fmodel=fmodel) assert approx_equal(map_stats.cc, 0.960, eps=0.01) edm = fmodel.electron_density_map() map1_coeffs = edm.map_coefficients("2mFo-DFc") map1 = map1_coeffs.fft_map( resolution_factor=0.25).apply_sigma_scaling().real_map() map2_coeffs = edm.map_coefficients("Fmodel") map2 = map2_coeffs.fft_map( resolution_factor=0.25).apply_sigma_scaling().real_map() xray_structure = fmodel.xray_structure map_stats2 = real_space_correlation.map_statistics_for_atom_selection( atom_selection=flex.bool(xrs.sites_cart().size(), True), map1=map1, map2=map2, xray_structure=xrs) assert approx_equal(map_stats2.cc, map_stats.cc, 0.01) # XXX other code outside cctbx depends on the current API - do not simply # change the test if this breaks! results = real_space_correlation.simple( fmodel=fmodel, pdb_hierarchy=hierarchy, log=null_out()) assert isinstance(results, list) assert isinstance(results[0], group_args) assert (results[0].n_atoms == 1) assert (results[0].id_str == " A GLY 1 N ") return True # test with synthetic twinned data def exercise_2 () : pdb_str = """\ CRYST1 12.000 8.000 12.000 90.02 89.96 90.05 P 1 1 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 ATOM 1 N ASN B 6 1.414 5.113 6.019 1.00 12.99 N ATOM 2 CA ASN B 6 2.720 4.776 5.445 1.00 13.30 C ATOM 3 C ASN B 6 3.763 5.209 6.438 1.00 14.40 C ATOM 4 O ASN B 6 4.125 6.391 6.507 1.00 14.92 O ATOM 5 CB ASN B 6 2.922 5.513 4.131 1.00 13.13 C ATOM 6 CG ASN B 6 1.798 5.250 3.160 1.00 13.77 C ATOM 7 OD1 ASN B 6 1.629 4.129 2.686 1.00 15.27 O ATOM 8 ND2 ASN B 6 1.022 6.266 2.875 1.00 11.07 N ATOM 9 N TYR B 7 4.222 4.248 7.230 1.00 15.70 N ATOM 10 CA TYR B 7 5.113 4.552 8.370 1.00 16.18 C ATOM 11 C TYR B 7 6.547 4.754 7.929 1.00 16.91 C ATOM 12 O TYR B 7 6.964 4.259 6.878 1.00 16.76 O ATOM 13 CB TYR B 7 5.042 3.449 9.417 1.00 16.35 C ATOM 14 CG TYR B 7 3.659 3.296 9.977 1.00 15.45 C ATOM 15 CD1 TYR B 7 2.756 2.398 9.402 1.00 16.68 C ATOM 16 CD2 TYR B 7 3.224 4.098 11.023 1.00 15.80 C ATOM 17 CE1 TYR B 7 1.476 2.267 9.896 1.00 14.46 C ATOM 18 CE2 TYR B 7 1.929 3.975 11.545 1.00 15.33 C ATOM 19 CZ TYR B 7 1.063 3.065 10.959 1.00 16.09 C ATOM 20 OH TYR B 7 -0.207 2.910 11.443 1.00 15.39 O ATOM 21 OXT TYR B 7 7.316 5.408 8.654 1.00 18.49 O END """ pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str) xrs = pdb_in.input.xray_structure_simple() fc = abs(xrs.structure_factors(d_min=1.5).f_calc()) fc = fc.set_observation_type_xray_amplitude() sigf = flex.double(fc.size(), 0.1) + (fc.data() * 0.03) fc = fc.customized_copy(sigmas=sigf) # and now add twinning fc_twin = fc.twin_data(twin_law='-l,-k,-h', alpha=0.4) flags = fc_twin.generate_r_free_flags(use_lattice_symmetry=True) fmodel = mmtbx.utils.fmodel_simple( f_obs=fc_twin, r_free_flags=flags, xray_structures=[xrs], scattering_table="n_gaussian") assert (fmodel.twin_law is not None) map_stats = real_space_correlation.extract_map_stats_for_single_atoms( xray_structure=xrs, pdb_atoms=pdb_in.hierarchy.atoms(), fmodel=fmodel) sel_cache = pdb_in.hierarchy.atom_selection_cache() sel = sel_cache.selection("chain B") map_stats_2 = real_space_correlation.extract_map_stats_for_single_atoms( xray_structure=xrs, pdb_atoms=pdb_in.hierarchy.atoms(), fmodel=fmodel, selection=sel) map_stats_3 = real_space_correlation.map_statistics_for_atom_selection( atom_selection=sel, fmodel=fmodel) if (__name__ == "__main__") : exercise_1() exercise_2() print "OK"