from __future__ import absolute_import, division, print_function from scitbx.array_family import flex import boost_adaptbx.boost.python as bp asu_map_ext = bp.import_ext("cctbx_asymmetric_map_ext") import iotbx.pdb from mmtbx.maps import correlation from libtbx.test_utils import approx_equal from cctbx import maptbx pdb_str=""" CRYST1 60.410 44.706 51.507 90.00 90.00 90.00 P 1 SCALE1 0.016554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019415 0.00000 ATOM 1 N GLY A 1 20.043 24.706 27.193 1.00 20.00 N ATOM 2 CA GLY A 1 20.000 24.301 25.742 1.00 20.00 C ATOM 3 C GLY A 1 21.037 23.234 25.510 1.00 20.00 C ATOM 4 O GLY A 1 21.529 22.615 26.472 1.00 20.00 O ATOM 5 N ASN A 2 21.396 23.017 24.246 1.00 20.00 N ATOM 6 CA ASN A 2 22.530 22.132 23.922 1.00 20.00 C ATOM 7 C ASN A 2 23.811 22.631 24.518 1.00 20.00 C ATOM 8 O ASN A 2 24.074 23.836 24.517 1.00 20.00 O ATOM 9 CB ASN A 2 22.706 21.975 22.432 1.00 20.00 C ATOM 10 CG ASN A 2 21.468 21.436 21.783 1.00 20.00 C ATOM 11 OD1 ASN A 2 21.027 20.321 22.107 1.00 20.00 O ATOM 12 ND2 ASN A 2 20.848 22.249 20.922 1.00 20.00 N ATOM 13 N ASN A 3 24.614 21.684 24.996 1.00 20.00 N ATOM 14 CA ASN A 3 25.859 21.998 25.680 1.00 20.00 C ATOM 15 C ASN A 3 27.097 21.426 24.986 1.00 20.00 C ATOM 16 O ASN A 3 27.180 20.213 24.739 1.00 20.00 O ATOM 17 CB ASN A 3 25.793 21.472 27.133 1.00 20.00 C ATOM 18 CG ASN A 3 27.046 21.833 27.952 1.00 20.00 C ATOM 19 OD1 ASN A 3 27.350 23.019 28.163 1.00 20.00 O ATOM 20 ND2 ASN A 3 27.781 20.809 28.397 1.00 20.00 N ATOM 21 N GLN A 4 28.047 22.322 24.689 1.00 20.00 N ATOM 22 CA GLN A 4 29.436 21.982 24.290 1.00 20.00 C ATOM 23 C GLN A 4 30.487 22.700 25.179 1.00 20.00 C ATOM 24 O GLN A 4 30.599 23.937 25.206 1.00 20.00 O ATOM 25 CB GLN A 4 29.708 22.242 22.802 1.00 20.00 C ATOM 26 CG GLN A 4 30.996 21.552 22.304 1.00 20.00 C ATOM 27 CD GLN A 4 31.556 22.138 21.002 1.00 20.00 C ATOM 28 OE1 GLN A 4 31.796 23.362 20.901 1.00 20.00 O ATOM 29 NE2 GLN A 4 31.802 21.255 20.000 1.00 20.00 N ATOM 30 N GLN A 5 31.206 21.915 25.962 1.00 20.00 N ATOM 31 CA GLN A 5 32.322 22.455 26.731 1.00 20.00 C ATOM 32 C GLN A 5 33.646 21.862 26.263 1.00 20.00 C ATOM 33 O GLN A 5 33.820 20.640 26.145 1.00 20.00 O ATOM 34 CB GLN A 5 32.108 22.277 28.238 1.00 20.00 C ATOM 35 CG GLN A 5 30.881 23.044 28.738 1.00 20.00 C ATOM 36 CD GLN A 5 30.396 22.508 30.045 1.00 20.00 C ATOM 37 OE1 GLN A 5 29.826 21.419 30.093 1.00 20.00 O ATOM 38 NE2 GLN A 5 30.601 23.281 31.130 1.00 20.00 N ATOM 39 N ASN A 6 34.566 22.758 25.947 1.00 20.00 N ATOM 40 CA ASN A 6 35.883 22.404 25.409 1.00 20.00 C ATOM 41 C ASN A 6 36.906 22.855 26.415 1.00 20.00 C ATOM 42 O ASN A 6 37.271 24.037 26.465 1.00 20.00 O ATOM 43 CB ASN A 6 36.117 23.110 24.084 1.00 20.00 C ATOM 44 CG ASN A 6 35.013 22.829 23.094 1.00 20.00 C ATOM 45 OD1 ASN A 6 34.850 21.698 22.642 1.00 20.00 O ATOM 46 ND2 ASN A 6 34.247 23.841 22.770 1.00 20.00 N ATOM 47 N TYR A 7 37.344 21.911 27.238 1.00 20.00 N ATOM 48 CA TYR A 7 38.211 22.238 28.390 1.00 20.00 C ATOM 49 C TYR A 7 39.655 22.425 27.976 1.00 20.00 C ATOM 50 O TYR A 7 40.093 21.905 26.946 1.00 20.00 O ATOM 51 CB TYR A 7 38.113 21.159 29.460 1.00 20.00 C ATOM 52 CG TYR A 7 36.717 21.023 29.993 1.00 20.00 C ATOM 53 CD1 TYR A 7 35.823 20.115 29.418 1.00 20.00 C ATOM 54 CD2 TYR A 7 36.262 21.850 31.011 1.00 20.00 C ATOM 55 CE1 TYR A 7 34.532 20.000 29.887 1.00 20.00 C ATOM 56 CE2 TYR A 7 34.956 21.743 31.507 1.00 20.00 C ATOM 57 CZ TYR A 7 34.099 20.823 30.922 1.00 20.00 C ATOM 58 OH TYR A 7 32.818 20.683 31.382 1.00 20.00 O ATOM 59 OXT TYR A 7 40.410 23.093 28.703 1.00 20.00 O END """ def exercise_d99(): pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str) ph = pdb_inp.construct_hierarchy() xrs = ph.extract_xray_structure(crystal_symmetry = pdb_inp.crystal_symmetry()) crystal_gridding = maptbx.crystal_gridding( unit_cell = xrs.unit_cell(), space_group_info = xrs.space_group_info(), resolution_factor = 0.25, d_min = 2., symmetry_flags = maptbx.use_space_group_symmetry) fc = xrs.structure_factors(d_min=2.).f_calc() fft_map = fc.fft_map(crystal_gridding=crystal_gridding) map = fft_map.real_map_unpadded() # o = maptbx.d99(map=map, crystal_symmetry=xrs.crystal_symmetry()) assert approx_equal(o.result.d99, 2.13, 0.03) def exercise_five_cc(): pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str) ph = pdb_inp.construct_hierarchy() #ph.write_pdb_file(file_name="m1.pdb") xrs = ph.extract_xray_structure(crystal_symmetry = pdb_inp.crystal_symmetry()) f_calc = xrs.structure_factors(d_min=2.0).f_calc()#.resolution_filter(d_max=6) fft_map = f_calc.fft_map(resolution_factor=0.25) m1 = fft_map.real_map_unpadded() # #xrs = xrs.set_b_iso(value=50) sc = xrs.sites_cart() #sc = sc + flex.vec3_double(sc.size(), [.5,.5,.5]) xrs = xrs.replace_sites_cart(new_sites=sc) ph.adopt_xray_structure(xrs) #ph.write_pdb_file(file_name="m2.pdb") o = correlation.five_cc(map=m1, xray_structure=xrs, d_min=2.0, compute_cc_box=True, compute_cc_image=True, box=False).result assert approx_equal(o.cc_box, 1.0) assert approx_equal(o.cc_image , 1.0) assert approx_equal(o.cc_mask , 1.0) assert approx_equal(o.cc_peaks , 1.0) assert approx_equal(o.cc_volume , 1.0) if (__name__ == "__main__"): exercise_d99() exercise_five_cc()