from __future__ import absolute_import, division, print_function import iotbx.pdb from cctbx.array_family import flex from libtbx import easy_run from cctbx import miller from libtbx.test_utils import approx_equal pdb_str = """ CRYST1 73.110 85.164 25.674 90.00 90.00 90.00 P 1 MODEL 1 ATOM 1 N MET A 1 6.018 9.573 5.000 1.00 30.00 N ATOM 2 CA MET A 1 6.167 8.775 6.243 1.00 30.00 C ATOM 3 C MET A 1 5.758 9.566 7.448 1.00 30.00 C ATOM 4 O MET A 1 5.000 9.074 8.283 1.00 30.00 O ATOM 5 CB MET A 1 7.620 8.264 6.399 1.00 30.00 C ATOM 6 CG MET A 1 7.823 7.287 7.573 1.00 30.00 C ATOM 7 SD MET A 1 6.760 5.817 7.493 1.00 30.00 S ATOM 8 CE MET A 1 7.423 5.000 8.970 1.00 30.00 C TER ENDMDL MODEL 2 ATOM 1 N MET A 1 29.179 17.377 7.934 1.00 30.00 N ATOM 2 CA MET A 1 29.606 16.685 9.177 1.00 30.00 C ATOM 3 C MET A 1 28.940 17.277 10.381 1.00 30.00 C ATOM 4 O MET A 1 28.410 16.545 11.217 1.00 30.00 O ATOM 5 CB MET A 1 31.145 16.731 9.331 1.00 30.00 C ATOM 6 CG MET A 1 31.686 15.890 10.506 1.00 30.00 C ATOM 7 SD MET A 1 31.222 14.137 10.425 1.00 30.00 S ATOM 8 CE MET A 1 32.135 13.614 11.902 1.00 30.00 C TER ENDMDL MODEL 3 ATOM 1 N MET A 1 47.992 33.026 10.855 1.00 30.00 N ATOM 2 CA MET A 1 48.638 32.534 12.098 1.00 30.00 C ATOM 3 C MET A 1 47.804 32.846 13.303 1.00 30.00 C ATOM 4 O MET A 1 47.573 31.973 14.138 1.00 30.00 O ATOM 5 CB MET A 1 50.059 33.129 12.253 1.00 30.00 C ATOM 6 CG MET A 1 50.865 32.539 13.426 1.00 30.00 C ATOM 7 SD MET A 1 51.062 30.736 13.345 1.00 30.00 S ATOM 8 CE MET A 1 52.103 30.574 14.821 1.00 30.00 C TER ENDMDL MODEL 4 ATOM 1 N MET A 1 59.934 54.401 13.778 1.00 30.00 N ATOM 2 CA MET A 1 60.716 54.173 15.021 1.00 30.00 C ATOM 3 C MET A 1 59.826 54.166 16.226 1.00 30.00 C ATOM 4 O MET A 1 59.923 53.268 17.062 1.00 30.00 O ATOM 5 CB MET A 1 61.828 55.239 15.176 1.00 30.00 C ATOM 6 CG MET A 1 62.793 54.977 16.348 1.00 30.00 C ATOM 7 SD MET A 1 63.625 53.365 16.266 1.00 30.00 S ATOM 8 CE MET A 1 64.654 53.587 17.743 1.00 30.00 C TER ENDMDL MODEL 5 ATOM 1 N MET A 1 63.411 78.601 16.713 1.00 30.00 N ATOM 2 CA MET A 1 64.223 78.668 17.954 1.00 30.00 C ATOM 3 C MET A 1 63.396 78.342 19.161 1.00 30.00 C ATOM 4 O MET A 1 63.810 77.538 19.995 1.00 30.00 O ATOM 5 CB MET A 1 64.878 80.062 18.109 1.00 30.00 C ATOM 6 CG MET A 1 65.874 80.164 19.281 1.00 30.00 C ATOM 7 SD MET A 1 67.228 78.958 19.199 1.00 30.00 S ATOM 8 CE MET A 1 68.110 79.536 20.674 1.00 30.00 C TER ENDMDL END """ def r(x,y): x = abs(x.deep_copy()).data() y = abs(y.deep_copy()).data() n = flex.sum(flex.abs(x-y)) d = flex.sum(flex.abs(x+y)) return n/d def exercise(prefix="tst_models_to_from_chains"): # inputs expected_n = 5 xrs = iotbx.pdb.input(source_info=None, lines=pdb_str).xray_structure_simple() input_file_name = "%s.pdb"%prefix of = open(input_file_name,"w") print(pdb_str, file=of) of.close() mi = flex.miller_index(((0,0,1), )) ms = miller.set(xrs.crystal_symmetry(), mi, anomalous_flag=False) complete_set = ms.complete_set(d_min=3) fc = complete_set.structure_factors_from_scatterers( xray_structure=xrs).f_calc() # models -> chains easy_run.call("phenix.models_as_chains %s"%input_file_name) pdb_inp = iotbx.pdb.input(file_name="chains_"+input_file_name) h = pdb_inp.construct_hierarchy() assert len(list(h.chains()))==expected_n assert len(list(h.models()))==1 xrs_c = pdb_inp.xray_structure_simple() fc_c = complete_set.structure_factors_from_scatterers( xray_structure=xrs_c).f_calc() # easy_run.call("phenix.chains_as_models chains_%s"%input_file_name) pdb_inp = iotbx.pdb.input(file_name="models_chains_"+input_file_name) h = pdb_inp.construct_hierarchy() assert len(list(h.chains()))==expected_n assert len(list(h.models()))==expected_n xrs_m = pdb_inp.xray_structure_simple() fc_m = complete_set.structure_factors_from_scatterers( xray_structure=xrs_m).f_calc() # assert approx_equal(0, r(fc, fc_c) ) assert approx_equal(0, r(fc, fc_m) ) assert approx_equal(0, r(fc_c, fc_m)) if (__name__ == "__main__"): exercise()