from __future__ import division import mmtbx from libtbx.utils import null_out import mmtbx.monomer_library.pdb_interpretation import mmtbx import mmtbx.secondary_structure import iotbx import libtbx.load_env pdb_str = """\ ATOM 1 N ALA 1 1.558 -2.549 -1.143 1.00 0.00 N ATOM 2 CA ALA 1 1.130 -3.826 -1.702 1.00 0.00 C ATOM 3 C ALA 1 -0.241 -3.705 -2.358 1.00 0.00 C ATOM 4 O ALA 1 -0.532 -4.386 -3.342 1.00 0.00 O ATOM 5 CB ALA 1 1.108 -4.897 -0.622 1.00 0.00 C ATOM 6 N ALA 2 -1.081 -2.834 -1.807 1.00 0.00 N ATOM 7 CA ALA 2 -2.422 -2.623 -2.338 1.00 0.00 C ATOM 8 C ALA 2 -2.392 -1.711 -3.560 1.00 0.00 C ATOM 9 O ALA 2 -3.170 -1.887 -4.497 1.00 0.00 O ATOM 10 CB ALA 2 -3.331 -2.042 -1.265 1.00 0.00 C ATOM 11 N ALA 3 -1.488 -0.736 -3.541 1.00 0.00 N ATOM 12 CA ALA 3 -1.351 0.207 -4.645 1.00 0.00 C ATOM 13 C ALA 3 -0.825 -0.487 -5.898 1.00 0.00 C ATOM 14 O ALA 3 -1.270 -0.201 -7.010 1.00 0.00 O ATOM 15 CB ALA 3 -0.437 1.356 -4.251 1.00 0.00 C ATOM 16 N ALA 4 0.124 -1.398 -5.708 1.00 0.00 N ATOM 17 CA ALA 4 0.699 -2.149 -6.817 1.00 0.00 C ATOM 18 C ALA 4 -0.333 -3.092 -7.426 1.00 0.00 C ATOM 19 O ALA 4 -0.387 -3.268 -8.643 1.00 0.00 O ATOM 20 CB ALA 4 1.922 -2.926 -6.355 1.00 0.00 C ATOM 21 N ALA 5 -1.152 -3.695 -6.569 1.00 0.00 N ATOM 22 CA ALA 5 -2.204 -4.597 -7.020 1.00 0.00 C ATOM 23 C ALA 5 -3.295 -3.830 -7.757 1.00 0.00 C ATOM 24 O ALA 5 -3.850 -4.313 -8.744 1.00 0.00 O ATOM 25 CB ALA 5 -2.792 -5.358 -5.842 1.00 0.00 C ATOM 26 N ALA 6 -3.597 -2.630 -7.271 1.00 0.00 N ATOM 27 CA ALA 6 -4.599 -1.778 -7.900 1.00 0.00 C ATOM 28 C ALA 6 -4.097 -1.252 -9.240 1.00 0.00 C ATOM 29 O ALA 6 -4.879 -1.036 -10.166 1.00 0.00 O ATOM 30 CB ALA 6 -4.971 -0.626 -6.981 1.00 0.00 C ATOM 31 N ALA 7 -2.788 -1.047 -9.335 1.00 0.00 N ATOM 32 CA ALA 7 -2.176 -0.571 -10.570 1.00 0.00 C ATOM 33 C ALA 7 -2.045 -1.703 -11.583 1.00 0.00 C ATOM 34 O ALA 7 -2.052 -1.472 -12.792 1.00 0.00 O ATOM 35 CB ALA 7 -0.816 0.047 -10.286 1.00 0.00 C ATOM 36 N ALA 8 -1.927 -2.929 -11.081 1.00 0.00 N ATOM 37 CA ALA 8 -1.805 -4.100 -11.941 1.00 0.00 C ATOM 38 C ALA 8 -3.169 -4.549 -12.452 1.00 0.00 C ATOM 39 O ALA 8 -3.290 -5.046 -13.572 1.00 0.00 O ATOM 40 CB ALA 8 -1.118 -5.234 -11.197 1.00 0.00 C ATOM 41 N ALA 9 -4.195 -4.370 -11.625 1.00 0.00 N ATOM 42 CA ALA 9 -5.552 -4.755 -11.995 1.00 0.00 C ATOM 43 C ALA 9 -6.141 -3.782 -13.010 1.00 0.00 C ATOM 44 O ALA 9 -6.957 -4.163 -13.849 1.00 0.00 O ATOM 45 CB ALA 9 -6.436 -4.832 -10.760 1.00 0.00 C ATOM 46 N ALA 10 -5.722 -2.523 -12.929 1.00 0.00 N ATOM 47 CA ALA 10 -6.206 -1.494 -13.841 1.00 0.00 C ATOM 48 C ALA 10 -5.523 -1.598 -15.200 1.00 0.00 C ATOM 49 O ALA 10 -6.184 -1.624 -16.238 1.00 0.00 O ATOM 50 CB ALA 10 -5.991 -0.112 -13.243 1.00 0.00 C TER """ def exercise_geo_out(): log = null_out() mon_lib_srv = mmtbx.monomer_library.server.server() ener_lib = mmtbx.monomer_library.server.ener_lib() processed_pdb_file = mmtbx.monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, raw_records=pdb_str.split('\n'), substitute_non_crystallographic_unit_cell_if_necessary=True, log=log) acp = processed_pdb_file.all_chain_proxies source = acp.pdb_inp.source_info() defpars = mmtbx.secondary_structure.sec_str_master_phil.fetch() custom_pars = defpars.fetch(source = iotbx.phil.parse( "h_bond_restraints.remove_outliers=False\n")) ss_manager = mmtbx.secondary_structure.manager( pdb_hierarchy=acp.pdb_hierarchy, params=custom_pars.extract()) ss_manager.find_automatically(log=log) ss_manager.initialize(log=log) proxies_for_grm = ss_manager.create_hbond_proxies( log = log, as_python_objects = False) custom_nb_excl = proxies_for_grm.exclude_nb_list grm = processed_pdb_file.geometry_restraints_manager( show_energies = False, show_nonbonded_clashscore = False, hydrogen_bond_proxies=proxies_for_grm.proxies, custom_nonbonded_exclusions = custom_nb_excl, assume_hydrogens_all_missing = True) from mmtbx.geometry_restraints import ramachandran params = ramachandran.master_phil.fetch().extract() params.rama_potential = "emsley" #params.rama_weight = sigma_on_ramachandran proxies = ramachandran.extract_proxies(acp.pdb_hierarchy, log=log) rama_lookup = ramachandran.lookup_manager(params) restraints_helper = mmtbx.geometry_restraints.manager( ramachandran_proxies=proxies, ramachandran_lookup=rama_lookup, hydrogen_bond_proxies=proxies_for_grm.proxies, hydrogen_bond_params=None) grm.set_generic_restraints(restraints_helper) atoms = acp.pdb_hierarchy.atoms() assert grm.generic_restraints_manager.get_n_hbonds() == 4 import StringIO str_result = StringIO.StringIO() grm.generic_restraints_manager.show_sorted_hbonds( by_value="residual", sites_cart = atoms.extract_xyz(), site_labels= [a.id_str() for a in atoms], f=str_result) assert str_result.getvalue() == """\ Hydrogen bond restraints: 4 Sorted by residual: hbond pdb=" O ALA 4 " pdb=" N ALA 8 " ideal model delta sigma weight residual 2.900 2.904 -0.004 5.00e-02 4.00e+02 4.93e-03 hbond pdb=" O ALA 2 " pdb=" N ALA 6 " ideal model delta sigma weight residual 2.900 2.903 -0.003 5.00e-02 4.00e+02 4.49e-03 hbond pdb=" O ALA 3 " pdb=" N ALA 7 " ideal model delta sigma weight residual 2.900 2.903 -0.003 5.00e-02 4.00e+02 2.92e-03 hbond pdb=" O ALA 5 " pdb=" N ALA 9 " ideal model delta sigma weight residual 2.900 2.902 -0.002 5.00e-02 4.00e+02 1.84e-03 """ str_result = StringIO.StringIO() grm.generic_restraints_manager.show_sorted_ramachandran( by_value="residual", sites_cart = atoms.extract_xyz(), site_labels= [a.id_str() for a in atoms], f=str_result) assert str_result.getvalue() == """\ Ramachandran plot restraints: 8 Sorted by residual: phi-psi angles formed by residual pdb=" C ALA 7 " 1.53e+01 pdb=" N ALA 8 " pdb=" CA ALA 8 " pdb=" C ALA 8 " pdb=" N ALA 9 " phi-psi angles formed by residual pdb=" C ALA 1 " 1.52e+01 pdb=" N ALA 2 " pdb=" CA ALA 2 " pdb=" C ALA 2 " pdb=" N ALA 3 " phi-psi angles formed by residual pdb=" C ALA 6 " 1.20e+01 pdb=" N ALA 7 " pdb=" CA ALA 7 " pdb=" C ALA 7 " pdb=" N ALA 8 " phi-psi angles formed by residual pdb=" C ALA 2 " 1.14e+01 pdb=" N ALA 3 " pdb=" CA ALA 3 " pdb=" C ALA 3 " pdb=" N ALA 4 " phi-psi angles formed by residual pdb=" C ALA 8 " 1.06e+01 pdb=" N ALA 9 " pdb=" CA ALA 9 " pdb=" C ALA 9 " pdb=" N ALA 10 " phi-psi angles formed by residual pdb=" C ALA 4 " 1.06e+01 pdb=" N ALA 5 " pdb=" CA ALA 5 " pdb=" C ALA 5 " pdb=" N ALA 6 " phi-psi angles formed by residual pdb=" C ALA 3 " 1.03e+01 pdb=" N ALA 4 " pdb=" CA ALA 4 " pdb=" C ALA 4 " pdb=" N ALA 5 " phi-psi angles formed by residual pdb=" C ALA 5 " 7.58e+00 pdb=" N ALA 6 " pdb=" CA ALA 6 " pdb=" C ALA 6 " pdb=" N ALA 7 " """ if (__name__ == "__main__") : if libtbx.env.has_module("ksdssp") : exercise_geo_out() print "OK" else : print "skipping test, ksdssp not available"