from __future__ import absolute_import, division, print_function # LIBTBX_SET_DISPATCHER_NAME phenix.secondary_structure_restraints from mmtbx.secondary_structure import sec_str_master_phil_str, \ sec_str_master_phil, manager import iotbx.pdb import mmtbx.model import iotbx.phil from scitbx.array_family import flex from libtbx.utils import Sorry from six.moves import cStringIO as StringIO import sys, os master_phil_str = """ show_all_params = False .type = bool .style = hidden filter_outliers = True .type = bool .style = hidden format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage csv .type = choice .style = hidden quiet = False .type = bool .style = hidden verbose = -1 .type = int .style = hidden output_prefix = None .type = str ignore_annotation_in_file = False .type = bool .help = ignore annotation that is present in input file file_name = None .type = path .multiple = True .optional = True .style = hidden %s """ % sec_str_master_phil_str master_phil = iotbx.phil.parse(master_phil_str, process_includes=True) def show_usage(): help_msg = """\ phenix.secondary_structure_restraints: tool for manipulating with secondary structure restraints. It can search and output them in various formats. Please note, that if HELIX/SHEET records are present in supplied .pdb file, automatic search will not be executed. These records will be outputted in choosen format instead. Usage examples: phenix.secondary_structure_restraints model.pdb phenix.secondary_structure_restraints model.pdb format=phenix_refine phenix.secondary_structure_restraints model.pdb ignore_annotation_in_file=True phenix.secondary_structure_restraints model.pdb search_method=from_ca Full scope of parameters: """ print(help_msg) master_phil.show() def run(args, params=None, out=sys.stdout, log=sys.stderr): # params keyword is for running program from GUI dialog if ( ((len(args) == 0) and (params is None)) or ((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ): show_usage() return # parse command-line arguments if (params is None): pcl = iotbx.phil.process_command_line_with_files( args=args, master_phil_string=master_phil_str, pdb_file_def="file_name") work_params = pcl.work.extract() # or use parameters defined by GUI else: work_params = params pdb_files = work_params.file_name work_params.secondary_structure.enabled=True assert work_params.format in ["phenix", "phenix_refine", "phenix_bonds", "pymol", "refmac", "kinemage", "pdb", 'csv'] if work_params.quiet : out = StringIO() pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files) pdb_structure = iotbx.pdb.input(source_info=None, lines=flex.std_string(pdb_combined.raw_records)) cs = pdb_structure.crystal_symmetry() corrupted_cs = False if cs is not None: if [cs.unit_cell(), cs.space_group()].count(None) > 0: corrupted_cs = True cs = None elif cs.unit_cell().volume() < 10: corrupted_cs = True cs = None if cs is None: if corrupted_cs: print("Symmetry information is corrupted, ", file=out) else: print("Symmetry information was not found, ", file=out) print("putting molecule in P1 box.", file=out) from cctbx import uctbx atoms = pdb_structure.atoms() box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center( sites_cart=atoms.extract_xyz(), buffer_layer=3) atoms.set_xyz(new_xyz=box.sites_cart) cs = box.crystal_symmetry() defpars = mmtbx.model.manager.get_default_pdb_interpretation_params() defpars.pdb_interpretation.automatic_linking.link_carbohydrates=False defpars.pdb_interpretation.c_beta_restraints=False defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None defpars.pdb_interpretation.allow_polymer_cross_special_position=True # defpars.pdb_interpretation.flip_symmetric_amino_acids=False # defpars.pdb_interpretation.sort_atoms=False model = mmtbx.model.manager( model_input=pdb_structure, crystal_symmetry=cs, stop_for_unknowns=False) model.process(pdb_interpretation_params=defpars) pdb_hierarchy = model.get_hierarchy() geometry = None if pdb_hierarchy.contains_nucleic_acid(): model.process(make_restraints = True) geometry = model.get_restraints_manager().geometry if len(pdb_hierarchy.models()) != 1 : raise Sorry("Multiple models not supported.") ss_from_file = None if (hasattr(pdb_structure, "extract_secondary_structure") and not work_params.ignore_annotation_in_file): ss_from_file = pdb_structure.extract_secondary_structure() m = manager(pdb_hierarchy=pdb_hierarchy, geometry_restraints_manager=geometry, sec_str_from_pdb_file=ss_from_file, params=work_params.secondary_structure, verbose=work_params.verbose) # bp_p = nucleic_acids.get_basepair_plane_proxies( # pdb_hierarchy, # m.params.secondary_structure.nucleic_acid.base_pair, # geometry) # st_p = nucleic_acids.get_stacking_proxies( # pdb_hierarchy, # m.params.secondary_structure.nucleic_acid.stacking_pair, # geometry) # hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy, # m.params.secondary_structure.nucleic_acid.base_pair) result_out = StringIO() # prefix_scope="refinement.pdb_interpretation" # prefix_scope="" prefix_scope="" if work_params.format == "phenix_refine": prefix_scope = "refinement.pdb_interpretation" elif work_params.format == "phenix": prefix_scope = "pdb_interpretation" ss_phil = None working_phil = m.as_phil_str(master_phil=sec_str_master_phil) phil_diff = sec_str_master_phil.fetch_diff(source=working_phil) if work_params.format in ["phenix", "phenix_refine"]: comment = "\n".join([ "# These parameters are suitable for use in e.g. phenix.real_space_refine", "# or geometry_minimization. To use them in phenix.refine add ", "# 'refinement.' if front of pdb_interpretation."]) if work_params.format == "phenix_refine": comment = "\n".join([ "# These parameters are suitable for use in phenix.refine only.", "# To use them in other Phenix tools remove ", "# 'refinement.' if front of pdb_interpretation."]) print(comment, file=result_out) if (prefix_scope != ""): print("%s {" % prefix_scope, file=result_out) if work_params.show_all_params : working_phil.show(prefix=" ", out=result_out) else : phil_diff.show(prefix=" ", out=result_out) if (prefix_scope != ""): print("}", file=result_out) elif work_params.format == "pdb": print(m.actual_sec_str.as_pdb_str(), file=result_out) elif work_params.format == "phenix_bonds" : raise Sorry("Not yet implemented.") elif work_params.format in ["pymol", "refmac", "kinemage", 'csv'] : m.show_summary(log=out) model.process(make_restraints=True) (hb_proxies, hb_angle_proxies, planarity_proxies, parallelity_proxies) = m.create_all_new_restraints( pdb_hierarchy=pdb_hierarchy, grm=model.get_restraints_manager().geometry, log=out) if hb_proxies.size() > 0: if work_params.format == "pymol" : file_load_add = "load %s" % work_params.file_name[0] # surprisingly, pymol handles filenames with whitespaces without quotes... print(file_load_add, file=result_out) bonds_in_format = hb_proxies.as_pymol_dashes( pdb_hierarchy=pdb_hierarchy) elif work_params.format == "kinemage" : bonds_in_format = hb_proxies.as_kinemage( pdb_hierarchy=pdb_hierarchy) elif work_params.format == "csv" : bonds_in_format = hb_proxies.as_csv( pdb_hierarchy=pdb_hierarchy) else : bonds_in_format = hb_proxies.as_refmac_restraints( pdb_hierarchy=pdb_hierarchy) print(bonds_in_format, file=result_out) if hb_angle_proxies.size() > 0: if work_params.format == "pymol": angles_in_format = hb_angle_proxies.as_pymol_dashes( pdb_hierarchy=pdb_hierarchy) print(angles_in_format, file=result_out) result = result_out.getvalue() out_prefix = os.path.basename(work_params.file_name[0]) if work_params.output_prefix is not None: out_prefix = work_params.output_prefix filename = "%s_ss.eff" % out_prefix if work_params.format == "pymol": filename = "%s_ss.pml" % out_prefix outf = open(filename, "w") outf.write(result) outf.close() print(result, file=out) return os.path.abspath(filename) # ============================================================================= # GUI-specific functions def validate_params(params): pass if __name__ == "__main__" : run(sys.argv[1:])