# LIBTBX_SET_DISPATCHER_NAME mmtbx.nonbonded_overlaps from __future__ import division, print_function from iotbx.cli_parser import run_program from mmtbx.programs import nonbonded_overlaps if __name__ == '__main__': run_program(program_class=nonbonded_overlaps.Program) # from __future__ import division # from __future__ import print_function # import mmtbx.monomer_library.pdb_interpretation as pdb_inter # import cctbx.geometry_restraints.nonbonded_overlaps as nbo # import mmtbx.validation.clashscore as mvc # from libtbx.utils import null_out # from libtbx.utils import Sorry # from libtbx.utils import Usage # import iotbx.phil # import sys # master_phil_str = """ # model = None # .type = path # .optional = False # .help = '''input PDB file''' # cif = None # .type = path # .optional = True # .help = '''Optional Crystallographic Information File (CIF)''' # verbose = True # .type = bool # keep_hydrogens = True # .type = bool # .help = '''Keep hydrogens in input file # (if there are no hydrogens in input file they will be added)''' # skip_hydrogen_test = False # .type = bool # .help = '''Ignore hydrogen considerations, check NBO on PDB file as-is ''' # nuclear = False # .type = bool # .help = '''Use nuclear hydrogen positions''' # time_limit = 120 # .type = int # .help = '''Time limit (sec) for Reduce optimization''' # show_overlap_type = *all sym macro selection # .type = choice(multi=False) # .help = '''When using cctbx method, this parameter allows selecting to show # all clashes 'all', clashes dues to symmetry operation 'sym' or clashes in # the macro molecule 'macro'.''' # substitute_non_crystallographic_unit_cell_if_necessary = False # .type = bool # .help = '''\ # Will replace the crystallographic unit cell when the model # crystallographic information is bad''' # show_normalized_nbo = False # .type = bool # .help = When True, will show non-bonded overlaps per 1000 atoms # show_non_binary_overlap_values = True # .type = bool # .help = use a function # """ # usage_string = """\ # phenix.clashscore file.pdb [params.eff] [options ...] # Options: # model=input_file input PDB file # cif=input_file input CIF file for additional model information # keep_hydrogens=True keep input hydrogen files (otherwise regenerate) # skip_hydrogen_test=False Ignore hydrogen considerations, # check NBO on PDB file as-is # nuclear=False use nuclear x-H distances and vdW radii # verbose=True verbose text output # time_limit=120 Time limit (sec) for Reduce optimization # show_overlap_type=all what type of overlaps to show (all,sym or macro) # show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms # substitute_non_crystallographic_unit_cell_if_necessary=false # fix CRYST1 records if needed # Example: # >>> mmtbx.nonbonded_overlaps xxxx.pdb keep_hydrogens=True # >>> mmtbx.nonbonded_overlaps xxxx.pdb verbose=false # """ # def run(args, out=None): # """ # Calculates number of non-bonded atoms overlaps in a model # prints to log: # When verbose=True the function print detailed results to log # When verbose=False it will print: # nb_overlaps_macro_molecule, # nb_overlaps_due_to_sym_op, # nb_overlaps_all # Args: # args (list): list of options. # model=input_file input PDB file # cif=input_file input CIF file for additional model information # keep_hydrogens=True keep input hydrogen files (otherwise regenerate) # nuclear=False use nuclear x-H distances and vdW radii # verbose=True verbose text output # time_limit=120 Time limit (sec) for Reduce optimization # show_overlap_type=all what type of overlaps to show # show_normalized_nbo=False Show non-bonded overlaps per 1000 atoms # substitute_non_crystallographic_unit_cell_if_necessary=false # fix CRYST1 records if needed # out : where to wrote the output to. # Returns: # nb_overlaps (obj): Object containing overlap and overlap per thousand # atoms information # """ # if not out: out = sys.stdout # if not args: # print(usage_string, file=out) # return None # cmdline = iotbx.phil.process_command_line_with_files( # args=args, # master_phil_string=master_phil_str, # pdb_file_def="model", # cif_file_def="cif", # usage_string=usage_string) # params = cmdline.work.extract() # if (params.model is None): # raise Usage(usage_string) # pdb_file_name = [x for x in args if x.endswith('.pdb')] # cif_file_name = [x for x in args if x.endswith('.cif')] # assert pdb_file_name # pdb_file_name = pdb_file_name[0] # if not params.skip_hydrogen_test: # pdb_with_h, h_were_added = mvc.check_and_add_hydrogen( # file_name=pdb_file_name, # model_number=0, # nuclear=params.nuclear, # verbose=params.verbose, # time_limit=params.time_limit, # keep_hydrogens=params.keep_hydrogens, # allow_multiple_models=False, # log=out) # if h_were_added: # pdb_file_name = pdb_file_name.replace('.pdb','_with_h.pdb') # open(pdb_file_name,'w').write(pdb_with_h) # files = [pdb_file_name] # if cif_file_name: # files += cif_file_name # pdb_processed_file = pdb_inter.run( # args=files, # assume_hydrogens_all_missing=False, # hard_minimum_nonbonded_distance=0.0, # nonbonded_distance_threshold=None, # substitute_non_crystallographic_unit_cell_if_necessary= # params.substitute_non_crystallographic_unit_cell_if_necessary, # log=null_out() ) # # test that CRYST1 records are ok # sps = pdb_processed_file.all_chain_proxies.special_position_settings # if not sps: # msg = 'None valid CRSYT1 records.\n' # msg += 'Consider running mmtbx.nonbonded_overlaps with the option:\n' # msg += 'substitute_non_crystallographic_unit_cell_if_necessary=true' # raise Sorry(msg) # grm = pdb_processed_file.geometry_restraints_manager() # xrs = pdb_processed_file.xray_structure() # sites_cart = xrs.sites_cart() # site_labels = xrs.scatterers().extract_labels() # hd_sel = xrs.hd_selection() # macro_mol_sel = nbo.get_macro_mol_sel(pdb_processed_file) # nb_overlaps = nbo.info( # geometry_restraints_manager=grm, # macro_molecule_selection=macro_mol_sel, # sites_cart=sites_cart, # site_labels=site_labels, # hd_sel=hd_sel) # if params.verbose: # nb_overlaps.show( # log=out, # nbo_type=params.show_overlap_type, # normalized_nbo=params.show_normalized_nbo) # else: # all = nb_overlaps.result.nb_overlaps_all # macro_molecule = nb_overlaps.result.nb_overlaps_macro_molecule # sym = nb_overlaps.result.nb_overlaps_due_to_sym_op # out_list = map(lambda x: str(round(x,2)),[macro_molecule,sym,all]) # print(', '.join(out_list), file=out) # return nb_overlaps # if (__name__ == "__main__"): # run(sys.argv[1:])