def opm_mempos(pdbfn, ballfn): """ get membrane position from opmdb pdb file """ geo_data = bbtmio.read_geo_file(pdbfn[:-3]+'geo') # an anchor used to find out the offset. ithas no meaning base_res_id = geo_data['startingSNs'][0] opmstruct = bbtmio.read_pdb_file(pdbfn[:-8]+'opmdb/'+pdbfn[-8:]) opmchain = opmstruct[0][ bbtmio.guess_chain_id(opmstruct, geo_data) ] for res in opmchain: if res.get_id()[1] == base_res_id: opm_base_z = res['CA'].get_coord()[2] break ball_data = bbtmio.read_ball_file(ballfn) my_base_z = ball_data['COORDZ'][0] # offset from my ball coords to opm pdb coords my_z_offset = opm_base_z - my_base_z # get the last chain, then the first res, then the first atom, and then the coord # just get the absolute value since membrane thickness is symetric in opm pdb file opm_half_thickness = abs( opmstruct[0].get_list()[-1].get_list()[0].get_list()[0].get_coord()[2] ) # my extracellular membrane position my_extra_z = opm_half_thickness - my_z_offset # my periplasm membrane position my_peri_z = -opm_half_thickness - my_z_offset return my_z_offset, my_extra_z, my_peri_z
'--overwrite', required=False, default=False, action='store_true', help='Overwrite the exisiting files') parser.add_argument( '--trim', required=False, default=False, action='store_true', help='chop off the parts of the barrel out of the membrane') # parse arguments args = vars(parser.parse_args()) files_to_clean = [] for pdbfn in glob.glob(args['src']): pdbcode = pdbfn[-8:-4] print( 'Processing ' + pdbcode ) structure = bbtmio.read_pdb_file(pdbfn) print( '\tPreparing bbin file' ) # check geo file geofn = pdbfn[:-4]+'.geo' if not os.path.isfile( geofn ): print( '\tFile '+pdbcode+'.geo not found. ' +pdbcode+ ' ignored\n' ) continue ################################################ # write bbin file bbinfn = pdbfn[:-4]+'.bbin' if os.path.isfile(bbinfn) and not args['overwrite']: print( '\tFile '+pdbcode+'.bbin exists. Nothing changed.\n' ) else: bbtmio.write_bbin_file(pdbfn, geofn)
