ó ±™xTc@ sÃdZddlmZddlZddlmZmZddlmZddl Z ddl Z ej j dƒZ d de jd„Ze jd„Zd „Zed kr¿ee jd ƒndS( sx Provides a command-line utility for fetching PDB files and their associated reflection data and electron density maps. iÿÿÿÿ(tdivisionN(tSorrytUsage(teasy_runs fetch_pdb .caption = PHENIX can automatically retrieve data from the PDB via the RCSB web server. If you intend to re-refine or re-build the structure we recommend creating a new project, but this is not required. Note that you may also use this tool to generate an MTZ file from the mmCIF structure factors (if available) and even calculate maps, but the options are more limited than what is available in the phenix.cif_as_mtz and phenix.maps GUIs. .style = auto_align caption_img:icons/custom/pdb_import64.png caption_width:400 { pdb_ids = None .type = strings .short_caption = PDB ID(s) .input_size = 400 .style = bold action = *pdb_only all_data all_plus_mtz all_plus_maps .type = choice .caption = Download_PDB_file(s) Download_all_data Download_all_data_and_convert_CIF_to_MTZ Download_all_data_and_create_maps .style = bold site = *rcsb pdbe pdbj .type = choice .caption = RCSB PDBe PDBj .short_caption = Mirror site .style = bold }c C s^|d k st‚g}g}d|jj}x#|jjD]}||g}|jjdkr|jddƒ|jjdkr”|jddƒn%|jjdkr¹|jdd ƒny9td |d |ƒ}|d j|ƒIJ|j |ƒWqPt k r}|j t |ƒƒqPXq;td ||gd |ƒ} || IJ|j | ƒq;W||fS(s= For use in PHENIX GUI only, fetches pdb files and their associated maps and/or reflection data from the PDB. Parameters ---------- args : list of str, optional params : libtbx.phil.scope_extract, optional out : file, optional Returns ------- output_files : list of str errors : list of str s --mirror=%stall_datat all_plus_mtzt all_plus_mapsis--allis--mtzs--mapstargstlogs N(RRR( tNonetAssertionErrort fetch_pdbtsitetpdb_idstactiontinserttrun2tjointextendt Exceptiontappendtstr( Rtparamstoutt output_filesterrorstmirrortidt data_filestetpdb_file((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/fetch_pdb.pytrun0s.    cC s6t|ƒdkr!tdƒ‚nddlm}t}t}}}d}d}d} g} x|D]ü} | dkrd}qd| d kr”d }qd| d kr©d }qd| d kr¾t}qd| dkrÙt}d}qd| dkrút}d}t}qd| dkrd}qd| jdƒrS| jdƒd} | d4kr`td| ƒ‚q`qd| j | ƒqdWt| ƒdkr…tdƒ‚n|dkrèg} x0| D](} | j || || |d|ƒƒqžWt| ƒdkrä| dS| Sg} x=| D]5} xBd5d6d7d8gD].\}}| j || || |d|ƒƒqW|rqddddg}t j d| | dj |ƒfƒt jjd | ƒrºt jd | d!| ƒ|d"| IJnt jjd!| ƒ| ds     )r