ó
R™xTc           @   s  d  d l  m Z d  d l m Z m Z d  d l m Z d  d l Z d  d l Z e j	 Z
 e j j d ƒ Z e d k sŠ e
 j e ƒ sŠ t ‚ e j j d ƒ Z e d k s½ e
 j e ƒ s½ t ‚ d „  Z d „  Z e d	 k rþ d  d l Z e d
 e j d ƒ n  d S(   iÿÿÿÿ(   t   division(   t   date_and_timet   user_plus_sys_time(   t   show_stringNt   PDB_MIRROR_PDBt
   CCI_PDBMTZc         C   s³  | \ } } d d  l  } | j j d | ƒ j ƒ  } | j ƒ  | j d d ƒ j ƒ  Hd  } d  } d d  l } | j	 j
 d | ƒ } xg | j d | ƒ D]S }	 |	 j ƒ  GH| d  k rÆ |	 j ƒ  rÆ |	 } q” | d  k r” |	 j ƒ  r” |	 } q” q” WH| d  k r/| d  k	 s
t ‚ | }
 | j ƒ  | j d d ƒ } n" | }
 | j ƒ  | j d d ƒ } Ht |  j ƒ d	 k rkd  Sd d
 l m } | d |  d t j | ƒ d |
 d | d | d | ƒ d  S(   Niÿÿÿÿt	   file_namet   tablet   it1992t   crystal_symmetryt	   algorithmt   shelxlt   xtal_3_7i    (   t   process_continuet   paramst   cod_idt   c_obst   i_obst   f_obst   structure_prep(   t	   iotbx.pdbt   pdbt   inputt   xray_structure_simplet   show_summaryt   scattering_type_registryt   showt   Nonet	   iotbx.mtzt   mtzt   objectt   as_miller_arrayst   infot   is_xray_amplitude_arrayt   is_xray_intensity_arrayt   AssertionErrort   show_comprehensive_summaryt	   f_as_f_sqt	   f_sq_as_ft   lent
   optimizerst   cctbx.omz.cod_refineR   t   opt   basename(   R   t   mtz_pdb_pairt   fn_mtzt   fn_pdbt   iotbxt   xsR   R   t   mtz_objt   maR   R   (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   process   sD    
	

c            si  d d l  m } d d  l } | j j d d ƒ } d t g } | d d j | ƒ d ƒ j d	 t ƒ j	 ƒ  j
 d
 |  d d ƒ } | j d | ƒ rš | ƒ  d  S| j } d Gt ƒ  GHH| j j ƒ  j ƒ  Ht j j ƒ  d d l m } | j d d  d d d t ƒ } | j ƒ  }	 g  }
 g  } xO | j D]D } | j d ƒ d k rX|
 j |	 j
 d | ƒ ƒ q!| j | ƒ q!W| j d |
 ƒ } | j ƒ  H| j ƒ  } g  } t | ƒ ‰  xqˆ  D]i} ‡  f d †  } t j | ƒ r | j  d' ƒ r | j  d ƒ r| ‰ | d d g ƒ } q| } | d g ƒ ‰ ná | d ‰ ‡ f d †  } t j ˆ ƒ r†x¶ d d g D]# } | | } t j | ƒ rUPqUqUW| ƒ  n{ t j t! | d ƒ ‰ t j ˆ ƒ sÄt" d t# ˆ ƒ ƒ ‚ n  t j t$ | d d !d | d  ƒ } t j | ƒ s| ƒ  n  | j ˆ | f ƒ q«Wd } xt% | ƒ D]\ } } | | j& j' | j& j( k rYq+n  t) ƒ  } y t
 | | ƒ Wnœ t* k
 r²t j+ d! IJt, j- ƒ  t j+ Jt j+ j ƒ  d  St. k
 rt j j ƒ  t j+ d" d# j | ƒ IJt, j- ƒ  t j+ Jt j+ j ƒ  | d 7} q+Xd$ | | j/ ƒ  f GHHt j j ƒ  q+WHd% G| GH| ƒ  Hd& Gt ƒ  GHt j j ƒ  d  S((   Niÿÿÿÿ(   t   option_parsert
   time_startt   nows   iotbx.pythont   usaget    s    [options] directory|file...t   easy_allt   argst	   min_nargsi   t   command_calls   TIME BEGIN pdb_dev:(   t
   cod_refinet	   max_atomst   f_calc_options_algorithms   direct *fftt   bulk_solvent_correctiont   =i    t   argt   sourcesc            si   d  ‡  f d † } y ˆ j ƒ  } Wn t k
 r? | d ƒ n X| j t ˆ  ƒ ƒ se | d | ƒ n  | S(   Nc            sV   d |  d j  ˆ  ƒ f } | d  k r2 | d 7} n | d t | ƒ 7} t | ƒ ‚ d  S(   Ns   %s file name (%s expected)s    or t   .s   : (   t   joinR   R   t   RuntimeError(   t   whatt   fnt   msg(   t   expected_exts(    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   raise_bad_filec   s
    t   Missingt
   Unexpected(   R   t   nextt   StopIterationt   endswitht   tuple(   RJ   RK   RB   (   t   arg_iter(   RJ   s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   get_nextb   s    s   .mtzs   .pdbs   .entc              s   t  d t ˆ  ƒ ƒ ‚ d  S(   Ns"   MTZ file found but no PDB file: %s(   RF   R   (    (   R-   (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   raise_mtz_but_no_pdbz   s    s   MTZ file not found: %si   R   s   .ent.gzs#   CAUGHT EXCEPTION: KeyboardInterrupts   CAUGHT EXCEPTION: %ss   , s    done_with: %s, %s (%.2f seconds)s   Number of exceptions caught:s   TIME END pdb_dev:(   s   .mtzs   .pdbs   .ent(0   t   iotbx.option_parserR4   t   libtbx.utilst   utilst
   show_timest   __file__RE   t   enable_chunkt   Truet   enable_multiprocessingR3   t(   run_multiprocessing_chunks_if_applicablet   optionsR   t   host_and_userR   t   syst   stdoutt   flusht	   cctbx.omzR=   t   get_master_philR   t!   command_line_argument_interpreterR:   t   findt   appendt   fetcht   extractt   iterR*   t   isfileRP   t   cci_pdbmtz_pathRF   R   t   pdb_v3_mirror_dirt	   enumeratet   chunkt   nt   iR   t   KeyboardInterruptt   stderrt	   tracebackt	   print_exct	   Exceptiont   elapsed(   R:   t   iotbx_option_parsert   libtbxRX   R<   t   command_linet   coR=   t   master_philt   argument_interpretert   phil_objectst   remaining_argsRB   t	   work_philR   t   mtz_pdb_pairsRS   R.   RT   t   extt   n_caughtt   i_pairR,   t   tm(    (   RR   R-   s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   run7   s´    					



$
 	

	t   __main__R:   i   (   t
   __future__R    RV   R   R   t   libtbx.str_utilsR   Rt   t   ost   pathR*   t   environt   getRm   R   t   isdirR#   Rl   R3   R†   t   __name__R`   t   argv(    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/omz/pdb_dev.pyt   <module>   s   	!!	)	w