ó
“™xTc           @   sÎ   d  d l  m Z d  d l m Z d  d l Z d  d l m Z d  d l m Z d  d l m	 Z	 m
 Z
 d  d l Z d  d l Z d „  Z e d k rÊ d  d l Z d  d l Z e d	 e j d
 d e j j ƒ n  d S(   iÿÿÿÿ(   t   division(   t	   cod_toolsN(   t   CifBuilderError(   t   CifParserError(   t   easy_picklet
   group_argsc         C   s>  d d l  m } d d  l } | j j d d ƒ } | d | d ƒ j d t ƒ j ƒ  j d  d d	 d
 ƒj d  d d	 d
 ƒj d  d d	 d
 ƒj d d d	 d
 ƒj
 d |  ƒ } | j d | t g ƒ rÍ | ƒ  d  S| j } | j } | j | j g j t ƒ d k st ‚ | j rd } n | j r*d } n d  } | j }	 | j }
 t j d | d | ƒ } | j ƒ  | j } | j } d } i  } i  } i  } t ƒ  } g  } | j | j ƒ  ƒ | j | j ƒ  ƒ x¹t | ƒ D]«\ } } | d 7} | | j j | j j  k rqÐn  y¤t! j" j# | ƒ } t$ j j% d | ƒ } |
 r>wÐn  t& } x| j' ƒ  j ƒ  D]ó } | j( d ƒ } t | j) ƒ  ƒ } | d6 k r¸t } | j* | ƒ |	 rJd | | f GHqJqWt+ t d d g ƒ j, | ƒ ƒ d k r| j* | ƒ |	 rJd G| GHqJqWt+ t d d  g ƒ j, | ƒ ƒ d k rW|	 r:d! G| GHn  | j* | ƒ qWqWW| rZwÐn  | j- d" ƒ rv| j. ƒ  n5 | j- d# ƒ r’| j/ ƒ  n t$ j j0 d$ | j' ƒ  ƒ WqÐt1 k
 rÅd% GHd  St2 k
 r‚} t3 | ƒ } |	 r| j4 d& ƒ s| j4 d' ƒ r| j5 | | ƒ qÐn  t6 j7 j8 ƒ  t6 j9 d( | | t3 | ƒ f IJ|	 rbt: j; ƒ  t6 j9 Jn  | j5 | | ƒ t6 j9 j8 ƒ  qÐt< k
 rþ} t6 j7 j8 ƒ  t3 | ƒ } | j5 | | ƒ t6 j9 d) | | | f IJ|	 rît: j; ƒ  t6 j9 Jn  t6 j9 j8 ƒ  qÐt= k
 rz} t6 j7 j8 ƒ  t3 | ƒ } | j5 | | ƒ t6 j9 d( | | | f IJ|	 rjt: j; ƒ  t6 j9 Jn  t6 j9 j8 ƒ  qÐXqÐWHd* | t+ | ƒ | f GH|
 sÏd+ Gt+ | ƒ GHd, Gt+ | ƒ GHd- Gt+ | ƒ GHn  H| ƒ  t> d. t+ | ƒ d/ t+ | ƒ d0 t+ | j? ƒ d1 | d2 | d3 | d4 | ƒ } t@ jA d5 | j j  | ƒ Hd  S(7   Niÿÿÿÿ(   t   option_parsert
   time_startt   nowt   usages    [options] [cod_id...]t   easy_alls   --parse_onlyt   actiont
   store_trues
   --cif_onlys
   --hkl_onlys   -vs	   --verboset   argst   command_calli   t   cift   hklt   cod_idst   exti    t	   file_patht   _cod_error_flagt   errorst	   retracteds    SKIPPING: _cod_error_flag %s: %st*   _space_group_symop_ssg_operation_algebraict   _space_group_ssg_names+   SKIPPING: COD entry with super-space group:t   _refln_index_mt   _refln_index_m_1s(   SKIPPING: COD entry with _refln_index_m:s   .cifs   .hklt	   cif_models#   CAUGHT EXCEPTION: KeyboardInterrupts$   No atomic coordinates could be founds>   No symmetry instructions could be extracted from the cif blocks   CAUGHT EXCEPTION: %s: %s: %ss   PARSING ERROR: %s: %s: %ss!   Number successfully parsed: %i/%is   Number skipped:s   Number of exceptions caught:s   Number of exceptions ignored:t   n_hklt   n_cift   n_hkl_cif_pairst   parsing_errorst   build_errorst   ignored_errorst   skippeds   result_%03i.pickle(   s   errorsR   (B   t   iotbx.option_parserR   t   libtbx.utilst   utilst
   show_timest   enable_chunkt   Truet   enable_multiprocessingt   optiont   Nonet   processt(   run_multiprocessing_chunks_if_applicablet   __file__t   optionsR   t   cif_onlyt   hkl_onlyt   countt   AssertionErrort   verboset
   parse_onlyR   t   build_hkl_cift   show_summaryR   R   t   sett   extendt   valuest	   enumeratet   chunkt   nt   it   ost   patht   basenamet   iotbxt   readert   Falset   modelt   gett   keyst   addt   lent   intersectiont   endswitht   build_crystal_structurest   build_miller_arrayst   cctbx_data_structures_from_cift   KeyboardInterruptR   t   strt
   startswitht
   setdefaultt   syst   stdoutt   flusht   stderrt	   tracebackt	   print_excR   t	   ExceptionR   t   hkl_cif_pairsR   t   dump(   R   t   command_namet   iotbx_option_parsert   libtbxR&   t   command_linet   coR   R   R4   R5   t   cod_hkl_cift	   hkl_filest	   cif_filest   n_totalR   R    R!   R"   t   files_to_parseR>   R@   t   cod_idt   cif_objt	   skip_filet	   cif_blockt   valueRG   t   et   e_strt   result(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cif/tests/tst_cod.pyt   run	   s   											'	 		 			
			
   	





	t   __main__R   i   R\   (   t
   __future__R    t	   iotbx.cifR   RB   t   iotbx.cif.buildersR   R   R^   R   R   R?   RW   Rn   t   __name__t   libtbx.load_envRS   t   argvt   envt   dispatcher_name(    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cif/tests/tst_cod.pyt   <module>   s   	�