ó
‹™xTc           @   s  d  d l  m Z d  d l Z d  d l Z d  d l Z e j Z e j j d ƒ Z	 e j j d ƒ Z
 e	 d k s‚ e j e	 ƒ s‚ t ‚ e
 d k s£ e j e
 ƒ s£ t ‚ d a d „  Z d „  Z d „  Z d „  Z d	 e f d
 „  ƒ  YZ d e f d „  ƒ  YZ d „  Z d „  Z d d „ Z d S(   iÿÿÿÿ(   t   divisionNt
   CCI_PDBMTZt   PDB_MIRROR_PDBc          C   sŒ   t  d  k rˆ t ƒ  a  xp t j t ƒ D]\ }  |  j d ƒ s@ q% n  t |  ƒ d k sX t ‚ |  j	 ƒ  |  k sp t ‚ t  j
 |  d  ƒ q% Wn  t  S(   Ns   .mtzi   i   (   t   __pdbmtz_codest   Nonet   sett   ost   listdirt   cci_pdbmtz_patht   endswitht   lent   AssertionErrort   lowert   add(   t   node(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   pdbmtz_codes   s    	 c         C   sÒ   d  } xÅ |  D]½ } | j d ƒ r | j d ƒ } | d k rÊ | | d j d ƒ d k rÊ | j ƒ  } t | ƒ d k rÇ y t | d ƒ } Wn t k
 rŸ qÄ X| d  k s¸ | | k rÄ | } qÄ qÇ qÊ q q W| S(   Ns   REMARK   2 t
   RESOLUTIONi    i
   t   ANGSTROMi   i   (   R   t
   startswitht   findt   splitR
   t   floatt
   ValueError(   t   remark_sectiont   resultt   linet   i_resolutiont   fldst
   resolution(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   extract_best_resolution   s    )  c         C   sV   t  j j ƒ  d GHd |  GHt  j j ƒ  t j ƒ  t  j j ƒ  d GHHt  j j ƒ  d  S(   Ns   >Begin exceptions   %s: Exceptions   >End exception(   t   syst   stderrt   flusht   stdoutt	   tracebackt	   print_exc(   t	   file_name(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   report_exception'   s    	
c         C   sT   t  j |  ƒ } | j d ƒ r) | d d !S| j d ƒ rC | d d !S| j d ƒ d S(	   Ns   .ent.gziõÿÿÿiùÿÿÿs   .entiøÿÿÿiüÿÿÿt   .i    (   t   opt   basenameR	   R   (   R$   t   bn(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   pdb_code_from_file_name2   s    t	   file_infoc           B   s    e  Z d  d g Z d d „ Z RS(   t   namet   atom_selection_stringc         C   sN   t  j | ƒ s8 d d l m } t d | | ƒ ƒ ‚ n  | |  _ | |  _ d  S(   Niÿÿÿÿ(   t   show_strings   Missing pdb file: %s(   R'   t   isfilet   libtbx.str_utilsR.   t   RuntimeErrorR,   R-   (   t   OR,   R-   R.   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   __init__>   s
    	N(   t   __name__t
   __module__t	   __slots__R   R3   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyR+   :   s   t   pdb_infoc           B   s)   e  Z d  d d d d d g Z d „  Z RS(   t   chunk_nt   chunk_iR$   R-   t   pdb_codet   pdb_inpc         C   s@   | |  _  | |  _ | j |  _ | j |  _ | |  _ | |  _ d  S(   N(   R8   R9   R,   R$   R-   R:   R;   (   R2   R8   R9   R+   R:   R;   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyR3   O   s    			(   R4   R5   R6   R3   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyR7   E   s   	c   
      c   sc  d d  l  } d d l m } d d  l } d Gt |  ƒ GHt j j ƒ  | j ƒ  } zÖ xÏ t |  ƒ D]Á \ } } | | | k r‚ q` n  d G| G| j	 GHt j j ƒ  t
 d | j	 ƒ }	 y< t d | d | d | d	 |	 d
 | j j d | j	 ƒ ƒ VWq` t k
 r‚  q` t k
 r t d t ƒ q` Xq` WWd  t j j ƒ  d | j ƒ  | GH| ƒ  GHt j j ƒ  Xd  S(   Niÿÿÿÿ(   t   format_cpu_timess   len(file_infos):s   i_file:R$   R8   R9   R+   R:   R;   s   total time: %.2f(   t	   iotbx.pdbt   libtbx.utilsR<   t   timeR
   R   R!   R    t	   enumerateR,   R*   R7   t   pdbt   inputt   KeyboardInterruptt	   ExceptionR%   R$   R   (
   t
   file_infosR8   R9   t   iotbxR<   R?   t   t0_totalt   i_fileR+   R:   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   pdb_inp_generatorW   s8      c          c   s   x g  D] }  |  Vq Wd  S(   N(    (   t   never(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   null_generatort   s     c      	   C   sÔ  d d l  m } d d  l } | j j d d ƒ } | d d j | ƒ d ƒ j d t ƒ j ƒ  j	 d	 | ƒ j
 d
 |  ƒ } | j d | ƒ r� | ƒ  | t ƒ  f Sd d l m } | j } t | ƒ d k rà t d  k	 rà t g } n  g  }	 xÀ| D]¸}
 t j |
 ƒ rƒt j |
 ƒ } | j d ƒ rt d  k	 s2t ‚ xKt t |
 ƒ j ƒ  j ƒ  ƒ D]Ç \ } } | j d  d ƒ } t | ƒ d k r­t d | |
 ƒ | d | | ƒ f ƒ ‚ n  | d } d  } t | ƒ d k rÜ| d } n  t j t | d d !d | ƒ } |	 j t d | d | ƒ ƒ qQWq¥| j d ƒ rjxO t |
 ƒ j ƒ  j ƒ  D] } |	 j t d | ƒ ƒ qGWq¥|	 j t d |
 ƒ ƒ qí t j  |
 ƒ r�t j |
 d ƒ } t j | ƒ rxÖ t | ƒ j ƒ  j ƒ  D]. } t j |
 | ƒ } |	 j t d | ƒ ƒ qÌWq¥t |	 ƒ } xQ t! j" |
 ƒ D]@ } | j# d" ƒ rt j |
 | ƒ } |	 j t d | ƒ ƒ qqWt |	 ƒ | k r¥t d | |
 ƒ ƒ ‚ q¥qí t d | |
 ƒ ƒ ‚ qí W| t$ d |	 d  | j% j& d! | j% j' ƒ f S(#   Niÿÿÿÿ(   t   option_parsert
   time_startt   nowt   usaget    s    [options] file|directory...t   easy_allt   callablet   argst   command_call(   R.   i    t
   pdb_codes_i   sB   Error interpreting pdb_codes file:
  %s  line number: %d  line: %si   s   pdb%s.ent.gzR,   R-   t   file_names_t   INDEXs   .ents   .ent.gzs   ent.Zs   .pdbs   .pdb.gzs   pdb.Zs5   No INDEX file and no pdb files found in directory: %ss   Not a file or directory: %sRE   R8   R9   (   s   .ents   .ent.gzs   ent.Zs   .pdbs   .pdb.gzs   pdb.Z((   t   iotbx.option_parserRL   R>   t   utilst
   show_timest   joint   enable_chunkt   Truet   enable_multiprocessingt    call_with_self_as_first_argumentt   processt(   run_multiprocessing_chunks_if_applicableRK   R0   R.   RS   R
   t   pdb_mirror_pdbR   R'   R/   R(   R   R   R@   t   opent   readt
   splitlinesR   R1   t   appendR+   t   isdirR   R   R	   RI   t   chunkt   nt   i(   RS   RT   t   command_line_add_optionst   iotbx_option_parsert   libtbxRZ   t   command_lineR.   t   caRE   t   argR)   t   i_lineR   R   R:   R-   R$   t   file_name_indext   relative_patht   prev_len_file_infos(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   runw   s€    				+&
		(   t
   __future__R    R"   R   R   t   pathR'   t   environt   getR   Rb   R   Rg   R   R   R   R   R%   R*   t   objectR+   R7   RI   RK   Ru   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mining.pyt   <module>   s"   	!!						