ó
šxTc           @   sK  d  d l  Z d  d l Z d  d l m Z d  d l Z d  d l m Z d  d l Z	 d  d l
 Z
 d e
 j f d „  ƒ  YZ d „  Z d „  Z d „  Z d	 „  Z d
 „  Z d „  Z d „  Z d „  Z d d „ Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z i d d 6Z d „  Z i d7 d 6Z d „  Z  d Z! d „  Z" d „  Z# d „  Z$ d  e% f d! „  ƒ  YZ& d" e% f d# „  ƒ  YZ' d$ e% f d% „  ƒ  YZ( d& e% f d' „  ƒ  YZ) d( e% f d) „  ƒ  YZ* d* e% f d+ „  ƒ  YZ+ d, e% f d- „  ƒ  YZ, d. e% f d/ „  ƒ  YZ- d0 e% f d1 „  ƒ  YZ. d2 e% f d3 „  ƒ  YZ/ d4 e% f d5 „  ƒ  YZ0 d6 „  Z1 d S(8   iÿÿÿÿN(   t   Sorry(   t   bioinformaticst   NullHandlerc           B   s   e  Z d  Z d „  Z RS(   s   
    No output
    c         C   s   d  S(   N(    (   t   selft   record(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   emit   s    (   t   __name__t
   __module__t   __doc__R   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR      s   c   	      C   s  t  j j j d | ƒ } g  } g  } g  } xÓ |  D]Ë } t j j | ƒ rœ y/ t  j j t | ƒ j	 ƒ  ƒ } | j
 | ƒ Wqü t k
 r˜ | j
 | ƒ qü Xq1 d | k rï y# | j d | ƒ } | j
 | ƒ Wqü t k
 rë | j
 | ƒ qü Xq1 | j
 | ƒ q1 W| | | f S(   Nt   master_philt   =t   arg(   t   libtbxt   philt   command_linet   argument_interpretert   ost   patht   isfilet   parset   filet   readt   appendt	   Exceptiont   process(	   t   argst   phil_masterR   t   phil_objectst   filest   unknownst   argumentt   file_paramst   command_line_params(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   process_command_line   s*    			c         K   s–   i  } g  } x} |  D]u } xl | j  ƒ  D]Q \ } } t g  | D] } | j | ƒ ^ q< ƒ r& | j | g  ƒ j | ƒ Pq& q& W| j | ƒ q W| | f S(   N(   t   itemst   anyt   endswitht
   setdefaultR   (   R   t   kwargst   sortedR   t	   file_namet   typet
   extensionst   ending(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   group_files_on_extension9   s    (c         C   s   t  j j d |  | f ƒ S(   Ns   %s=%s(   R   R   R   (   t	   parametert   value(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   phil_assignJ   s    c         C   s   d t  j j |  ƒ d | f S(   Ns   %s_%si    (   R   R   t   splitext(   R(   t   label(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   autorootO   s    c         C   s   d t  |  | ƒ | f S(   Ns   %s.%s(   R2   (   R(   R1   t	   extension(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   autonameT   s    c         C   s<   d j  g  |  D]( } d | | k r( d n d | f ^ q ƒ S(   Nt    s   %s%st   *t    (   t   join(   t   possiblet   defaultt   n(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   choice_stringY   s    c         C   s?   d d d d |  | f j  d ƒ d d d g } d j | ƒ S(   Nt   #iO   s   %s %siM   s   
(   t   centerR8   (   t   programt   versiont   banner(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt
   get_banner`   s    c      	   C   sà   t  |  ƒ } g  |  D] } t  | ƒ ^ q } g  | D] } d | ^ q2 } d j |  ƒ g } xv | D]n }	 t  |	 ƒ | k s t ‚ | j d j g  t | |	 | | ƒ D]$ \ }
 } } } | |
 | |  ^ q¡ ƒ ƒ qa Wd j | ƒ S(   Ns   %%%dss     s   
(   t   lenR8   t   AssertionErrorR   t   zip(   t   captionst   formatst   linest   countt   ct   widthst   wt   wformatst   tablet   lt   ft   vt   wf(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   format_tablek   s    Ec         C   s  g  } g  } | d  k r. d  g t |  ƒ } n  xÔ t |  | t | Œ  | ƒ D]· \ } } } }	 | g g  | D] }
 | |
 ^ qi } | sŒ t ‚ t g  | D] } t | ƒ ^ q– ƒ } |	 d  k	 rÏ t | |	 ƒ } n  d | } | j g  | D] } | | |  ^ qæ ƒ qJ Wt | Œ  S(   Ns   %%%ds(   t   NoneRC   RE   RD   t   maxt   minR   (   RF   RG   RH   t
   max_widthst   columnsRK   RJ   RP   t   valuest   mwRQ   t
   convertedst   cvt   widtht   wformat(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   format_table_entries~   s    .$%
,c         C   s:   g  } x$ |  D] } | j  d j | ƒ ƒ q Wd j | ƒ S(   Ns     s   
(   R   R8   (   RH   RN   RO   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   assemble_table”   s    c         C   sp   t  j d |  ƒ } | r* t  j | ƒ } n	 t ƒ  } | j t  j d ƒ ƒ | j | ƒ | j t  j ƒ | | f S(   Nt   names   %(message)s(	   t   loggingt	   getLoggert   StreamHandlerR   t   setFormattert	   Formattert
   addHandlert   setLevelt   INFO(   Ra   t   outt   loggert   handler(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt
   get_loggerž   s    	c         C   s;   |  r t  j |  ƒ } n	 t ƒ  } | j t  j d ƒ ƒ | S(   Ns   %(message)s(   Rb   Rd   R   Re   Rf   (   Rj   Rl   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   get_handler¯   s
    	c         C   sw   t  j j |  ƒ r& | j d |  ƒ nM t  j j |  ƒ rU | j d ƒ t d |  ‚ n | j d |  ƒ t  j |  ƒ d  S(   Ns    Using existing output folder: %ss3   Cannot create output folder: existing non-directorys   Existing non-directory: %ss   Creating output directory: %s(   R   R   t   isdirt   infot   existst   errorR    t   mkdir(   t   folderRk   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   create_output_folder¼   s    c         C   s4   g  } x' |  D] } | j  | j d | ƒ ƒ q W| S(   NR(   (   R   t	   from_file(   t
   file_namest   object_typet   objsRP   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   read_in_filesÌ   s    c         C   s   t  j j |  ƒ \ } } | S(   N(   R   R   R0   (   R(   Ra   R3   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR3   Ö   s    R7   t   ac         C   s,   | d k r |  S|  t  k r$ t  |  Sd |  S(   Ni   s   %ss(   t   PLURAL_FOR_NOUN(   t   wordRI   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   inflectà   s
    t   ist   aret   bec         C   s?   | d k r' |  d k r d Sd |  Sn |  d k r7 d S|  Sd  S(   Ni   R   s   %ssR€   (    (   t   verbRI   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt	   conjugateð   s    s%   REMARK PHASER ENSEMBLE MODEL %s ID %sc         C   s.   |  s d n	 t  |  ƒ } t d | d | f S(   Ni    s   %ds   %.1f(   t   intt   PHASER_MODEL_IDENTITY_REMARK(   t   midt   identityt   index(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt    get_phaser_model_identity_remark  s    c         C   sr   d d  l  } | j t d
 |  ƒ } | s4 t d ‚ n  | j d ƒ } | d k rU d n d | t | j d	 ƒ ƒ f S(   Niÿÿÿÿs   \s*(\d+)s
   (\d*\.\d+)s   Incorrect remark formati   t   0R7   s   %4si   (   s   \s*(\d+)s
   (\d*\.\d+)(   t   ret   matchR…   t
   ValueErrort   groupt   float(   t   textR‹   RŒ   R†   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt"   parse_phaser_model_identity_remark  s    	c          C   su   d d l  m }  d d l m } m } m } |  d | j d | j d d d d d d d g ƒ d	 | j d
 d ƒ ƒ ƒ S(   Niÿÿÿÿ(   t   format_cryst1_and_scale_records(   t   uctbxt   sgtbxt   crystalt   crystal_symmetryt	   unit_cellt
   parametersi   iZ   t   space_group_infot   number(	   t	   iotbx.pdbR’   t   cctbxR“   R”   R•   t   symmetryR—   R™   (   R’   R“   R”   R•   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   dummy_cryst1_record  s    	$t	   ChainInfoc           B   sM   e  Z d  Z d „  Z e d „  ƒ Z e d „  ƒ Z e d „  ƒ Z d „  Z RS(   s)   
    Stores information about chains
    c         C   s(   | |  _  | |  _ | |  _ | |  _ d  S(   N(   t   pdbt   m_indext   c_indexR‡   (   R   R    R¡   R¢   R‡   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   __init__(  s    			c         C   s   |  j  j j ƒ  |  j S(   N(   R    t   objectt   modelsR¡   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   model0  s    c         C   s   |  j  j ƒ  |  j S(   N(   R¦   t   chainsR¢   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   chain6  s    c         C   s%   |  j  j |  j j |  j j |  j f S(   N(   R    Ra   R¦   t   idR¨   R¢   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt
   identifier<  s    c         C   s#   d |  j  j |  j j |  j j f S(   Ns   chain (%s, '%s', '%s')(   R    Ra   R¦   R©   R¨   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   __str__B  s    		(	   R   R   R   R£   t   propertyR¦   R¨   Rª   R«   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRŸ   #  s   	t	   PDBObjectc           B   sY   e  Z d  Z d d „ Z d „  Z d „  Z e d „  ƒ Z e d „  ƒ Z e d „  ƒ Z	 RS(   s$   
    Opened and parsed PDB file
    c         C   s   | |  _  | |  _ | |  _ d  S(   N(   Ra   R¤   t   remarks(   R   t   rootRa   R®   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   P  s    		c         C   sÆ   i  } xZ |  j  D]O } y t d | ƒ \ } } Wn t k
 rE q n X| j | g  ƒ j | ƒ q Wi  } xV |  j j ƒ  D]E } x< t | j ƒ  | j	 | j
 g  ƒ ƒ D] \ } } | | | <q¤ Wqy W| S(   NR�   (   R®   R‘   R�   R%   R   R¤   R¥   RE   R§   t   getR©   (   R   t   cid_int   rR†   R‡   t   identity_forR¦   R¨   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   match_identity_recordsW  s    1c         C   s�   g  } |  j  ƒ  } xw t |  j j ƒ  ƒ D]` \ } } xQ t | j ƒ  ƒ D]= \ } } | j t d |  d | d | d | j | ƒ ƒ ƒ qG Wq( W| S(   NR    R¡   R¢   R‡   (   R´   t	   enumerateR¤   R¥   R§   R   RŸ   R°   (   R   t   infosR³   R¡   R¦   R¢   R¨   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   get_chain_infosm  s    "c         C   sc   y t  j j d | d t ƒ } Wn t k
 r= } t | ‚ n X|  d | j ƒ  d | d | j ƒ  ƒ S(   NR(   t   raise_sorry_if_format_errorR¯   Ra   R®   (   t   iotbxR    t   inputt   Truet   IOErrorR    t   construct_hierarchyt   remark_section(   t   clsR(   Rº   t   e(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRv   €  s    c         C   sZ   d d  l  } y | j | ƒ j ƒ  } Wn t k
 rC } t | ‚ n X|  j d | d | ƒ S(   Niÿÿÿÿt   pdb_strRa   (   t   gzipt   GzipFileR   R¼   R    t   from_string(   R¿   R(   RÂ   t   dataRÀ   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   from_gzipped_file‘  s    	c         C   s@   t  j j d | d | ƒ } |  d | j ƒ  d | d | j ƒ  ƒ S(   NRH   t   source_infoR¯   Ra   R®   (   R¹   R    Rº   R½   R¾   (   R¿   RÁ   Ra   Rº   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÄ   ¢  s
    (    (
   R   R   R   R£   R´   R·   t   classmethodRv   RÆ   RÄ   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR­   K  s   		t   AlignmentObjectc           B   s5   e  Z d  Z d „  Z e d „  ƒ Z e d „  ƒ Z RS(   s*   
    Opened and parsed alignment file
    c         C   s/   | j  s t d | ‚ n  | |  _ | |  _ d  S(   Ns   Empty alignment: %s(   t
   alignmentsR    Ra   R¤   (   R   t	   alignmentRa   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   ²  s    		c         C   sd   y t  | ƒ j ƒ  } Wn& t k
 r> } t d | | f ‚ n X|  j d | d t d | ƒ d | ƒ S(   Ns   Error while reading %s: %st   ali_strR3   R(   Ra   (   R   R   R¼   R    RÄ   R3   (   R¿   R(   RÌ   RÀ   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRv   »  s    	c         C   so   t  j d | ƒ } | s( t d | ‚ n  | | ƒ \ } } | rP t d | ‚ n  | s\ t ‚ |  d | d | ƒ S(   NR3   s   Unknown format: %ss   Incorrect format:
%sRË   Ra   (   R   t   alignment_parser_for_extensionR    RD   (   R¿   RÌ   R3   Ra   t   parsert   alit   errors(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÄ   Ë  s    (   R   R   R   R£   RÈ   Rv   RÄ   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÉ   ­  s   		t   SequenceObjectc           B   s5   e  Z d  Z d „  Z e d „  ƒ Z e d „  ƒ Z RS(   s*   
    Opened and parsed alignment file
    c         C   s   | |  _  | |  _ d  S(   N(   Ra   R¤   (   R   t	   sequencesRa   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   â  s    	c         C   sU   y t  | ƒ j ƒ  } Wn& t k
 r> } t d | | f ‚ n X|  j d | d | ƒ S(   Ns   Error while reading %s: %st   seq_strRa   (   R   R   R¼   R    RÄ   (   R¿   R(   RÓ   RÀ   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRv   è  s
    c         C   sŠ   t  j d | ƒ \ } } | s% | r5 t d | ‚ n  x? | D]7 } | j s< t j j t j j | ƒ ƒ d | _ q< q< W|  d | d | ƒ S(   NRÅ   s   Incorrect format:
%si    RÒ   Ra   (   R   t   parse_sequenceR    Ra   R   R   R0   t   basename(   R¿   RÓ   Ra   t   seqsRÐ   t   seq(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÄ   ô  s    	,(   R   R   R   R£   RÈ   Rv   RÄ   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÑ   Ý  s   	t   HomologySearchObjectc           B   s&   e  Z d  Z d „  Z e d „  ƒ Z RS(   s0   
    Opened and parsed homology search data
    c         C   s   | |  _  | |  _ d  S(   N(   Ra   R¤   (   R   t   searchRa   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£     s    	c         C   sö   t  | ƒ j ƒ  } | j d ƒ rY y t j d | ƒ } Wqã t k
 rU } t | ‚ qã XnŠ | j d ƒ rÚ d d l m } | j	 ƒ  | j
 ƒ  g } xP | D]3 } y | d | ƒ } Wn t k
 rÈ } q— n XPq— Wt d ‚ n	 t d ‚ |  d	 | d
 | ƒ S(   Ns   .hhrt   outputs   .xmliÿÿÿÿ(   t   homologyRÅ   s+   No XML parser was able to process this files   Unknown homology search fileRÙ   Ra   (   t   openR   R$   R   t   hhsearch_parserR�   R    t   phaser.pipelineRÛ   t   get_ncbi_blast_parsert   get_ebi_blast_parsert   RuntimeError(   R¿   R(   RÅ   t   resultRÀ   RÛ   t   parserst   p(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRv     s&    		(   R   R   R   R£   RÈ   Rv   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRØ     s   	t   FileArgumentc           B   s2   e  Z d  Z d „  Z d „  Z d „  Z d „  Z RS(   s   
    A file
    c         C   s   | |  _  d  S(   N(   R(   (   R   R(   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   9  s    c         C   s   | j  d |  ƒ d  S(   NR   (   t   process_file(   R   t   accumulator(    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR   >  s    c         C   s   t  j j |  j ƒ d S(   Ni   (   R   R   R0   R(   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR3   C  s    c         C   s   d |  j  S(   Ns	   %s <file>(   R(   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR«   H  s    (   R   R   R   R£   R   R3   R«   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRå   4  s
   			t   PhilArgumentc           B   sV   e  Z d  Z d „  Z d „  Z d „  Z e d „  ƒ Z e d „  ƒ Z e d „  ƒ Z	 RS(   s!   
    A phil read from a file
    c         C   s   | |  _  d  S(   N(   R   (   R   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   R  s    c         C   s   | j  d |  ƒ d  S(   NR   (   t   process_phil(   R   Rç   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR   W  s    c         C   s   d |  j  j ƒ  S(   Ns   Phil:
%s(   R   t   as_str(   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR«   \  s    c         C   s@   y t  j j | ƒ } Wn t k
 r2 t d ‚ n X|  d | ƒ S(   Ns   Incorrect PHIL formatR   (   R   R   R   R   R�   (   R¿   t   stringR   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRÄ   a  s
    c         C   s   |  j  d t | ƒ j ƒ  ƒ S(   NRë   (   RÄ   RÜ   R   (   R¿   R(   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRv   m  s    c         C   s@   y | j  d | ƒ } Wn t k
 r2 t d ‚ n X|  d | ƒ S(   NR   s$   Incorrect PHIL command line argumentR   (   R   R   R�   (   R¿   t   interpreterR   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   command_line_arguments  s
    (
   R   R   R   R£   R   R«   RÈ   RÄ   Rv   Rí   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRè   M  s   			t   UnknownArgumentc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   s%   
    An argument that is unknown
    c         C   s   | |  _  d  S(   N(   R   (   R   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   „  s    c         C   s   | j  d |  ƒ d  S(   NR   (   t   process_unknown(   R   Rç   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR   ‰  s    c         C   s   |  j  S(   N(   R   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR«   Ž  s    (   R   R   R   R£   R   R«   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRî     s   		t   PhilArgumentFactoryc           B   s   e  Z d  „  Z d „  Z RS(   c         C   s   t  j j j d | ƒ |  _ d  S(   NR	   (   R   R   R   R   Rì   (   R   R	   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   •  s    c         C   s²   t  j j | ƒ rN y t j d | ƒ } Wq® t k
 rJ t d | ƒ } q® Xn` d | k rŸ y t j d |  j d | ƒ } Wq® t k
 r› t	 d | ƒ } q® Xn t	 d | ƒ } | S(   NR(   R
   Rì   R   (
   R   R   R   Rè   Rv   R�   Rå   Rí   Rì   Rî   (   R   R   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   __call__œ  s    		(   R   R   R£   Rñ   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRð   “  s   	t   PhilAccumulatorc           B   sD   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   sH   
    Unifies Phil command line handling (using the visitor pattern)
    c         C   s(   | |  _  g  |  _ g  |  _ g  |  _ d  S(   N(   R	   t   philst   file_handlerst   unknown_handlers(   R   R	   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   º  s    			c         C   s   |  j  j | ƒ d  S(   N(   Rô   R   (   R   Rl   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   register_file_handlerÃ  s    c         C   s\   xU |  j  D]: } y | d | d |  j ƒ } Wn t k
 rB q
 n XPq
 W|  j d | ƒ d  S(   NR   Ró   (   Rô   Ró   Rá   Rï   (   R   R   Rl   Râ   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRæ   È  s    c         C   s   |  j  j | j ƒ d  S(   N(   Ró   R   R   (   R   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRé   ×  s    c         C   sW   xP |  j  D]8 } y | d | d |  j ƒ Wn t k
 r@ q
 n XPq
 Wt d | ‚ d  S(   NR   Ró   s   Unknown argument: %s(   Rõ   Ró   Rá   R    (   R   R   Rl   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRï   Ü  s    c         C   s   |  j  j d |  j ƒ S(   Nt   sources(   R	   t   fetchRó   (   R   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   mergeë  s    (	   R   R   R   R£   Rö   Ræ   Ré   Rï   Rù   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRò   µ  s   						t   ExtensionFileHandlerc           B   s   e  Z d  „  Z d „  Z RS(   c         C   s   | |  _  | |  _ d  S(   N(   R*   t   template(   R   R*   Rû   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyR£   ò  s    	c         C   sI   | j  ƒ  |  j k r8 | j t j j |  j | j ƒ ƒ St d | ‚ d  S(   Ns   Cannot process argument: %s(	   R3   R*   R   R   R   R   Rû   R(   Rá   (   R   R   Ró   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRñ   ø  s    (   R   R   R£   Rñ   (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyRú   ð  s   	c         C   sv   d d d } d d l  m } d d  l } | j j ƒ  } | d =| d d d	 | |  | f f d
 | ƒ} | j ƒ  d  S(   Ns3   read_pdb( '%s' ); graphics_to_ca_representation(0);s;   set_show_symmetry_master( 1 ); symmetry_as_calphas( 0, 1 );s$   auto_read_make_and_draw_maps( '%s' )iÿÿÿÿ(   t   Popent   LD_LIBRARY_PATHt   coots   --pythons   -ct   env(   t
   subprocessRü   R   t   environt   copyt   communicate(   t   pdb_filet   mtz_filet   SCRIPT_TEMPLATERü   R   Rÿ   Rä   (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   display_in_coot  s    	(   s   iss   are(2   t   libtbx.philR   t   libtbx.phil.command_linet   libtbx.utilsR    R›   R¹   R   t   os.pathR   Rb   t   HandlerR   R!   R,   R/   R2   R4   R<   RB   RS   RT   R_   R`   Rm   Rn   Ru   Rz   R3   R|   R~   t   CONJUGATED_FOR_INFINITIVERƒ   R…   R‰   R‘   Rž   R¤   RŸ   R­   RÉ   RÑ   RØ   Rå   Rè   Rî   Rð   Rò   Rú   R  (    (    (    s>   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/tbx_utils.pyt   <module>   sX   
	#								
				
	
	
				(b0&12";