ó
«™xTc           @   s3  d  d l  m Z d  d l m Z d  d l m Z m Z m Z d  d l Z	 d  d l	 m
 Z
 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  d l m Z e j ƒ  Z e	 j j e j ƒ  ƒ Z d „  Z e d k r/e e j d ƒ n  d S(   iÿÿÿÿ(   t   division(   t   crystal(   t   Sorryt   date_and_timet	   multi_outN(   t   reflection_file_reader(   t   reflection_file_utils(   t   crystal_symmetry_from_any(   t   pair_analyses(   t   StringIO(   t	   pre_scalet
   make_param(   t   fa_estimationc      	   C   sŸ  t  |  ƒ d k r% t j d d ƒ nvd |  k r9 d GHnbd |  k rM d GHnNd |  k rl t j d d ƒ n/d |  k r‹ t j d d ƒ nt ƒ  } d	 |  k r¼ | j d
 d d t j ƒ n  t ƒ  } t ƒ  } | j d
 d d | ƒ t ƒ  } | d IJ| J| t ƒ  IJ| J| Jg  } t j	 d d ƒ } d  } xˆ|  D]€} d  }	 t }
 | d	 k r\t }
 n  t j j | ƒ ry t j j d | ƒ }	 Wn$ t k
 r�‚  n t k
 r­n X|	 d  k	 rÐ| j |	 ƒ t }
 n  |	 d  k r÷t j d | d t ƒ } n  | d  k	 rt| } t }
 qtn_ y8 | j d | ƒ }	 |	 d  k	 rL| j |	 ƒ t }
 n  Wn$ t k
 rc‚  n t k
 rsn X|
 s5| d IJ| d I| IJ| d IJ| Jt d | ƒ ‚ q5q5Wt j d | ƒ } | j ƒ  } d  } t j d | j j j  j! j" ƒ } | j j j  j# d  k r;| j$ ƒ  | j j j  _# | d IJn  | j j j  j% d  k rx| j% ƒ  | j j j  _% | d IJn  | j j j  j# d  k rŸt d ƒ ‚ n  | j j j  j% d  k rÆt d ƒ ‚ n  t& j' d | j j j  j% d t( | j j j  j# ƒ ƒ } } t j d | ƒ } t j) d | ƒ } | d IJ| d  IJ| j d! | d | j j j* ƒ | d" IJ| Jt+ j, d# | d$ t d% g  ƒ } d  } | j- d | j j j  j! j" d& | j j j  j! j. d' t d( d) ƒ } | j/ ƒ  } | j0 ƒ  j1 | j2 ƒ  d8 k ƒ } | j1 | j3 ƒ  d k ƒ } | j4 ƒ  r.| j5 ƒ  } n | j6 ƒ  rIt7 | ƒ } n  | j8 ƒ  sdt d* ƒ ‚ n  | j9 d+ | ƒ d  } | j- d | j j j  j: j" d& | j j j  j: j. d' t d( d, ƒ } | j/ ƒ  } | j0 ƒ  j1 | j2 ƒ  d9 k ƒ } | j1 | j3 ƒ  d k ƒ } | j4 ƒ  r| j5 ƒ  } n | j6 ƒ  r:t7 | ƒ } n  | j8 ƒ  sUt d- ƒ ‚ n  | j9 d+ | ƒ | j; ƒ  r‰| j< ƒ  j= | ƒ } n  | j; ƒ  r­| j< ƒ  j= | ƒ } n  | J| d. IJ| d/ IJ| j> d0 | ƒ | Jt? j@ | | j j jA jB | j j jC ƒ } | jD jE ƒ  } ~ | J| d1 IJ| d2 IJ| j> d0 | ƒ | Jt? j@ | | j j jA jB | j j jC ƒ } | jD jE ƒ  } ~ tF jG | | | j j jA jH ƒ } | jD jE ƒ  } | jI jE ƒ  } ~ | J| d3 IJ| d4 IJ| JtJ jK | | ƒ } | J| d5 IJ| d4 IJ| J| jL ƒ  d  k	 s!tM ‚ | jL ƒ  d  k	 s9tM ‚ | jN jL ƒ  d  k	 sTtM ‚ | jN jO d6 d7 | j j jP jQ ƒ } | jR ƒ  jS d | j j jP jT ƒ d  S(:   Ni    t   expert_levels   --helps   no help availables   --hs   --show_defaultss   --show_defaults_alli
   s   --quiett   labelt   stdoutt   file_objectt
   log_buffers   #phil __OFF__t
   home_scopet   scalingt	   file_namet   ensure_read_accesst   args2   ##----------------------------------------------##s%   ## Unknown phil-file or phil-command:s'   Unknown file format or phil command: %st   sourcess   Using symmetry of native datas   Using cell of native datas   No space group defineds   No unit cell definedt	   unit_cellt   space_group_symbolt   python_objects   Effective parameterss   #phil __ON__t   outs   #phil __END__t   crystal_symmetryt   force_symmetryt   reflection_filest   labelst   ignore_all_zerost   parameter_scopes(   scaling.input.SIR_scale.xray_data.natives'   miller_array_native is not a real arrayt   infos,   scaling.input.SIR_scale.xray_data.derivatives+   miller_array_derivative is not a real arrays   Native datas   ===========t   fs   Derivative datas   ===============s   Making delta f'ss   ----------------s   writing mtz filet   column_root_labelt   F(   i    i    i    (   i    i    i    (U   t   lent   master_paramst   showR   t   registert   sysR   R	   R   t!   command_line_argument_interpretert   Nonet   Falset   Truet   ost   patht   isfilet   iotbxt   philt   parset   KeyboardInterruptt	   Exceptiont   appendR   t   any_reflection_filet   processR   t   fetcht   extractR   t   extract_fromR   t   inputt	   xray_datat   nativeR   t   space_groupt   space_group_infoR   R   t   symmetryt   strt   formatR   R   t   reflection_file_servert   get_xray_dataR   R"   t
   map_to_asut   selectt   indicest   datat   is_xray_intensity_arrayt	   f_sq_as_ft   is_complex_arrayt   abst   is_real_arrayt   set_infot
   derivativet   anomalous_flagt   average_bijvoet_matest   set_observation_typet   show_comprehensive_summaryR
   t
   pre_scalert   scaling_strategyt   pre_scaler_protocolt   basict   x1t	   deep_copyR   t   combined_scalingt   iso_protocolt   x2R   t   delta_generatort   observation_typet   AssertionErrort   abs_delta_ft   as_mtz_datasett   outputt   outlabelt
   mtz_objectt   writet   hklout(   t   argst   logt   string_buffert   string_buffer_plotst	   log_plotst   phil_objectst   argument_interpretert   reflection_fileR   t   command_line_paramst   arg_is_processedt   effective_paramst   paramst   crystal_symmetry_natR   t
   new_paramst   xray_data_servert   miller_array_nativet   info_nativet   miller_array_derivativet   info_derivativet   native_pre_scalet   derivative_pre_scalet   scalert	   delta_gent   mtz_dataset(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/sir_scale.pyt   run   sj   				
			  		  

		


						





		

t   __main__i   (    t
   __future__R    t   cctbxR   t   libtbx.utilsR   R   R   t
   iotbx.philR2   R   R   R   t   mmtbx.scalingt   mmtbxR   t   libtbx.str_utilsR	   R
   R   R*   R/   R   t	   phil_legot   params_generatorR3   R4   t   default_sirR'   R�   t   __name__t   argv(    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/sir_scale.pyt   <module>   s"   	ø