ó
‚™xTc           @   s±   d  d l  m Z d  d l Z d  d l Z d  d l m Z d  d l m Z d  d l m	 Z	 d  d l
 m Z d  d l m Z d d	 „ Z d
 „  Z e d k r­ e e j d ƒ n  d S(   iÿÿÿÿ(   t   divisionN(   t   miller(   t   iotbx_option_parser(   t   crystal_symmetry_from_pdb(   t   Sorry(   t   flexs   mmtbx.csv_to_mtzc         C   sÄ  t  |  ƒ d k r d g }  n  y{ t d d | d d | ƒ j ƒ  j d  d d d	 d
 t d d d d ƒj d  d d d	 d
 t d d d d ƒj d |  ƒ } Wn@ t k
 rÛ } t | ƒ d k rË t | ƒ GHn  t	 j
 d ƒ n X| j } | j j ƒ  d  k s| j j ƒ  d  k r9| j j r9t j d | j j ƒ } q9n  | j ƒ  d  k s]| j ƒ  d  k rpt d | ƒ ‚ n  t  | j ƒ d k r­d t  | j ƒ G| j GHt d ƒ ‚ n  | j d } t j j | ƒ sßt d | ƒ ‚ n  t j ƒ  } t j ƒ  } t j ƒ  } t d | ƒ \ }	 }
 |	 d } t j | t j |
 d ƒ ƒ } x% |
 d D] } | j t | ƒ ƒ qLWx% |
 d D] } | j t | ƒ ƒ qtWx% |
 d D] } | j t | ƒ ƒ qœWt  | ƒ t  | ƒ k s×t  ‚ t  | ƒ t  | ƒ k sõt  ‚ t j! | | | ƒ } | j" d ƒ r&| j# ƒ  n& | j" d ƒ rB| j$ ƒ  n
 | j# ƒ  t j d | d | j% ƒ  ƒ j! d | ƒ } | j& d  | ƒ } | j' d! | d  d" ƒ | j( ƒ  } | j) d | j j* ƒ d  S(#   Ni    s   --helpt   usages"   %s [reflection_csv_file] [options]t   descriptions,   Example: %s 1m5u-sf.csv --use_model=1m5u.pdbs   --output_filet   actiont   storet   defaultt   typet   stringt   helps   Output mtz file name.s   --use_models>   Use PDB model to make better guess about reflection data type.t   argst   0t	   file_namesq   Crystal symmetry is not defined. Please use the --symmetry option.
Type %s without arguments to see more options.i   s-   %d arguments are given from the command line:s'   Please specify one reflection csv file.s   File is not found: %si   i   t   Ft   It   crystal_symmetryt   indicest   datat   column_root_labelt   miller_arrays   R-free-flags(+   t   lenR   t   enable_symmetry_comprehensivet   optiont   Nonet   Falset   processt	   Exceptiont   strt   syst   exitt   symmetryt	   unit_cellt   space_group_infot   optionst	   use_modelR   t   extract_fromR   R   t   ost   patht   isfileR   t   doublet   intt   parse_csv_fileR   t   sett   miller_indext   appendt   floatt   AssertionErrort   arrayt
   startswitht#   set_observation_type_xray_amplitudet#   set_observation_type_xray_intensityR   t   as_mtz_datasett   add_miller_arrayt
   mtz_objectt   writet   output_file(   R   t   command_namet   command_linet   eR   R   R   t   sigmast   flagst
   column_idst   columnst   data_label_roott   mst   dt   sigt   flagt   mat   flags_mat   mtz_datasetR9   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/csv_as_mtz.pyt   run   sŠ     
			 		

				c         C   sH  t  |  ƒ } | j ƒ  j ƒ  j d ƒ } g  } x | D] } | j g  ƒ q4 Wxð | j ƒ  D]â } | j ƒ  j d ƒ } xÄ t | ƒ D]¶ \ } } | d k r§ t | ƒ }	 q€ | d k rÂ t | ƒ }
 q€ | d k rÝ t | ƒ } q€ | d k r!|	 |
 | f } | d j | ƒ | | d j | ƒ q€ | | d j | ƒ q€ WqX W| | f S(   Nt   ,i    i   i   i   (   t   opent   readlinet   stript   splitR0   t	   readlinest	   enumerateR,   (   R   t   fRA   R   t   idt   linet   tempt   it   valuet   ht   kt   lt   hkl(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/csv_as_mtz.pyR-   R   s(    t   __main__i   (   t
   __future__R    R    R(   t   cctbxR   t   iotbx.option_parserR   t	   iotbx.pdbR   t   libtbx.utilsR   t   cctbx.array_familyR   RK   R-   t   __name__t   argv(    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/csv_as_mtz.pyt   <module>   s   G	