ó
—™xTc           @   s:  d  d l  m Z d  d l m Z m 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 l Z d  d	 l m Z d  d
 l m Z d  d l m Z d  d l Z d  d l Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ d „  Z d „  Z d e f d „  ƒ  YZ d d d „ Z d „  Z d S(   iÿÿÿÿ(   t   division(   t   re_sg_uct   crystal_symmetry_from_re_match(   t   crystal(   t   uctbx(   t   sgtbx(   t   adptbx(   t   xrayN(   t   eltbx(   t   adopt_init_args(   t   easy_picklet   sdb_sitec           B   s   e  Z d  „  Z d d „ Z RS(   c
   
      C   s   t  |  t ƒ  ƒ d  S(   N(   R	   t   locals(
   t   selft   actiont   segidt   typet   xt   yt   zt   bt   qt   g(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   __init__   s    c         C   sî   t  j j d |  j d t d t ƒ } | d  k rW t  j j d |  j d t d t ƒ } n  | d  k rl d } n  |  j |  j	 |  j
 f } | d  k	 r¢ | j | ƒ } n  t j d d j |  j |  j f ƒ d | d t j |  j ƒ d |  j d	 | ƒ S(
   Nt   labelt   exactt   optionalt   unknownt   _t   sitet   ut	   occupancyt   scattering_type(   R   t   xray_scatteringt   get_standard_labelR   t   Falset   Truet   NoneR   R   R   R   t   fractionalizeR   t	   scatterert   joinR   t   b_as_uR   R   (   R   t	   unit_cellR    R   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   as_xray_scatterer   s      	 		N(   t   __name__t
   __module__R   R%   R+   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyR      s   	t   sdb_filec           B   s,   e  Z d  „  Z d „  Z d e d d „ Z RS(   c         C   s   t  |  t ƒ  ƒ d  S(   N(   R	   R   (   R   t	   file_nameR*   t   space_group_infot   sites(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyR   '   s    c         C   s   t  j d |  j d |  j ƒ S(   NR*   R0   (   R   t   symmetryR*   R0   (   R   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   crystal_symmetry*   s    		g      à?c         C   s£   |  j  ƒ  j d | d | ƒ } | j ƒ  d  k	 s6 t ‚ | j ƒ  d  k	 sN t ‚ t j t j	 d | d | ƒ ƒ } x- |  j
 D]" } | j | j | j ƒ  ƒ ƒ qy W| S(   Nt   other_symmetryt   forceR3   t   min_distance_sym_equiv(   R3   t   join_symmetryR*   R%   t   AssertionErrorR0   R   t	   structureR   t   special_position_settingsR1   t   add_scattererR+   (   R   R3   t   force_symmetryR6   R9   R   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   as_xray_structure/   s    	 N(   R,   R-   R   R3   R%   R#   R=   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyR.   %   s   		c         C   sU   |  s
 d  St  |  j d ƒ ƒ } | t | ƒ d k s; t ‚ | j |  j d ƒ ƒ d  S(   Ni   i   (   t   intt   groupt   lenR8   t   append(   t   mt   buffert   seq_no(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   generic_add_str=   s
     c         C   s[   |  s
 d  St  |  j d ƒ ƒ } | t | ƒ d k s; t ‚ | j t |  j d ƒ ƒ ƒ d  S(   Ni   i   (   R>   R?   R@   R8   RA   t   float(   RB   RC   RD   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   generic_add_floatC   s
     t   raw_parametersc           B   sk   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z RS(   c         C   sp   | |  _  d  |  _ d  |  _ g  |  _ g  |  _ g  |  _ g  |  _ g  |  _ g  |  _	 g  |  _
 g  |  _ g  |  _ d  S(   N(   R/   R%   R*   R0   R   R   R   R   R   R   R   R   R   (   R   R/   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyR   K   s    											c         C   s   t  | |  j ƒ d  S(   N(   RE   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt
   add_actionY   s    c         C   s   t  | |  j ƒ d  S(   N(   RE   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt	   add_segidZ   s    c         C   s   t  | |  j ƒ d  S(   N(   RE   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_type[   s    c         C   s   t  | |  j ƒ d  S(   N(   RG   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_x\   s    c         C   s   t  | |  j ƒ d  S(   N(   RG   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_y]   s    c         C   s   t  | |  j ƒ d  S(   N(   RG   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_z^   s    c         C   s   t  | |  j ƒ d  S(   N(   RG   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_b_   s    c         C   s   t  | |  j ƒ d  S(   N(   RG   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_q`   s    c         C   s   t  | |  j ƒ d  S(   N(   RE   R   (   R   RB   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   add_ga   s    c         C   sÌ  t  |  j ƒ t  |  j ƒ k s$ t ‚ t  |  j ƒ t  |  j ƒ k sH t ‚ t  |  j ƒ t  |  j ƒ k sl t ‚ t  |  j ƒ t  |  j ƒ k s� t ‚ t  |  j ƒ t  |  j ƒ k s´ t ‚ t  |  j ƒ t  |  j ƒ k sØ t ‚ t  |  j	 ƒ t  |  j ƒ k sü t ‚ t  |  j
 ƒ t  |  j ƒ k s t ‚ g  } x‡ t t  |  j ƒ ƒ D]p } | j t |  j | |  j | |  j | |  j | |  j | |  j | |  j | |  j	 | |  j
 | ƒ	 ƒ q<Wt |  j |  j |  j | ƒ S(   N(   R@   R   R   R8   R   R   R   R   R   R   R   t   xrangeRA   R   R.   R/   R*   R0   (   R   R1   t   i(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   as_sdb_sitesc   s"    $$$$$$$$	(   R,   R-   R   RI   RJ   RK   RL   RM   RN   RO   RP   RQ   RT   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyRH   I   s   										i@B c         C   sÜ  g  } d  } d  } d } d } x›|  D]“} | d k rZ | t | ƒ 7} | | k rZ PqZ n  t j d | ƒ }	 |	 r„ |	 j d ƒ } n  t j t | ƒ }	 |	 r® t d |	 ƒ } n  t j d | ƒ }	 |	 r•| d  k rt | ƒ d }
 | rõ |
 d 7}
 n  | d  k rd |
 } q| d |
 } n  | r;| j | j	 ƒ  ƒ n  t
 | ƒ } | d  k rhd  | _ d  | _ n$ | j ƒ  | _ | j ƒ  | _ d  } d  } n  | s¡q% n  t j d | ƒ }	 |	 r×t j |	 j d ƒ ƒ | _ n  | j t j d	 | ƒ ƒ | j t j d
 | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ | j t j d | ƒ ƒ q% W| rØ| j | j	 ƒ  ƒ n  | S(   Ni    s   \{\+\s+file:\s*(\S*)i   RB   s4   \{\-\s+begin\s+block\s+parameter\s+definition\s+\-\}s   block_%ds   _%ds   \{===>\}\s*sg=\s*"(\S+)"\s*;s"   site\.action_(\d+)\s*=\s*"([^"]*)"s!   site\.segid_(\d+)\s*=\s*"([^"]*)"s    site\.type_(\d+)\s*=\s*"([^"]*)"s   site\.x_(\d+)\s*=\s*([^\s;]*)s   site\.y_(\d+)\s*=\s*([^\s;]*)s   site\.z_(\d+)\s*=\s*([^\s;]*)s   site\.b_(\d+)\s*=\s*([^\s;]*)s   site\.q_(\d+)\s*=\s*([^\s;]*)s   site\.g_(\d+)\s*=\s*"([^"]*)"(   R%   R@   t   ret   searchR?   t   matchR   R   RA   RT   RH   R*   R0   R   RI   RJ   RK   RL   RM   RN   RO   RP   RQ   (   t   linesR/   t   max_characterst	   sdb_filest
   block_namet   current_symmetryt   n_characterst   pt   lineRB   RS   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   multi_sdb_parserv   sj    
   		  c         C   sN  d |  k } d |  k } d  } d  } x| |  D]t } | j d ƒ rh | j d d ƒ d } t j | ƒ } q+ | j d ƒ r+ | j d d ƒ d } t j | ƒ } q+ q+ Wx¤|  D]œ} | j d ƒ rÅ qª n  t | d ƒ }	 |	 j ƒ  }
 |	 j	 ƒ  t
 |
 | ƒ } xJ| D]B} | d  k	 r| | _ n  | d  k	 r6| | _ n  d	 G| j GH| j d  k	 rfd
 G| j j ƒ  GHn  | j d  k	 r„d G| j GHn  | ræx´ | j D]K } | j G| j G| j G| j GHd G| j G| j G| j G| j G| j GHq”Wn[ | j ƒ  } | j ƒ  j ƒ  | rAt j j | j ƒ d d } d G| GHt j | | ƒ n  Hq Wqª Wd  S(   Ns
   --show_raws   --pickles   --unit_cell=t   =i   s   --space_group=s   --t   rs   file:s
   unit cell:s   space group:t    s   .pickles   Writing:(   R%   t
   startswitht   splitR   R*   R   R0   t   opent	   readlinest   closeR`   R/   t
   parametersR1   R   R   R   R   R   R   R   R   R   R=   t   show_summaryt   show_scattererst   ost   pathR
   t   dump(   t   argst   show_rawt   write_pickleR*   R0   t   argt   paramst   symbolR/   t   fRX   RZ   t   sdbR   t   xray_structuret   file_name_pickle(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   run³   sN     
  /	(   t
   __future__R    t    iotbx.cns.crystal_symmetry_utilsR   R   t   cctbxR   R   R   R   R   t   cctbx.eltbx.xray_scatteringR   t   libtbxR	   R
   RU   Rl   t   objectR   R.   RE   RG   RH   R%   R`   Ry   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/cns/sdb_reader.pyt   <module>   s&   		-=