ó
ï™xTc           @   sb   d  d l  m Z d  d l m Z d  d l m Z m Z m Z d  d l Z	 d e
 f d „  ƒ  YZ d S(   iÿÿÿÿ(   t   division(   t   xray(   t   constraintst   least_squarest
   restraintsNt   modelc           B   sM   e  Z d  „  Z e e ƒ Z d „  Z e e ƒ Z d „  Z d „  Z d „  Z RS(   c         O   s    d d l  m } | |  | | Ž S(   Niÿÿÿÿ(   t   smtbx_refinement_model_from(   t   iotbx.shelxR   (   t   clst   argst   kwdst   _(    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyt
   from_shelx   s    c   	      C   só   d d l  m } t j j d | ƒ } t | ƒ d k sC t d ƒ ‚ | j ƒ  d } | | ƒ j d | ƒ } d } x< | D]4 } | j
 ƒ  rx | j ƒ  d k	 rx | j ƒ  } Pqx qx W| d k	 sÂ t ‚ |  d | d	 | d
 g  d t j ƒ  d t j ƒ  ƒ S(   s‹   
    We could try to read in the weighting scheme.
    As for constraints and restraints, the CIF format does not support them
    yet
    iÿÿÿÿ(   t   any_reflection_filet	   file_pathi   s*   CIF should contain only one xray structurei    t   crystal_symmetryt   fo_sqt   xray_structureR   t   restraints_managert   weighting_schemeN(   t   iotbx.reflection_file_readerR   R   t	   structuret   from_cift   lent   AssertionErrort   valuest   as_miller_arrayst   Nonet   is_xray_intensity_arrayt   sigmast   as_xray_observationsR   t   managerR   t   sigma_weighting(	   R   R   t   reflectionsR   t   xs_dictt   xst   masR   t   ma(    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyR      s    c         C   sI   | |  _  | |  _ | |  _ | |  _ | |  _ t j j |  j ƒ |  _ d  S(   N(   R   R   R   R   R   t   smtbxt   utilst   connectivity_table(   t   selfR   R   R   R   R   (    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyt   __init__$   s    						c         C   sK   |  j  j ƒ  x7 |  j  j ƒ  D]& } | j j t ƒ | j j t ƒ q Wd  S(   N(   R   t   convert_to_anisotropict
   scattererst   flagst   set_grad_u_anisot   Truet   set_grad_u_isot   False(   R)   t   sc(    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyt   make_anisotropic.   s    c         C   sC   t  j |  j |  j  |  j ƒ } t j |  j | d |  j d |  j ƒS(   NR   R   (	   R   t   reparametrisationR   R(   R   t   crystallographic_lsR   R   R   (   R)   R4   (    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyR   4   s    	(   t   __name__t
   __module__R   t   classmethodR   R*   R3   R   (    (    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyR      s   			
	(   t
   __future__R    t   cctbxR   t   smtbx.refinementR   R   R   t   smtbx.utilsR&   t   objectR   (    (    (    sG   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/__init__.pyt   <module>   s   