ó
-™xTc           @   sõ   d  d l  m Z d  d l 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 „  Z d e f d	 „  ƒ  YZ d
 e f d „  ƒ  YZ d e f d „  ƒ  YZ d „  Z d „  Z e d k rñ e e j d ƒ n  d S(   iÿÿÿÿ(   t   divisionN(   t   flex(   t   miller(   t   Sorry(   t   adopt_init_argsc      	   C   sÛ   t  |  ƒ } t | ƒ d k r3 d } t | ƒ ‚ n  t d | d d t | d ƒ d | d ƒ } | j ƒ  x+ | j D]  } | j d t | d ƒ ƒ qt Wt	 d	 | j d
 | j
 d t | d ƒ d d ƒ j d | d ƒ d  S(   Ni   sp   Bad inputs.
Usage example:
  phenix.diffuse pdb=m.pdb probabilities=0.5,0.5 sampling=1 resolution=4.0 prefix=tstt   pdb_file_namet   pdbt   samplingt   probabilitiest   d_mint
   resolutiont   modelst   crystal_symmetryt   scale_factoriè  t   prefix(   t   get_input_dictt   lenR   t   ensemblet   intt
   get_modelsR   t
   initializet   floatt   diffuset   symmetryt   write_mtz_file(   t   argt   argst   msgt   datat   model(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyt   run   s     

		R   c           B   s   e  Z d  „  Z d „  Z RS(   c         C   sx   t  |  t ƒ  ƒ t j j d | ƒ } | j ƒ  |  _ | j ƒ  |  _ g  | j	 d |  j ƒ D] } | j
 ƒ  ^ qY |  _ d  S(   Nt	   file_nameR   (   R   t   localst   iotbxR   t   inputt   construct_hierarchyt	   hierarchyt   crystal_symmetry_from_cryst1R   t   xray_structures_simplet   expand_to_p1t   xray_structures_p1(   t   selfR   R   R   t   pdb_inpt   xrs(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyt   __init__"   s    c      	   C   s.  g  |  _  |  j j  ƒ  } g  } |  j d  k	 r£ t |  j ƒ } x: t d t | ƒ ƒ D]# } t | | ƒ } | j | ƒ qR Wt | ƒ t | ƒ k r× t	 d ƒ ‚ q× n4 x1 | D]) } t d t | ƒ ƒ } | j | ƒ qª WxP t
 | ƒ D]B \ } } t d t d |  j | d | | ƒ } |  j  j | ƒ qä Wd  S(   Ni    sA   The number of models and number of given probabilities must matchi   R   t   xray_structure_p1t   probability(   R   R$   R   t   Nonet   get_probabilitiest   rangeR   R   t   appendR   t	   enumerateR   R(   (   R)   R   t   weightst	   new_probst   it   dt   model_t   m(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   *   s(    	(   t   __name__t
   __module__R,   R   (    (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR       s   	R   c           B   s   e  Z d  „  Z d „  Z RS(   c         C   s>   t  |  t ƒ  ƒ | j ƒ  j ƒ  j ƒ  j ƒ  d k s: t ‚ d  S(   Ni   (   R   R    R   t   space_groupt   typet   numbert   AssertionError(   R)   R   R-   R.   (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR,   C   s    c         C   sW   |  j  j d | ƒ j ƒ  } | |  j |  _ t | ƒ j ƒ  j ƒ  } | |  j |  _ d  S(   NR	   (	   R-   t   structure_factorst   f_calcR.   t
   f_weightedt   abst#   set_observation_type_xray_amplitudet	   f_as_f_sqt   f_squared_weighted(   R)   R	   t   ft	   f_squared(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   G   s    (   R:   R;   R,   R   (    (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   A   s   	R   c           B   s2   e  Z d  Z d „  Z d „  Z d „  Z d „  Z RS(   s7   Class for all diffuse maps produced in reciprocal spacec         C   s'   t  |  t ƒ  ƒ i  |  _ |  j ƒ  d  S(   N(   R   R    t   latticet   calculate_map(   R)   R   R   R   R   (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR,   P   s    	c         C   sµ   d  } d  } x_ |  j D]T } | j j ƒ  | j j ƒ  } } | d  k rV | } | } q | | } | | } q W|  j d j j d | t j | ƒ d ƒ |  _ |  j	 d |  j ƒ d  S(   Ni    R   i   t   miller_array(
   R/   R   RB   R   RF   t   customized_copyR   RC   t   diffuse_signalt   write_squared_amplitudes(   R)   t   sum_fct   sum_fc_squareR   t   xt   y(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyRJ   U   s    	
c         C   s.  t  |  j ƒ d } d } d d „ } x| D]ú \ } } | d | d d |  j ƒ } | d | d d |  j ƒ } | d | d d |  j ƒ }	 | | }
 | |  j k rµ i  |  j | <n  | |  j | k rÜ i  |  j | | <n  |	 |  j | | k rd |  j | | |	 <n  |  j | | |	 c |
 7<q, Wd  S(	   Ni   g•Ö&è.>c         S   s$   t  t t |  ƒ t | ƒ | ƒ ƒ S(   N(   R   t   roundR   (   RQ   t   st   eps(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyt   converth   s    RQ   i    RT   i   i   (   R   R   RI   (   R)   RK   t   correction_factorRU   RV   t   hklt	   intensityt   h_intt   k_intt   l_intt   intensity_new(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyRN   d   s    
c         C   sD  t  j ƒ  } t  j ƒ  } t  j ƒ  } |  j d k s9 t ‚ x¤ |  j D]™ } x� |  j | D]� } xx |  j | | D]e } | j | | | g ƒ t d |  j | | | ƒ |  j } | j | ƒ | j t j	 | ƒ ƒ qo WqW WqC Wt
 j d t
 j |  j | ƒ d | d | ƒ }	 |	 j ƒ  |	 j d d ƒ }
 |
 j ƒ  j | d ƒ d  S(	   Ni    s   %4dt
   miller_setR   t   sigmast   column_root_labelt   Is   .mtz(   R   t   miller_indext   doubleR   R?   RI   R2   R   t   matht   sqrtR   t   arrayt   setR   t#   set_observation_type_xray_intensityt   as_mtz_datasett
   mtz_objectt   write(   R)   R   t   indicest   i_obst   sig_it   key_ht   key_kt   key_lt   iot   mat   mtz_dataset(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   v   s     &"
(   R:   R;   t   __doc__R,   RJ   RN   R   (    (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   M   s
   			c         C   sm   t  ƒ  } xD |  D]< } | j d ƒ } t | ƒ d k r | d | | d <q q Wd | k ri d  | d <n  | S(   Nt   =i   i   i    R   (   t   dictt   splitR   R/   (   R   t   dicR   t   spl(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR   Š   s    	c         C   sc   t  j g  |  j d ƒ D] } t | ƒ ^ q ƒ } t d t  j | ƒ ƒ d k r_ t d ƒ ‚ n  | S(   Nt   ,g      ð?gü©ñÒMbP?s.   Sorry, the given probabilities must sum to one(   R   Rc   Rx   R   RC   t   sumR   (   R"   R7   t   result(    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyR0   ”   s    1t   __main__i   (   t
   __future__R    t   syst	   iotbx.pdbR!   Rd   t   cctbx.array_familyR   t   cctbxR   t   libtbx.utilsR   t   libtbxR   R   t   objectR   R   R   R   R0   R:   t   argv(    (    (    sH   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/command_line/diffuse.pyt   <module>   s   	!=	
	