ó
Ç™xTc           @   s)  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	 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 e j j d	 ƒ Z d
 „  Z d „  Z d „  Z d „  Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d „  Z d S(   iÿÿÿÿ(   t   divisionN(   t   flex(   t   wk1995(   t   bessel_i1_over_i0(   t   max_lik(   t   miller(   t   adopt_init_argssò    free_reflections_per_bin = 140
    .type = int
  number_of_macromolecule_atoms_absent = 225
    .type = int
  n_atoms_included = 0
    .type = int
  bf_atoms_absent = 15.0
    .type = float
  final_error = 0.0
    .type = float
  absent_atom_type = "O"
    .type = str
  method = *est calc
    .type = choice
  estimation_algorithm = *analytical iterative
    .type = choice
  verbose = -1
    .type = int
  interpolation = True
    .type = bool
  number_of_waters_absent = 613
    .type = float
c         C   s[   t  j d |  j ƒ  d t j | j ƒ  ƒ d | j ƒ  d | j ƒ  d |  j ƒ  d |  j ƒ  ƒ S(   Nt   f_obst   f_modelt   alphat   betat   space_groupt   miller_indices(   R   t   fo_fc_alpha_over_eps_betat   dataR   t   absR   t   indices(   R   R   R	   R
   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR   &   s    	c         C   sL   t  j d |  j ƒ  d | j ƒ  d | d | d |  j ƒ  d |  j ƒ  ƒ j ƒ  S(   NR   R   R	   R
   R   R   (   R   t   fom_and_phase_errorR   R   R   t   fom(   R   t   f_calcR	   R
   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt   figures_of_merit_1   s    c         C   sL   t  j d |  j ƒ  d | j ƒ  d | d | d |  j ƒ  d |  j ƒ  ƒ j ƒ  S(   NR   R   R	   R
   R   R   (   R   R   R   R   R   t   phase_error(   R   R   R	   R
   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR   <   s    	c         C   s2   | d k r t  d |  ƒ } n t j |  ƒ } | S(   Ni    g       @(   R   t   matht   tanh(   t   tt   lcentt   result(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR   H   s    t   alpha_beta_calcc           B   s#   e  Z d  „  Z d „  Z d „  Z RS(   c         C   s%  | |  _  | d k s t ‚ | d k s- t ‚ | j ƒ  d k sE t ‚ d t j | j ƒ  j ƒ  ƒ |  _ |  j j ƒ  | j ƒ  j ƒ  k sŽ t ‚ | j ƒ  j	 ƒ  |  _
 |  j
 d k s¸ t ‚ | |  _ | |  _ | |  _ | d  k rè d } n  | |  _ | d k st ‚ | d  k rd } n  | |  _ d  S(   Ni    g      ð?i   g        t   C(   t   ft   AssertionErrort   sizeR   t   pow2t
   d_spacingsR   t   ssR   t   order_zt   nsymt   n_atoms_absentt   n_atoms_includedt   bf_atoms_absentt   Nonet   final_errort   absent_atom_type(   t   selfR   R%   R&   R'   R)   R*   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt   __init__V   s$    	"'			 		 	c   
      C   s!  g  } g  } |  j  |  j } |  j  |  j } x” |  j D]‰ } t j d | |  j d t j d ƒ } | j | ƒ |  j	 | ƒ t j |  j
 d | ƒ } | j d | d | | | d ƒ q6 Wt j | ƒ } t j | ƒ }	 t j d |  j d | ƒ } t j d |  j d |	 ƒ } | | f S(   Ng      Ð¿i   i   g      @g      ð?t
   miller_setR   (   R$   R&   R%   R"   R   t   expR)   t   pit   appendt   form_factorR'   R   t   doubleR   t   arrayR   (
   R+   R	   R
   t   n_partt   n_lostt   ssit   akt   factt
   alpha_datat	   beta_data(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt
   alpha_beta{   s     )()c         C   s‚   t  |  j ƒ j ƒ  } | j ƒ  } | j ƒ  } | j ƒ  } | } x< t d ƒ D]. } | | | t j | | | d ƒ 7} qL W| S(   Ni   g      @(	   R   R*   t   fetcht
   array_of_at
   array_of_bt   ct   xrangeR   R.   (   R+   R"   t   tablet   a_wkt   b_wkt   c_wkt	   result_wkt   i(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR1   ‘   s    ,(   t   __name__t
   __module__R,   R;   R1   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR   T   s   	%	t   alpha_beta_est_managerc           B   s/   e  Z d  „  Z d „  Z d „  Z d d „ Z RS(   c      	   C   s1  t  |  t ƒ  ƒ t |  j ƒ |  j j ƒ  j ƒ  k s: t ‚ |  j j ƒ  j ƒ  |  j j ƒ  j ƒ  k sj t ‚ |  j j	 ƒ  j
 |  j j	 ƒ  ƒ d k s— t ‚ t |  j ƒ |  _ |  j j t ƒ d k r| | j t ƒ k rë | j t ƒ |  _ n  |  j j |  j ƒ |  _ |  j j |  j ƒ |  _ n  |  j j t ƒ d k rk|  j j |  j ƒ |  _ |  j j |  j ƒ |  _ n  |  j j d |  j ƒ g  |  _ g  |  _ g  |  _ x³ |  j j ƒ  j ƒ  D]œ } |  j j ƒ  j | ƒ } |  j j | ƒ } |  j j | ƒ }	 | j t ƒ d k r²|  j j | j ƒ  ƒ |  j j |	 j ƒ  ƒ |  j j | j	 ƒ  ƒ q²q²Wxk t |  j |  j |  j ƒ D]N \ }
 } } |
 j ƒ  | j ƒ  k o±| j ƒ  k o±d k n snt ‚ qnWt j d |  j d |  j d |  j d |  j j ƒ  ƒ } | j ƒ  | j ƒ  |  _  |  _! |  j" ƒ  \ |  _ |  _ d  S(   Ni   i    t   reflections_per_bint   fo_testt   fm_testR   R   (#   R   t   localst   lent   flagsR   R   R   R   R   R   t   all_eqR   t   countt   Truet   free_reflections_per_bint   selectt
   f_obs_testt   f_calc_testt   setup_binner_counting_sortedt   fo_test_setst   fm_test_setst   indices_setst   binnert
   range_usedt	   selectionR0   t   zipR   t   alpha_beta_estR   R	   R
   t   alpha_in_zonest   beta_in_zonest   alpha_beta_for_each_reflection(   R+   R   R   RS   RO   t   interpolationt   i_bint   selt   sel_f_obs_testt   sel_f_calc_testt   at   bR?   t   obj(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR,   ¡   sD    *0-
			+C		c         C   s   |  j  |  j f S(   N(   R	   R
   (   R+   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR;   Ù   s    c         C   sü   t  | ƒ d k rø | d } | d } xZ t d t  | ƒ d d ƒ D]< } | | d } | | | d } | | | <| } | } qC Wxr t d t  | ƒ d ƒ D]U } | | d k  rœ y | | d | | <Wqñ t k
 rí | | d | | <qñ Xqœ qœ Wn  | S(   Ni   i    g      @g{®Gáz„?(   RN   t   ranget	   Exception(   R+   t   xt   x1t   x2RF   t   x3t   tmp(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt   smoothÜ   s     

#

   c   	      C   s€  | d  k r |  j } n  t j | j ƒ  ƒ } t j | j ƒ  ƒ } | j d t |  j ƒ ƒ | j ƒ  } |  j	 t
 k rÓ t j |  j |  j ƒ ƒ } t j |  j |  j ƒ ƒ } | j | d ƒ } | j | d ƒ } ns |  j	 t k rFxa t | j ƒ  |  j |  j ƒ D]> \ } } } | j | ƒ } | j | | ƒ | j | | ƒ qWn  t j d | d | ƒ } t j d | d | ƒ } | | f S(   Nt   n_binsi    R-   R   (   R(   R   R   R2   R   t   setup_binnerRN   R`   R[   Rc   RR   Rr   Ra   t   interpolatet   FalseR^   R\   R]   t   set_selectedR   R3   (	   R+   R   R	   R
   R[   t   azt   bzRd   Re   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyRb   í   s(     N(   RG   RH   R,   R;   Rr   R(   Rb   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyRI   Ÿ   s   	8		R;   c           B   s>   e  Z d d d d d d d d d d d d d  „ Z d „  Z RS(   c   3      C   s£	  t  |  t ƒ  ƒ |  j d k sC |  j d k sC |  j d k sC t ‚ |  j d  k	 sX t ‚ |  j d k rT|  j d  k	 s| t ‚ |  j j ƒ  j	 ƒ  |  j
 j ƒ  j	 ƒ  k s¬ t ‚ |  j j	 ƒ  |  j j ƒ  j	 ƒ  k sÖ t ‚ |  j
 j ƒ  j |  j j ƒ  ƒ d k st ‚ t d |  j d t |  j
 ƒ d |  j d |  j d	 |  j ƒ j ƒ  \ |  _ |  _ n  |  j d k rP|  j d  k	 s‡|  j
 d  k	 s‡t ‚ |  j d  k	 r¢|  j } n	 |  j
 } |  j d  k	 sÀt ‚ |  j d  k	 sÕt ‚ |  j d  k	 sêt ‚ |  j d  k	 sÿt ‚ t d
 | d |  j d |  j d |  j d |  j d |  j ƒ j ƒ  \ |  _ |  _ n  |  j d k rŸ	|  j d  k	 stt ‚ |  j d  k	 s‰t ‚ |  j
 d  k	 sžt ‚ |  j d  k	 s³t ‚ |  j d  k	 sÈt ‚ |  j d  k	 sÝt ‚ |  j d  k	 sòt ‚ |  j d  k	 st ‚ |  j d  k	 st ‚ |  j d  k	 s1t ‚ |  j j ƒ  j	 ƒ  |  j
 j ƒ  j	 ƒ  k oo|  j j	 ƒ  k n szt ‚ |  j
 j ƒ  j |  j j ƒ  ƒ d k s§t ‚ t d
 |  j d |  j d |  j d |  j d |  j d |  j ƒ j ƒ  \ |  _ |  _ t d |  j d t |  j
 ƒ d |  j d |  j d	 |  j ƒ j ƒ  \ |  _ |  _ t j  d |  j d |  j ƒ } t j  d |  j d |  j ƒ } t j  d |  j d |  j ƒ } t j  d |  j d |  j ƒ } d t! j" | j# ƒ  j ƒ  ƒ } g  } g  } xØ t$ |  j |  j | ƒ D]¾ \ } } } | d k r&d } n  | d k r;d } n  | d k rPd } n  | d k red } n  d t% j& d | } | j' t% j( t% j) | ƒ | ƒ ƒ | j' t% j( t% j) | ƒ | ƒ ƒ qWt j  d |  j d t! j* | ƒ ƒ } t j  d |  j d t! j* | ƒ ƒ } |  j j+ t, ƒ d k r“| j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ }  n  |  j j+ t, ƒ d k r | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ } | j- |  j ƒ }  n  | j. d |  j ƒ | j/ | ƒ | j/ | ƒ |  j/ | ƒ | j/ | ƒ | j/ | ƒ d GHd GHx| j0 ƒ  j1 ƒ  D]}! | j0 ƒ  j2 |! ƒ }" | j- |" ƒ }# | j- |" ƒ }$ | j- |" ƒ }% |  j- |" ƒ }& | j- |" ƒ }' | j- |" ƒ }( |# j ƒ  j	 ƒ  }) |  j t3 k r²d }* x¾ |* |) k  r®|% j ƒ  |* }+ |% j ƒ  j+ |+ ƒ |) d k r¡|& j ƒ  |* }, |& j ƒ  j+ |, ƒ |) d k r¡Pq¡n  |* d 7}* q0Wn< |  j t, k rît! j4 |% j ƒ  ƒ }+ t! j4 |& j ƒ  ƒ }, n  t! j4 |# j ƒ  ƒ }- t! j4 |$ j ƒ  ƒ }. t! j4 |' j ƒ  ƒ }/ t! j4 |( j ƒ  ƒ }0 | j0 ƒ  j5 |! ƒ d }1 | j0 ƒ  j5 |! ƒ d }2 d |1 |2 |) |+ |, |0 |- |. |/ f	 GHq‘Wn  d  S(   Nt   calct   estt   calc_and_esti   R   R   RS   RO   Rc   R   R%   R&   R'   R)   R*   R-   R   g      ð?g        g�íµ ÷Æ°>g      Ài   i    RJ   sM       Resolution           Estimated and calculated alpha, beta and model errorsM      d1        d2    nref alpha_e    beta_e    err_e alpha_c   beta_c     err_ci   s5   %8.4f %8.4f %5d %6.5f %12.3f %5.3f %6.5f %12.3f %5.3f(6   R   RM   t   methodR   t   verboseR(   Rc   R   R   R   R   RO   R   RP   RI   R   RS   R;   R	   R
   R%   R&   R'   R*   R   R)   t
   alpha_calct	   beta_calcR_   t	   alpha_estt   beta_estR   R3   R   R    R!   R^   R   R/   R0   t   sqrtt   logR2   RQ   RR   RT   Rt   t   use_binning_ofR[   R\   R]   Rv   t   meant   bin_d_range(3   R+   R   R   RS   RO   R~   R%   R&   R'   R)   R*   R}   Rc   R   t   alpha_calc_mat   beta_calc_mat   alpha_est_mat   beta_est_maR"   t
   omega_calct	   omega_estt   act   aeR6   t   coefft   omega_calc_mat   omega_est_mat   omega_calc_ma_testt   omega_est_ma_testt   alpha_calc_ma_testt   beta_calc_ma_testt   alpha_est_ma_testt   beta_est_ma_testRd   Re   t   sel_alpha_calc_ma_testt   sel_beta_calc_ma_testt   sel_alpha_est_ma_testt   sel_beta_est_ma_testt   sel_omega_calc_ma_testt   sel_omega_est_ma_testR   RF   t   v_alpha_estt
   v_beta_estR   R€   t   omega_ct   omega_et   d1t   d2(    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR,     s   0*-			!$ 					!,-								( 	 	 	 	#'$$	
 c         C   s   |  j  |  j f S(   N(   R	   R
   (   R+   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR;   “  s    N(   RG   RH   R(   R,   R;   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR;     s   „c   
      C   s½   t  j ƒ  } | d k r4 t  j |  j ƒ  j ƒ  d ƒ Sd „  } d t  j |  j ƒ  j ƒ  ƒ } |  j ƒ  j ƒ  } xH | D]@ } | | | ƒ t	 j
 | d | ƒ }	 | j |	 | | ƒ qu W| S(   Ni    c         S   s   t  | ƒ j ƒ  } | j ƒ  } | j ƒ  } | j ƒ  } | } x< t d ƒ D]. } | | | t j | | |  d ƒ 7} qI W| S(   Ni   g      @(   R   R<   R=   R>   R?   R@   R   R.   (   R6   R*   RA   RB   RC   RD   RE   RF   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyR1   ™  s    ,g      ð?g      @(   R   R2   R   R   R    R!   R   R   R#   R   R.   R0   (
   t   miller_arrayR%   R'   R*   R   R1   R"   R$   R6   R8   (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt
   sigma_miss–  s     		%(   t
   __future__R    R   t   cctbx.array_familyR   t   cctbx.eltbx.xray_scatteringR   t   scitbx.mathR   t   mmtbxR   t   cctbxR   t   libtbxR   t
   iotbx.philt   iotbxt   philt   parset   alpha_beta_paramsR   R   R   R   t   objectR   RI   R;   R¦   (    (    (    sB   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/maxlik.pyt   <module>   s(   						Kd“