ó
ï™xTc           @   sÈ   d  d l  m Z 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 j j
 j Z d  d l j j
 j j Z d e j f d „  ƒ  YZ d	 e f d
 „  ƒ  YZ d „  Z d „  Z d S(   iÿÿÿÿ(   t   division(   t   random_structure(   t   crystalt   xray(   t   flex(   t   constraintsNt   random_xray_structurec           B   s   e  Z e d  „ Z RS(   c         K   sn   t  t |  ƒ j | | � | r# d  S| d rj | d rj x0 |  j ƒ  D] } | j j t ƒ j t ƒ qD Wn  d  S(   Nt	   use_u_isot   use_u_aniso(   t   superR   t   __init__t
   scattererst   flagst   set_use_u_isot   Truet   set_use_u_aniso(   t   selft   space_group_infot   u_iso_xor_u_anisot   kwdst   sc(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyR
      s     (   t   __name__t
   __module__R   R
   (    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyR   
   s   t	   test_casec           B   s6   e  Z d  e f d „  ƒ  YZ e d „ Z e e ƒ Z RS(   t   __metaclass__c           B   s   e  Z d  „  Z RS(   c         C   sÙ   g  } x6 | D]. } y | j  | j ƒ Wq t k
 r: q Xq WxE | j ƒ  D]7 \ } } t | ƒ rL | j d ƒ rL | j | ƒ qL qL Wg  | D] } | j | f ^ qŽ }	 |	 j ƒ  g  |	 D] \ }
 } | ^ qº |  _ d  S(   Nt   exercise(	   t   extendt	   exercisest   AttributeErrort   itemst   callablet
   startswitht   appendR   t   sort(   t   clst	   classnamet   basest	   classdictR   t   baset   namet   attrt   ext   dsut   foo(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyR
      s    "
(   R   R   R
   (    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyR      s   c         O   sd   | r |  j  GHn  xL |  j D]A } | r5 d | j  Gn  |  | | Ž  } | | ƒ | r d GHq q Wd  S(   Ns   	%s ... t   OK(   R   R   (   R"   t   verboset   argsR   R   t   o(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyt   run%   s      
 (   R   R   t   typeR   t   FalseR0   t   classmethod(    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyR      s   c      
   C   s|  |  j  ƒ  } | j } | j } | j ƒ  } | j j d t d t ƒ } g  } x*t | ƒ D]\ } }	 | | }
 | | d k r„ qX n  d } g  } d } xŒ |	 j	 ƒ  D]~ \ } } |
 d k pØ | | d k pØ |
 | | k sá q£ n  | | d k r| | j
 ƒ  7} | j | ƒ q£ | | j
 ƒ  7} q£ Wt } t } d  } d } | d k rOqX n™| d k r| d k r¨| | d k rƒt j } qþt j } | | d	 k rþd
 } qþqè| d k rÖ| | d k rÖt j } t } qè| d k rè| | d k rèt j } qènç | d k r»| d k r5| | d k r5t j } qè| d k r]| | d k r]t j } qè| d k rè| | d	 k rèd
 } x6 | D]+ } | j t j d | d | d | ƒ ƒ q†Wqèn- | d k rè| d k rèt j } d
 } qèn  | d  k	 rX | d | d | d | d | ƒ } | j | ƒ | | j j ƒ  r;qX n  x6 | D]+ } | j t j d | d | d | ƒ ƒ qBWqX qX W| S(   Nt   skip_j_seq_less_than_i_seqt    all_interactions_from_inside_asut   Ht   Di    g333333ó?i   t   Ct   Og      ø?i   t   Ni   t   u_eq_scatterer_idxt   u_iso_scatterer_idxt
   multipliert   rotatingt
   stretchingt   pivott   constrained_site_indices(   R6   R7   (   R6   R7   (   R8   R:   (   R8   R:   (   R   t   conformer_indicest   sym_excl_indicest   extract_scattering_typest   pair_asu_tablet   extract_pair_sym_tableR2   R   t	   enumerateR   t   sizeR    t   Nonet   geometrical_hydrogenst   terminal_linear_ch_sitet   terminal_tetrahedral_xh_sitet   secondary_planar_xh_sitet   tertiary_xh_sitet   terminal_planar_xh2_sitest   secondary_xh2_sitest   adp_constraintst    u_iso_proportional_to_pivot_u_eqt   terminal_tetrahedral_xh3_sitesR   R   (   t	   structuret   connectivity_tableR   RB   RC   t   sc_typest   pair_sym_tablet   h_constraintst   i_seqt
   j_seq_dictt   conformer_it   h_countRA   t   pivot_neighbour_countt   j_seqt   sym_opsR>   R?   t   constraint_typet   u_eq_multipliert   idxt   current(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyt   generate_hydrogen_constraints.   s–    			
  						 	c        ;   C   sð  t  j d t j d dPd d	 ƒ d
 t j t  j d d d dQd dRƒ t  j d d d dSd dTƒ t  j d d! d dUd d% ƒ t  j d d& d dVd dWƒ t  j d d0 d dXd d4 ƒ t  j d d5 d dYd dZƒ t  j d d? d d[d dC ƒ t  j d dD d d\d d]ƒ t  j d dN d d^d dR ƒ t  j d dS d d_d d`ƒ t  j d d[ d dad dbƒ t  j d de d dcd di ƒ t  j d dj d ddd deƒ t  j d ds d dfd dw ƒ t  j d dx d dgd dhƒ t  j d d‚ d did d† ƒ t  j d d‡ d djd dkƒ t  j d d‘ d dld d• ƒ t  j d d– d dmd dnƒ t  j d d  d dod dpƒ t  j d dª d dqd d® ƒ t  j d d¯ d drd dsƒ t  j d d¹ d dtd d½ ƒ t  j d d¾ d dud dvƒ t  j d dÇ d dwd dË ƒ t  j d dÌ d dxd dyƒ t  j d dÕ d dzd d½ ƒ t  j d dÙ d d{d dÝ ƒ t  j d dÞ d d|d d}ƒ t  j d dè d d~d dì ƒ t  j d dí d dd d€ƒ t  j d dõ d d�d dù ƒ t  j d dú d d‚d dƒƒ t  j d dd d„d d…ƒ t  j d dd d†d dƒ t  j d dd d‡d dƒ t  j d dd dˆd d‰ƒ t  j d dd dŠd d"ƒ t  j d d#d d‹d dŒƒ t  j d d-d d�d d1ƒ t  j d d2d dŽd d�ƒ t  j d d9d d�d d=ƒ t  j d d>d d‘d d’ƒ t  j d dGd d“d dKƒ t  j d dLd d”d dKƒ f- ƒ ƒ S(•  Nt   crystal_symmetryt	   unit_cellgoƒÀÊ!@g~Œ¹k	y!@gé·¯çÌ%@iZ   gåÐ"Ûù¾Y@t   space_group_symbols   hall:  P 2ybR   t   labelt   O1t   siteg‘*ŠWYÛÀ¿g]©gA(ïí?gz©Ø˜×ì?t   ugb�oï:?gµRäG.?g}’;l"3'?gfLÁgÓñ¾g·_>Y1\?gTäqs*É¾t   O2g=¹¦@fgË¿gù*8é?gšÚRLñ?gÚuoEb‚J?grQ-"ŠÉ;?gpD÷¬k´,?g¼yªCn†?g™ò!¨½
?t   H2gæêÇ&ùÍ¿gÏ½‡Kì?gt}¢ñ?góèFXTÄ©?t   O3g½U×¡š’Â¿gŠSÍ¬¥à?gÂÚ;á%ë?g•ñï3.L?giUMu/?gÙ“Àæ<C?g†ÆAœ‡#¿g*T7Û3?g1]ˆÕa¿t   H3g˜Ãî;†Ç²¿g¶÷©*4Ý?gsGÿËµèê?g;¨Äu°?t   O4g»^š"ÀéÉ?gJA·—4Æâ?gK\Ç¸ââé?grQ-"ŠÉK?g¢&ú|”7?gMÛ¿²Ò¤4?gÐî�b€D3?g�íµ ÷Æ0?gˆ»z?t   H4g�ÙYôNÎ?gÅçN°ÿ:â?gÕ¯t><Ëç?g)[$íF«?t   O5g{JÎ‰=´Ï?gCâKºì?gø¬8Uç?g°Víš�Ö8?g/PR`L9?g‹à+Ù±1?g
ØFìó¾grQ-"ŠÉ?g�íµ ÷Æ°>t   H5gÕ@ó9w»Ô?gö]üo¥î?gDÃbÔµvè?g«êåwš¤?t   O6g\“nKä‚Ç¿g%ìjòÔó?gÜJ¯ÍÆÊæ?g¢'eRC+?gÒûÆ×žY?g�íµ ÷ÆÀ>g$Diâ¿t   O7g(eRC€Ý¿g||BvÞ†ñ?g£#¹ü‡tê?gH£'ÛÀ=?gpD÷¬k´<?g8„*5{ 5?g�¾IÓ hþ>gOÊ¤†6 ?gÅ­‚èÚ?t   H7gH1@¢	×¿g0�ÖmPûð?g;¨ÄuŒ+ë?go½¦¥¨?t   O8g–ëm3ââ¿giÉãiùÁó?gEcíïl�Þ?gmUÙY6?gç4´;¤8?g›©¾ó‹2?gÞ 3ßÁO?g¢&ú|”÷¾t   H8gÆûqûåã¿gá³up°7õ?g6#ƒÜE˜ß?g´Ø€q¥?t   O9g�EÓÙÉàÒ¿gæ}“¦Að?gì4ÒRy;Û?g©ÜD-Í­@?gÕýL½n1?gyxÏ�å)?g!>°ã¿@ ¿g·_>Y1\?g-Cëâ6
¿t   H9gØñ_ �Ó¿g,ü¨†ýí?gB±4-±Ý?gÔÖˆ`\¢?t   O10gŠéB¬þ¿?gæ!S>•ñ?g²¹jž#òà?g()° ¦<?g&z‹‡÷<?gúœ»]/M1?g«ZÒQf?g†ÆAœ‡#?gÕÌZ
Hû?t   H10gøŠn½¦Å?gÄxÍ«:kð?g«–t”ƒYâ?g£<órØ¥?t   O11gšÎNGÉ»¿gtÑ�ñ(•ï?g#gaO;|å?gOèõ'ñ¹3?gñhãˆµø$?g€Ÿqá@H&?g?«Ì”Ößò¾g·_>Y1\ý>gTäqs*É>t   C1gB"mãOTÊ¿gC8Ùé?gT5AÔ}€ë?gÃ L£ÉÅ8?gôPÛ†Q0?g—åë2ü§+?g{…÷¿gñhãˆµøô>g·_>Y1\Ý>t   H1g#Ù#ÔÒ¿g•k*‹Âè?gÍä›mnÌè?g9í)9'ö ?t   C2gPª}:3Ô¿g�@gÒ¦jè?g­À�Õ­žî?gŽ±^‚S??góWÈ\9?g°t><K�1?gTäqs*Ù>gÚæÆô„%?g€Ÿqá@H?t   H2Bgxã§qoÚ¿g£ZD“·ê?gLþ'÷î?g o–ê¦?t   C3g—7‡kµ‡­¿gÊÂ××:å?gô‹ôúë?gVÓõD×…??g¾†à¸Œ›*?g„¹ÝË}r¿g
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¼“O�m)?gü©ñÒMb ?gTäqs*Ù¾t   H6gqãósC£?g)ßÞ5ñ?gÈÓòWyê?g•Ô	h"l˜?t   C7gÖß—ªÀ¿g,×Ûf*Dò?g›sôøã?gro~ÃDƒ4?gd?‹¥H¾"?g{…÷(?g       €gÖÿ9Ì—?g�íµ ÷Æ°¾t   C8gr6Ü,¦?g(}!ä¼?ó?gu€Ô&Nã?g}’;l"37?g�*ß3¡1?g3ˆìø/0?gñhãˆµøô¾gTäqs*ù>t   H8Ag&o€™ïà—?gž_” ¿Ðô?g�üÁÀsïá?g[¶Ö	m¡?t   H8Bgä�È"M¼¿?g²œ„Ò‚ó?g‚ïäÓãå?t   C9g‹ú$wØDÒ¿g"ãQ*áIò?g‰±L¿D<à?gêAA)Z¹'?g?«Ì”Ößâ>g!>°ã¿@?gÉÇî%?t   H9BgO\ŽW zÑ¿g‰”M¹Âó?g8¢{Ö5ZÝ?gŒÊÂ××š?t   C10gd²¸ÿÈtÜ¿g Nyt#¬ò?g:Ë,B±â?g,amŒ�ð2?gF–Ì±¼«.?g¼yªCn†+?g?«Ì”Ößò>g?«Ì”Öß?gñhãˆµø?t   H10BghÐÐ?ÁÅÞ¿g]¿`7lñ?g_Ï×,—ã?g‚ý×¹i3ž?t   C11g¢ÑÄÎ×¿gé&1¬\ô?g’we¨å?g§@fgÑ;5?gR×ÚûT*?gXþ|[°T?t   H11g7ßˆîY×Ø¿gN} yçö?gyÌ|¿ä?g…÷ ?t   C12gÛÁˆ}Ý¿gåE&à×ô?gÁoCŒ×<é?gvk™Çó9?g—åë2ü§;?gçfh<1?g6wô¿\‹?gÕÌZ
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Hû¿(   g(�H0ÕLâ¿g¶€Ðzø²ô?g’;l"3—è?(   gW@ÜÕ«Ø¿gp{‚Äv÷ô?gñ+Öp‘{ë?(   R   RT   R   t   symmetryR   t   xray_scatterert	   scatterer(    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyt   sucrose|   s    				 	 		 		 		 		 	 		 		 		 		 	 		 		 		 			 		 		 	 			 		 		 		 		(   t
   __future__R    t   cctbx.developmentR   t   cctbxR   R   t   cctbx.array_familyR   t   smtbx.refinementR   t    smtbx.refinement.constraints.adpt
   refinementt   adpRQ   t2   smtbx.refinement.constraints.geometrical.hydrogenst   geometricalt	   hydrogensRJ   t   xray_structureR   t   objectR   Rd   R›   (    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/development.pyt   <module>   s   
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