ó
ð™xTc           @   sÈ   d  d l  m Z d  d l m Z d  d l m Z d  d l m Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ	 d	 e f d
 „  ƒ  YZ
 d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d S(   iÿÿÿÿ(   t   division(   t   flex(   t   crystal(   t   adp_restraintst   adp_similarity_restraintsc           B   s&   e  Z d d d d d  d d d „ Z RS(   g{®Gáz¤?g      @c      	   C   s  | | g j  d  ƒ d k s! t ‚ | d  k	 rH t | ƒ d k rH d  } n  | d  k ra d | } n  | d  k r| t j ƒ  } n  | d  k ré | j d | ƒ } t j d | ƒ }	 | j	 ƒ  j
 ƒ  }
 |	 j |
 d t j d ƒ ƒ|	 j ƒ  } n  | j ƒ  } xt | ƒ D]\ } } | d  k	 r,| | k r,qn  xÕ | j ƒ  D]Ç \ } } | d  k	 rc| | k rcq9n  xš | D]’ } | j ƒ  rû| | j ƒ  d k } | | j ƒ  d k } | s´| rÅd | | } n d | | } | j t j d	 | | f d
 | ƒ ƒ n  PqjWq9WqW| |  _ d  S(   Ni   i    i   t   buffer_thicknesst   asu_mappingst   exclude_scattering_typest   Ht   Dt   i_seqst   weight(   R   R	   (   t   countt   Nonet   AssertionErrort   lenR   t   shared_adp_similarity_proxyR   R   t   pair_asu_tablet
   scattererst   extract_scattering_typest   add_covalent_pairsR   t
   std_stringt   extract_pair_sym_tablet   full_simple_connectivityt	   enumeratet   itemst
   is_unit_mxt   sizet   appendt   adp_similarity_proxyt   proxies(   t   selft   xray_structuret   pair_sym_tableR   R
   t   sigmat   sigma_terminalR   R   R   t   scattering_typest   connectivityt   i_seqt
   j_seq_dictt   j_seqt   sym_opst   sym_opt   i_is_terminalt   j_is_terminalR   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyt   __init__   s@    ! 	   N(   t   __name__t
   __module__R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR      s   		t   rigid_bond_restraintsc           B   s&   e  Z d d d d d  d d d „ Z RS(   g{®Gáz„?g      @c         C   sQ  | | g j  d
 ƒ d k s! t ‚ | d
 k	 rH t | ƒ d k rH d
 } n  | d
 k r] | } n  | d
 k rx t j ƒ  } n  | d
 k rå | j d | ƒ } t j d | ƒ }	 | j	 ƒ  j
 ƒ  }
 |	 j |
 d t j d ƒ ƒ|	 j ƒ  } n  | j ƒ  } t ƒ  } xGt | ƒ D]9\ } } | d
 k	 r1| | k r1qn  x| | D] } | d
 k	 r`| | k r`q<n  | | k  r}| | | } n | | | } x‚ | D]z } | j ƒ  r’| | k  r’| | f | k r’| j | | f ƒ d | | } | j t j d | | f d	 | ƒ ƒ Pq’q’W| | j ƒ  d k r<x| | D]} | d
 k	 rU| | k rUq1n  | | k r1xÑ | D]Æ } | j ƒ  rh| | k  r—| | | } n | | | } x‚ | D]z } | j ƒ  r¬| | k  r¬| | f | k r¬| j | | f ƒ d | | } | j t j d | | f d	 | ƒ ƒ Pq¬q¬WPqhqhWq1q1Wq<q<WqW| |  _ d
 S(   sv    sigma_12 and sigma_13 are the effective standard deviations used for
        1,2- and 1,3-distances respectively
    i   i    R   R   R   R   R	   R
   R   N(   R   R	   (   R   R   R   R   R   t   shared_rigid_bond_proxyR   R   R   R   R   R   R   R   R   R   t   setR   R   t   addR   t   rigid_bond_proxyR   R   (   R   R    R!   R   R
   t   sigma_12t   sigma_13R   R   R   R$   R%   t   ij_seqsR&   R'   R(   t	   j_sym_opst	   k_sym_opsR*   R   t   k_seq(    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR-   *   sn    ! 	 		   N(   R.   R/   R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR0   )   s   		t   isotropic_adp_restraintsc           B   s#   e  Z d d d d  d d d „ Z RS(   gš™™™™™¹?g      @c         C   s§  | d  k r d | } n  | d  k	 r@ t | ƒ d k r@ d  } n  | d  k r[ t j ƒ  } n  | j ƒ  j ƒ  } | j ƒ  j ƒ  }	 | d  k rÚ | j d | ƒ }
 t j	 d |
 ƒ } | j
 | d t j d ƒ ƒ| j ƒ  } n  | j ƒ  } x± t | ƒ D]£ \ } } | d  k	 r| | k rqó n& | | d k r3qó n |	 | sCqó n  | j ƒ  d k rfd | | } n d | | } | j t j d	 | f d
 | ƒ ƒ qó W| |  _ d  S(   Ni   i    R   R   R   R   R	   i   R
   R   (   R   R	   (   R   R	   (   R   R   R   t   shared_isotropic_adp_proxyR   R   t   extract_use_u_anisoR   R   R   R   R   R   R   R   R   R   R   t   isotropic_adp_proxyR   (   R   R    R!   R   R
   R"   R#   R   R$   t   use_u_anisoR   R   R%   R&   t
   neighboursR   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR-   g   s8      	  
 N(   R.   R/   R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR;   f   s   t   fixed_u_eq_adp_restraintsc           B   s   e  Z d d d  d „ Z RS(   gš™™™™™¹?c   
   	   C   s¸   | d  k r t j ƒ  } n  d | | } | d  k rr g  t | j ƒ  ƒ D]! \ } } | j d k rH | ^ qH } n  x6 | D]. }	 | j t j d |	 f d | d | ƒ ƒ qy W| |  _ d  S(   Ni   R   R	   R
   R   t
   u_eq_ideal(   R   R	   (	   R   R   t   shared_fixed_u_eq_adp_proxyR   R   t   scattering_typeR   t   fixed_u_eq_adp_proxyR   (
   R   R    RB   R   R
   R"   R   t   it   sR&   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR-   „   s    N(   R.   R/   R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyRA   ƒ   s   t   adp_u_eq_similarity_restraintsc           B   s   e  Z d d d  d „ Z RS(   gš™™™™™¹?c         C   s¶   | d  k r t j ƒ  } n  d | | } | d  k rr g  t | j ƒ  ƒ D]! \ } } | j d k rH | ^ qH } n  t | ƒ d k sŠ t ‚ | j t j	 d | d | ƒ ƒ | |  _
 d  S(   Ni   R   R	   R
   R   (   R   R	   (   R   R   t    shared_adp_u_eq_similarity_proxyR   R   RD   R   R   R   t   adp_u_eq_similarity_proxyR   (   R   R    R   R
   R"   R   RF   RG   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR-   ’   s    N(   R.   R/   R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyRH   ‘   s   t    adp_volume_similarity_restraintsc           B   s   e  Z d d d  d „ Z RS(   gš™™™™™¹?c         C   s¶   | d  k r t j ƒ  } n  d | | } | d  k rr g  t | j ƒ  ƒ D]! \ } } | j d k rH | ^ qH } n  t | ƒ d k sŠ t ‚ | j t j	 d | d | ƒ ƒ | |  _
 d  S(   Ni   R   R	   R
   R   (   R   R	   (   R   R   t"   shared_adp_volume_similarity_proxyR   R   RD   R   R   R   t   adp_volume_similarity_proxyR   (   R   R    R   R
   R"   R   RF   RG   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyR-       s    N(   R.   R/   R   R-   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyRK   Ÿ   s   N(   t
   __future__R    t   cctbx.array_familyR   t   cctbxR   R   t   objectR   R0   R;   RA   RH   RK   (    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/adp_restraints.pyt   <module>   s   #=