ó
ï™xTc           @   s˜   d  d l  m Z d  d l Z d  d l Z e j j d ƒ d  d l Td  d l	 m
 Z
 d  d l m Z d  d l m Z d  d l Z d e f d	 „  ƒ  YZ d S(
   iÿÿÿÿ(   t   divisionNt   smtbx_refinement_restraints_ext(   t   *(   t   parameter_map(   t   adp_restraint_params(   t   adopt_optional_init_argst   managerc           B   s}   e  Z d Z d Z d Z d Z d Z d Z d Z	 d Z
 d Z d Z d Z d Z d  „  Z d d d d „ Z d „  Z d „  Z RS(   c         K   s   t  |  | ƒ d  S(   N(   R   (   t   selft   kwds(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyt   __init__   s    t    c         C   s-  | j  ƒ  } | j ƒ  } | j ƒ  j | ƒ } | j ƒ  j ƒ  } | j ƒ  }	 | j ƒ  j ƒ  }
 | d  k ru t j	 } n  |  j
 d  k	 rÂ |  j
 j d d d | d | d |
 d | d | d | ƒ | Jn  |  j d  k	 r|  j j d d d | d | d |
 d | d | d | ƒ | Jn  |  j d  k	 r\|  j j d d d | d |
 d | d | d | d | ƒ | Jn  |  j d  k	 r£|  j j d d d | d |
 d | d | d | ƒ | Jn  |  j d  k	 rð|  j j d d d | d | d |
 d | d | d | ƒ | Jn  |  j d  k	 r=|  j j d d d | d |
 d | d | d | d | ƒ | Jn  |  j d  k	 r�|  j j d d d |
 d	 | d
 | d |	 d | d | d | ƒ | Jn  |  j d  k	 rã|  j j d d d |
 d	 | d
 | d |	 d | d | d | ƒ | Jn  |  j d  k	 r6|  j j d d d |
 d	 | d
 | d |	 d | d | d | ƒ | Jn  |  j d  k	 rƒ|  j j d d d | d |
 d	 | d | d | d | ƒ | Jn  |  j d  k	 rÖ|  j j d d d |
 d	 | d
 | d |	 d | d | d | ƒ | Jn  |  j d  k	 r)|  j j d d d |
 d	 | d
 | d |	 d | d | d | ƒ | Jn  d  S(   Nt   by_valuet   residualt	   unit_cellt
   sites_cartt   site_labelst   ft   prefixt	   max_itemst   u_cartt   u_isot   use_u_aniso(   R   R   t
   scattererst   extract_u_cartt   extract_u_isoR   t   extract_labelst   Nonet   syst   stdoutt   bond_proxiest   show_sortedt   angle_proxiest   dihedral_proxiest   chirality_proxiest   planarity_proxiest   bond_similarity_proxiest   adp_similarity_proxiest   adp_u_eq_similarity_proxiest   adp_volume_similarity_proxiest   rigid_bond_proxiest   isotropic_adp_proxiest   fixed_u_eq_adp_proxies(   R   t   xray_structureR   R   R   R   R   R   R   R   R   (    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyR   "   s      c         C   s€   d d  l  } | j j j | | d |  j d |  j d |  j d |  j d |  j d |  j	 d |  j
 d	 |  j d
 |  j d |  j ƒ
d  S(   NiÿÿÿÿR   R   R    R#   R'   R$   R(   R%   R&   R)   (   t   iotbx.cif.restraintst   cift
   restraintst   add_to_cif_blockR   R   R    R#   R'   R$   R(   R%   R&   R)   (   R   t	   cif_blockR*   t   iotbx(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyR.   v   s    										c      	   C   sï  d } | j  } g  |  j |  j |  j f D] } | d  k	 r( | ^ q( } t g  | D] } | j ƒ  ^ qP ƒ } |  j d  k	 r´ x$ |  j D] } | | j j ƒ  7} q„ W| j	 |  j ƒ n  g  } |  j
 d  k	 ró | j	 |  j
 ƒ | d |  j
 j ƒ  7} n  |  j d  k	 r<| j	 |  j ƒ x' |  j D] }	 | t |	 j ƒ 7} qWn  |  j d  k	 r…| j	 |  j ƒ x' |  j D] }	 | t |	 j ƒ 7} qeWn  |  j d  k	 r¾| j	 |  j ƒ | d |  j j ƒ  7} n  |  j d  k	 ró| j	 |  j ƒ | |  j j ƒ  7} n  |  j d  k	 r(| j	 |  j ƒ | |  j j ƒ  7} n  t | | ƒ }
 x0 | D]( } t | j ƒ  | j ƒ  | | |
 ƒ q>W| j ƒ  j | j ƒ  ƒ } t d | j ƒ  d | d | j ƒ  j ƒ  d | j ƒ  ƒ } x* | D]" } t | j ƒ  | | | |
 ƒ qÅW|
 S(   Ni    i   R   R   R   R   (   t   n_parametersR   R   R    R   t   sumt   sizeR#   t   i_seqst   appendR$   R%   t   lenR&   R(   R)   R'   t   linearised_eqns_of_restraintt   linearise_restraintsR   R   R   R   R   R   R   (   R   R*   R   t   n_restraintst   n_paramst   proxiest   geometry_proxiest   proxyt   adp_proxiest   pt   linearised_eqnsR   t   params(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyt   build_linearised_eqns†   sb    	%N(   t   __name__t
   __module__R   R   R   R    R!   R"   R#   R$   R'   R(   R)   R%   R&   R	   R   R.   RB   (    (    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyR      s$   	Q	(   t
   __future__R    t   scitbx.sparset   scitbxt   boost.pythont   boostt   pythont
   import_extR   t
   cctbx.xrayR   t   cctbx.adp_restraintsR   t   libtbxR   R   t   objectR   (    (    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/smtbx/refinement/restraints/__init__.pyt   <module>   s   
