ó
¶™xTc           @   sš   d  d l  m Z d  d l m 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	 „  Z e d
 „ Z d S(   iÿÿÿÿ(   t   division(   t   approx_equalN(   t   flex(   t   matrix(   t   adptbx(   t   rotatable_bondsc      
   C   s¼  t  j j } g  } x£|  j ƒ  D]•} xŒ| j ƒ  D]~} xu| j ƒ  D]g} x^| j ƒ  D]P} xG| j ƒ  D]9} | | j ƒ d k rk t	 j
 d | d | ƒ }	 |	 d  k	 r¤xô |	 D]é }
 g  } t j ƒ  } t j ƒ  } |
 d } |
 d } x^ t | j ƒ  ƒ D]J \ } } | | k r'| j | j ƒ qü | | k rü | j | j ƒ qü qü Wt | ƒ d k sbt ‚ t | ƒ d k szt ‚ | j | | g ƒ | j | ƒ q± Wq¤qk qk WqX WqE Wq2 Wq W| S(   Nt   common_amino_acidt   residuet   mon_lib_srvi    i   i   (   t   iotbxt   pdbt   common_residue_names_get_classt   modelst   chainst   residue_groupst
   conformerst   residuest   resnameR   t   axes_and_atoms_aa_specifict   NoneR   t   size_tt	   enumeratet   atomst   appendt   i_seqt   lent   AssertionError(   t   pdb_hierarchyR   t	   get_classt   axes_and_atoms_i_seqst   modelt   chaint   residue_groupt	   conformerR   t   aaat   aaa_t   tmp_t   axist   movingt   axis_t   atoms_R   t   atom(    (    s<   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/tls/ladp.pyt   get_axes_and_atoms_i_seqs
   s6    	

  +c         C   s  t  j | ƒ } | d d k s% t ‚ t | d d d g ƒ sD t ‚ t  j | ƒ } | j d ƒ | j d ƒ | j d ƒ f } t j |  d | d d |  d | d d |  d | d d | d d d | d d d | d d d ƒ d t j } t j |  d | d d |  d | d d |  d | d d | d d d | d d d | d d d ƒ d t j } t j |  d | d d |  d | d d |  d | d d | d d d | d d d | d d d ƒ d t j } t | d ƒ st ‚ d  S(   Ni    i   i   i´   g     €V@(	   R   t   eigenvaluesR   R   t   eigensystemt   vectorst   matht   acost   pi(   R%   t   u_cartt   evt   est   evst   a1t   a2t   a3(    (    s<   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/tls/ladp.pyt   check_u_cart%   s    *‚‚‚c         C   sò  t  j d } |  j ƒ  } |  j ƒ  } t j ƒ  } t j | j ƒ  d d d d d d g ƒ }	 xY t | ƒ D]K \ }
 } | r‰ |
 | k } n |
 | k } | rh | j	 | d d ƒ qh qh Wxt | ƒ D]\ }
 } | rå |
 | k } n |
 | k } | rÄ xÚ| D]Ï} t j
 | | d d ƒ } t j
 | | d d ƒ } | | } t  j | d d | d d | d d ƒ } | | \ } } } | | | g } t j | d | | | | | | | d | | | | | | | d f	 ƒ } xç | d D]Û } | | } t j
 | ƒ | } t j d | d | d | d d | d | d | d d f	 ƒ } | | | | j ƒ  | j ƒ  } t d | d | ƒ | | j j t ƒ t t j
 |	 | ƒ t j
 | ƒ ƒ |	 | <qîWqþ WqÄ qÄ W|  j d |	 d | ƒ |  S(   Ni´   i    i   i   R%   R1   t	   selection(   R.   R0   t
   sites_cartt
   scatterersR   R   t   sym_mat3_doublet   sizeR   t   extendt   doublet   sqrtR   t   sqrt	   transposet   as_sym_mat3R8   t   flagst   set_use_u_anisot   Truet   listt
   set_u_cart(   t   xray_structureR   t   valuet   deptht   enable_recursiont   scR:   R;   t   all_selectionst   u_cartsR   R#   t   queryt   rt   aaait   G1t   G2t   gt   dgt   lxt   lyt   lzt   lt   Lt   i_seq_movingt	   site_cartt   deltat   AR1   (    (    s<   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/tls/ladp.pyt   set_ladp3   sH    *   
/N
?"&(   t
   __future__R    t   libtbx.test_utilsR   R.   t	   iotbx.pdbR	   t   scitbx.array_familyR   t   scitbxR   t   cctbxR   t   mmtbx.utilsR   R*   R8   RF   R`   (    (    (    s<   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/tls/ladp.pyt   <module>   s   		