ó
Âšó>c           @   s   d  d l  m Z d  d l Z d  d l m Z d  d l  m Z d  d l Z d e j f d     YZ d e	 f d     YZ
 d	   Z d
   Z d   Z d S(   i˙˙˙˙(   t   FSSPN(   t   Generic(   t   Alphabett	   FSSPAlignc           B   s   e  Z d    Z RS(   c         C   s   i  | j  d <i  | j  d <d  S(   Nt   abs2pdbt   pdb2abs(   t   annotations(   t   selft
   new_record(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt   _add_numbering_table   s    (   t   __name__t
   __module__R	   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyR      s   t   FSSPMultAlignc           B   s   e  Z d    Z RS(   c         C   s   g  |  _  g  |  _ i  |  _ d  S(   N(   t   abs_rest   pdb_rest   data(   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt   __init__   s    		(   R
   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyR      s   c         C   s  i  } x* | j  d  j j   D] } d | | <q Wxg t d t |  d  D]L } xC | j  |  j j   D]) } | | c | j  |  j | j 7<ql WqM W| j   } | j   t j t	 j
 t	 j j   } x4 | D], } | j |  | j |  | j | |  qŘ W| S(   sC   Returns a biopython multiple alignment instance (Bio.Align.Generic)i   t    (   t   abst   pos_align_dictt   keyst   ranget   lent   aat   sortR   t	   AlignmentR   t   Gappedt   IUPACt   extended_proteint   add_sequencet   pdb2t   chain2(   t   sum_dictt
   align_dictt   mult_align_dictt   jt   it	   seq_ordert
   fssp_align(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt
   mult_align   s     +
c         C   sń   t  j   } t j |  } xP |  j   D]B } t |  | |  } | | k r( | | k r( |  | | | <q( q( W| j   }	 |	 j   x` | j j   D]O }
 i  | j |
  _	 x4 |	 D], } | j |
  j	 | | j |
  j	 | <qł Wq W| | f S(   s   filters a passed summary section and alignment section according to a numeric
   attribute in the summary section. Returns new summary and alignment sections(
   R    t   FSSPSumDictt   copyt   deepcopyR   t   getattrR   t   abs_res_dictR   R   (   R    R!   t   filter_attributet	   low_boundt
   high_boundt   new_sum_dictt   new_align_dictt   prot_numt
   attr_valuet   prot_numberst   pos_num(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt   filter6   s    
.c   	      C   ső   t  j   } t j |  } xT | D]L } xC |  j   D]5 } |  | j |  | j | k r5 |  | | | <q5 q5 Wq" W| j   } | j   x` | j j   D]O } i  | j	 |  _
 x4 | D], } | j	 |  j
 | | j	 |  j
 | <qˇ Wq W| | f S(   s    Accepts a list of names. Returns a new Summary block and Alignment block which
       contain the info only for those names passed.(   R    R(   R)   R*   R   R   R   R   R,   R   R   (	   R    R!   t	   name_listR0   R1   t   cur_pdb_nameR2   R4   R5   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt   name_filterL   s    
.(   t   BioR    R)   t	   Bio.AlignR   R   t   timeR   R   t   dictR   R'   R6   R9   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/FSSP/FSSPTools.pyt   <module>   s   	$	