*ë
G5@;c       s·      d  k  Z   d k l Z  d  k Z  d k l Z  d k l Z  d  k Z  d e i f d „  ƒ  YZ	  d e  i  f d „  ƒ  YZ
  d „  Z 7 d	 „  Z M d
 „  Z d  S(   N(   s   FSSP(   s   Generic(   s   Alphabets	   FSSPAlignc      s    	 d „  Z  RS(   Nc    s'   	 
 h  | i d < h  | i d <d  S(   Ns   abs2pdbs   pdb2abs(   s
   new_records   annotations(   s   selfs
   new_record(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   _add_numbering_table	 s   (   s   _add_numbering_table(    (    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys	   FSSPAlign s   s   FSSPMultAlignc      s     d „  Z  RS(   Nc    s+     g  |  _  g  |  _  h  |  _ d  S(   N(   s   selfs   abs_ress   pdb_ress   data(   s   self(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   __init__ s   (   s   __init__(    (    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   FSSPMultAlign s   c  	  sQ     h  }  x2 | i d ƒ i i ƒ  d  r }  d | | <q- W xw t d t | ƒ d ƒ d  rW }  xK | i | ƒ i i ƒ  d  r, }  | | c | i | ƒ i | i	 7<q Wqf W | i ƒ  }  | i ƒ    t i t i t i i ƒ ƒ } " x? | d " r2 } # | i |  | i |  | i $ | | ƒ qW& | Sd S(   sC   Returns a biopython multiple alignment instance (Bio.Align.Generic)i   i    s    N(   s   mult_align_dicts
   align_dicts   abss   pos_align_dicts   keyss   js   ranges   lens   is   aas	   seq_orders   sorts   Generics	   Alignments   Alphabets   Gappeds   IUPACs   extended_proteins
   fssp_aligns   add_sequences   sum_dicts   pdb2s   chain2(   s   sum_dicts
   align_dicts   is   mult_align_dicts   js
   fssp_aligns	   seq_order(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys
   mult_align s$   	 	 	 	.! 	c    s4  7 9 : t  i ƒ  }
 ; t i | ƒ }	 ? xa |  i ƒ  d ? rN } @ t
 |  | | ƒ } A | | j o
 | | j o C |  | |
 | <n q9 WD |
 i ƒ  } E | i ƒ  F xs |	 i i ƒ  d F r] } G h  |	 i | ƒ _ H x< | d H r/ } I | i | ƒ i | |	 i | ƒ i | <qé Wq¿ WK |
 |	 f Sd S(   s   filters a passed summary section and alignment section according to a numeric
   attribute in the summary section. Returns new summary and alignment sectionsi    N(   s   FSSPs   FSSPSumDicts   new_sum_dicts   copys   deepcopys
   align_dicts   new_align_dicts   sum_dicts   keyss   prot_nums   getattrs   filter_attributes
   attr_values	   low_bounds
   high_bounds   prot_numberss   sorts   abs_res_dicts   pos_nums   abss   pos_align_dict(   s   sum_dicts
   align_dicts   filter_attributes	   low_bounds
   high_bounds   prot_numberss   pos_nums
   attr_values   prot_nums   new_align_dicts   new_sum_dict(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   filter7 s"    	 	 	1c 	   s<  M O P t  i ƒ  } Q t i | ƒ } R xi | d R r\ } S xP |  i
 ƒ  d S r= } T |  | i |  | i | j o U |  | | | <n qN Wq3 WV | i
 ƒ  } W | i ƒ  X xs | i i
 ƒ  d X r] } Y h  | i | ƒ _ Z x< | d Z r/ } [ | i | ƒ i | | i | ƒ i | <qñ WqÇ W] | | f Sd S(   s„    Accepts a list of names. Returns a new Summary block and Alignment block which
       contain the info only for those names passed.i    N(   s   FSSPs   FSSPSumDicts   new_sum_dicts   copys   deepcopys
   align_dicts   new_align_dicts	   name_lists   cur_pdb_names   sum_dicts   keyss   prot_nums   pdb2s   chain2s   prot_numberss   sorts   abs_res_dicts   pos_nums   abss   pos_align_dict(	   s   sum_dicts
   align_dicts	   name_lists   pos_nums   prot_numberss   prot_nums   new_align_dicts   cur_pdb_names   new_sum_dict(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   name_filterM s$    	 	" 	 	1(   s   UserDicts   Bios   FSSPs   copys	   Bio.Aligns   Generics   Alphabets   times	   Alignments	   FSSPAligns   FSSPMultAligns
   mult_aligns   filters   name_filter(   s   copys   UserDicts   times
   mult_aligns   filters   Generics   name_filters   FSSPMultAligns	   FSSPAligns   FSSPs   Alphabet(    (    s+   /mit/seven/lib/python/Bio/FSSP/FSSPTools.pys   ? s   $