ó
{™xTc        "   @   sQ  d  d l  m Z d  d l m Z m Z m Z d  d l m Z m Z m Z m	 Z	 m
 Z
 d  d l m Z d e f d „  ƒ  YZ d  d l m Z d „  Z e d	 i d
 e d	 i d e d e d d d d ƒ e d d d d ƒ e	 d d d d d d ƒ g ƒ f e d d ƒ 6d e d d ƒ f e d d ƒ 6d e d e d d d e d ƒ d e d d ƒ e d d d e d ƒ d e d d ƒ e d d d e d ƒ d d ƒ e d d d e d ƒ d e d d ƒ e d d d e d ƒ d d ƒ e d d  d e d  ƒ d d ƒ g d	 i d! e d e d d" ƒ d# e d e d d$ d d$ d e ƒ e d d d d ƒ e d d% d d% ƒ e d d& d d& d e ƒ g ƒ ƒ f e d d! ƒ 6d' e d e d d( ƒ d# e d e d d$ d d$ d e ƒ e d d d d ƒ e d d% d d% ƒ e	 d d) d d) d d ƒ g ƒ ƒ f e d d' ƒ 6ƒ f e d d ƒ 6d* e d e d d+ d d+ ƒ e d d, d d, ƒ e d d- d d- ƒ g ƒ f e d d. ƒ 6ƒ f e d d/ ƒ 6d0 e d e d d1 ƒ d# e d e d d$ d d$ d e ƒ e d d( d d( ƒ e d d2 d d3 ƒ e d d& d d& d e ƒ e d d4 d d4 ƒ g d	 i d e d e d d5 ƒ d# e d e d d$ d d$ d e ƒ e d d6 d e d d6 ƒ d e ƒ e d d7 d e d d7 ƒ d e ƒ e d d8 d e d d8 ƒ d e ƒ e d d9 d e d d9 ƒ d e d d ƒ e d d: d e d d: ƒ d e ƒ e d d; d e d d; ƒ d e ƒ e d d< d e d d< ƒ ƒ g d	 i d= e d e d d+ d d+ d e ƒ e d d, d d, d e ƒ e
 d d> ƒ g ƒ f e d d? ƒ 6d@ e d e d d+ d d+ d e ƒ e d d, d d, d e ƒ e
 d d> ƒ g ƒ f e d dA ƒ 6ƒ ƒ f e d d ƒ 6ƒ ƒ f e d0 ƒ 6ƒ Z e d e d dB ƒ dC e dD e dE e ƒ Z dF S(G   iÿÿÿÿ(   t   division(   t   Singlet   Multiplet   DataAttribute(   t   Textt   TextWithDefaultt	   Attributet   AttributeWithDefaultt   Value(   t   Parsert   Resultc           B   s2   e  Z d  Z d „  Z d „  Z d „  Z d „  Z RS(   s(   
  Homology search by WU-BLAST at EBI
  c         C   s   | |  _  d  S(   N(   t   root(   t   selfR   (    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyt   __init__   s    c         C   s   |  j  j | 3d  S(   N(   R   t   hits(   R   t	   max_count(    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyt   restrict   s    c      
   c   sþ   d d l  m } xç |  j j D]Ù } | j j d ƒ } d t | ƒ k  sM t ‚ t | ƒ d k rr | d } d } n | d  \ } } | j d d	 d
 | | f g d | j	 d j
 j | j	 d j j g d d ƒ } | j d | d | d | j d | ƒ Vq Wd  S(   Niÿÿÿÿ(   t   bioinformaticst   _i    i   t    i   t   namest   targets   %s_%st
   alignmentst   programs   WU-BLASTt
   identifiert   chaint
   annotationt	   alignment(   t   iotbxR   R   R   R   t   splitt   lent   AssertionErrort   clustal_alignmentR   t   queryt   seqt   matcht   homology_search_hitt   description(   R   R   t   ht   piecest   pdbR   R   (    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyR      s"    
		&			c         C   s   t  |  j j ƒ S(   N(   R   R   R   (   R   (    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyt   __len__1   s    (   t   __name__t
   __module__t   __doc__R   R   R   R)   (    (    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyR
      s
   			(   t   QNamec         C   s   t  d |  ƒ j S(   Ns   http://www.ebi.ac.uk/schema(   R-   t   text(   t   tag(    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyt   ebi_qualified8   s    t   child_data_taggedt   headerR   t   extractionst	   attributet   namet   versiont   citationt   defaultR   R/   t   commandt   commandLinet
   parameterst   scorest
   conversiong        R   i    t   matrixt   expectation_uppert   expectationUppert
   statisticst   filtert	   sequencest   sequencet	   processort   numbert   typet   lengtht	   databasest   databaset   createdt   timet   startt   endt   searcht   timeInfot   HeaderR   t   hitR   t   idR%   R   t   scoret   bitst   expectationt   probabilityt   identityt	   positivest   patternR!   R"   t   querySeqR#   t   matchSeqt   EBIApplicationResultt   buildert   restypet   cElementTreeN(   t
   __future__R    t   iotbx.bioinformatics.xmlbuildR   R   R   R   R   R   R   R   R	   t   objectR
   t   xml.etree.cElementTreeR-   R0   t   floatt   intt   BUILDERt   Truet   parse(    (    (    sS   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ebi_wu_blast_xml.pyt   <module>   s   (/	1D	;!"Q