ó
šxTc        +   @   sS  d  d l  Z d  d l Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ e d e ƒ Z e d e ƒ Z	 d „  Z
 d „  Z d	 e f d
 „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ e d e d d d d d  e
 ƒ e d d! d d" d  e
 ƒ e d d# d d$ d  e
 ƒ e d d% d d& d  e
 ƒ e d d' d d( d  e
 ƒ e d d) d d* d  e
 ƒ e d d+ d d, d  e ƒ e d e d e d d- d d. d  e
 ƒ e d d/ d d0 d  e	 ƒ e d d1 d d2 d  e	 ƒ e d d3 d d4 d  e	 ƒ e d d5 d d6 d  e
 ƒ g d7 e d d8 ƒ ƒ g d7 e d d9 d d: ƒ ƒ e d e d d; d d< d  e ƒ e d d' d d= d  e
 d> d? ƒ e d d) d d@ d  e
 d> d? ƒ e d d+ d dA d  e d> dB ƒ e d e d d; d dC d  e ƒ e d dD d dE d  e
 ƒ e d dF d dG d  e
 ƒ e d dH d dI d  e
 ƒ e d dJ d dK d  e ƒ e d e d d; d dL d  e ƒ e d dM d dN d  e	 ƒ e d dO d dP d  e	 ƒ e d dQ d dR d  e	 ƒ e d e d dS d dT d  e ƒ e d dU d dV d  e ƒ e d dW d dX d  e d> dB ƒ e d dY d dZ d  e
 ƒ g d7 e d d[ ƒ ƒ e d e d dS d d\ d  e ƒ e d dU d d] d  e ƒ e d dW d d^ d  e d> dB ƒ e d dY d d_ d  e
 ƒ g d7 e d d` ƒ ƒ e d da d db d  e ƒ e d dc d dd d  e ƒ e d de d df d  e d> dB ƒ e d dJ d dg d  e ƒ e d dh d di d  e
 ƒ g d7 e d dj d dk ƒ ƒ g d7 e d dl d dm ƒ ƒ e d e d e d dn d do d  e ƒ e d dp d dq d  e ƒ e d dr d ds d  e ƒ e d dt d du d  e	 ƒ e d dv d dw d  e	 ƒ e d dx d dy d  e	 ƒ e d dz d d{ d  e	 ƒ g d7 e d d| ƒ ƒ g d7 e d d} d d~ ƒ ƒ g d7 e d d d d€ ƒ ƒ g	 d7 e ƒ Z d� e f d‚ „  ƒ  YZ dƒ „  Z e d e d e d e d d„ d… d„ d  e
 ƒ e d d! d… d! d  e
 ƒ e d d† d… d† d  e
 d> d? ƒ g d7 e d e d ƒ d d ƒ ƒ e d e d d‡ d… d‡ d  e
 ƒ g d7 e d e dˆ ƒ ƒ ƒ e d e d e d d‰ d… d‰ d  e ƒ e d d„ d… d„ d  e
 ƒ e d d d… d d  e
 ƒ e d dJ d… dJ d  e ƒ g d7 e d e dŠ ƒ d dŠ ƒ ƒ e d e d d‰ d… d‰ d  e ƒ e d d„ d… d„ d  e
 ƒ e d d d… d d  e
 ƒ e d d‹ d… d‹ d  e
 d> d? ƒ g d7 e d e dŒ ƒ d dŒ ƒ ƒ e d d� d e d� ƒ d  e	 d> dŽ ƒ e d d� d e d� ƒ d  e d> dB ƒ e d d- d e d- ƒ d  e
 d> d? ƒ e d d� d e d‘ ƒ d  e	 d> dŽ ƒ e d d} d e d} ƒ d  e
 d> d? ƒ e d d5 d e d5 ƒ d  e
 d> d? ƒ g d7 e d e d9 ƒ d d9 ƒ ƒ e d e d dS d… dS d  e
 ƒ e d dU d… dU d  e
 ƒ e d d’ d… d’ d  e
 ƒ g d7 e d e d“ ƒ d d” ƒ ƒ g d7 e d e d• ƒ ƒ ƒ e d e d e d d‰ d… d‰ d  e ƒ e d d– d… d– d  e
 ƒ e d dD d… d— d  e
 ƒ e d dJ d… dJ d  e ƒ e d d˜ d… d˜ d  e
 ƒ e d e d d‰ d… d‰ d  e ƒ e d dO d e dO ƒ d  e	 ƒ e d d™ d e d™ ƒ d  e	 ƒ e d dš d e dš ƒ d  e	 ƒ e d d› d e d› ƒ d  e	 d> dŽ ƒ e d da d e da ƒ d  e	 ƒ e d dœ d e dœ ƒ d  e	 ƒ e d e d dS d… dS d  e ƒ e d dU d… dU d  e ƒ e d dY d  e
 ƒ g d7 e d e d� ƒ d d[ ƒ ƒ e d e d dS d… dS d  e ƒ e d dU d… dU d  e ƒ e d dY d  e
 ƒ g d7 e d e dž ƒ d dŸ ƒ ƒ e d d  d e d  ƒ d  e
 ƒ g
 d7 e d e d� ƒ d d� ƒ ƒ g d7 e d e dl ƒ d dl ƒ ƒ g d7 e d e d¡ ƒ ƒ ƒ g d7 e ƒ Z d¢ e f d£ „  ƒ  YZ d¤ „  Z d¥ „  Z d¦ „  Z d§ „  Z e d e d e d d¨ d… d¨ d  e
 ƒ e d d© d… d© d  e
 ƒ e d dª d… dª d  e
 ƒ e d d« d… d¬ d  e ƒ e d e d d­ d… d­ d  e
 ƒ e d d® d… d® d  e
 ƒ e d d© d… d© d  e
 ƒ e d dª d… dª d  e
 ƒ e d d¯ d… d¯ d  e ƒ e d d° d… d° d  e
 ƒ e d d± d… d± d  e
 ƒ e d e d d² d… d² d  e
 ƒ e d d³ d… d³ d  e
 ƒ e d d´ d… d´ d  e
 ƒ e d dµ d… dµ d  e
 ƒ e d d¶ d… d¶ d  e
 ƒ e d d· d… d· d  e
 ƒ e d d¸ d… d¸ d  e
 ƒ e d d¹ d… d¹ d  e
 ƒ e d dº d… dº d  e
 ƒ e d d» d  e
 ƒ g
 d7 e d d¼ d d¼ ƒ ƒ e d e d d½ d… d½ d  e ƒ e d d¾ d… d¾ d  e
 ƒ e d d¿ d… d¿ d  e
 ƒ e d dÀ d… dÀ d  e ƒ e d dÁ d… dÁ d  e
 ƒ g d7 e d dÂ d dÂ ƒ ƒ g	 d7 e d dÃ d dÄ ƒ ƒ g d7 e d dÅ d d[ ƒ ƒ g d7 e ƒ Z dÆ e f dÇ „  ƒ  YZ dÈ „  Z  dÉ „  Z! d S(Ê   iÿÿÿÿNt   DataNodec           B   s   e  Z d  Z RS(   sB   
    A storage class that allows setting arbitrary attributes
    (   t   __name__t
   __module__t   __doc__(    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR       s   t   Convertc           B   s    e  Z d  Z d „  Z d „  Z RS(   s&   
    Conversion to a certain type
    c         C   s   | |  _  d  S(   N(   t   type(   t   selfR   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   __init__   s    c         C   sF   y |  j  | ƒ } Wn, t k
 rA } t d | |  j  | f ‚ n X| S(   Ns    %s cannot be converted to %s: %s(   R   t
   ValueErrort   RuntimeError(   R   t   datat   valuet   e(    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   __call__   s    (   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR      s   	R   c         C   s   |  S(   N(    (   R
   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   <lambda>#   s    c         C   s   |  j  d | d | ƒ d S(   s#   
    Direct attachment to node
    t   elemt   nodeN(   t   populate(   t
   processingR   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   Direct&   s    t   Childc           B   s    e  Z d  Z d „  Z d „  Z RS(   s   
    Attach a child node
    c         C   s   | |  _  | |  _ d  S(   N(   t   tagt	   attribute(   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   3   s    	c         C   sg   | j  |  j ƒ } | d  k r1 t d |  j ‚ n  t ƒ  } t | |  j | ƒ | j d | d | ƒ d  S(   Ns   Missing %s tagR   R   (   t   findR   t   NoneR	   R    t   setattrR   R   (   R   R   R   R   t
   elem_childt
   node_child(    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   9   s    	(   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   .   s   	t	   Submergedc           B   s    e  Z d  Z d „  Z d „  Z RS(   s/   
    Climb the tree, but keep current node
    c         C   s   | |  _  d  S(   N(   R   (   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   J   s    c         C   sK   | j  |  j ƒ } | d  k r1 t d |  j ‚ n  | j d | d | ƒ d  S(   Ns   Missing %s tagR   R   (   R   R   R   R	   R   (   R   R   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   O   s    (   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   E   s   	t   Raisedc           B   s    e  Z d  Z d „  Z d „  Z RS(   s8   
    Climb node hierarchy, but keep current element
    c         C   s   | |  _  d  S(   N(   R   (   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   ^   s    c         C   s6   t  ƒ  } t | |  j | ƒ | j d | d | ƒ d  S(   NR   R   (   R    R   R   R   (   R   R   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   c   s    	(   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   Y   s   	t   Multiplec           B   s    e  Z d  Z d „  Z d „  Z RS(   s%   
    Attach an array of children
    c         C   s   | |  _  | |  _ d  S(   N(   R   R   (   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   o   s    	c         C   s‹   | j  |  j ƒ } | d  k r1 t d |  j ‚ n  g  } t | |  j | ƒ x: | D]2 } t ƒ  } | j d | d | ƒ | j | ƒ qQ Wd  S(   Ns   Missing %s tagR   R   (	   R   R   R   R	   R   R   R    R   t   append(   R   R   R   R   R   t   arrayt   elem_grandchildR   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   u   s    	(   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   j   s   	t   MultipleEntryc           B   s    e  Z d  Z d „  Z d „  Z RS(   s"   
    Attach nodes as an array
    c         C   s   | |  _  | |  _ d  S(   N(   R   R   (   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   Š   s    	c         C   sf   g  } t  | |  j | ƒ xF | j |  j ƒ D]2 } t ƒ  } | j d | d | ƒ | j | ƒ q, Wd  S(   NR   R   (   R   R   t   findallR   R    R   R   (   R   R   R   R   R    R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   �   s    	(   R   R   R   R   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR"   …   s   	t   NodeProcessingc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   s"   
    Processing data XML node
    c         C   s   | |  _  | |  _ d  S(   N(   t   instructionst
   attachment(   R   R%   R&   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR       s    	c         C   s    |  j  d |  d | d | ƒ d  S(   NR   R   R   (   R&   (   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   process¦   s    c         C   s.   x' |  j  D] } | j d | d | ƒ q
 Wd  S(   NR   R   (   R%   R'   (   R   R   R   t   instruction(    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   «   s    (   R   R   R   R   R'   R   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR$   ›   s   		t   TextProcessingc           B   s#   e  Z d  Z d d „ Z d „  Z RS(   s$   
    Converts text to some type
    c         C   s(   | |  _  | |  _ | |  _ | |  _ d  S(   N(   R   R   t
   conversiont   default(   R   R   R   R*   R+   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   ¶   s    			c         C   su   | j  |  j ƒ } | d  k rL |  j d  k r@ t d |  j ‚ qU |  j } n	 | j } t | |  j |  j | ƒ ƒ d  S(   Ns   Missing %s tag(	   R   R   R   R+   R	   t   textR   R   R*   (   R   R   R   t   childR   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR'   ¾   s    	N(   R   R   R   R   R   R'   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR)   ±   s   t   AttributeProcessingc           B   s#   e  Z d  Z d d „ Z d „  Z RS(   s,   
    Converts an attribute to some type
    c         C   s(   | |  _  | |  _ | |  _ | |  _ d  S(   N(   R   t   keywordR*   R+   (   R   R   R/   R*   R+   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   Ô   s    			c         C   sp   |  j  | j k r@ |  j d  k r4 t d |  j  ‚ qP |  j } n | j |  j  } t | |  j |  j | ƒ ƒ d  S(   Ns   Missing %s attribute(   R/   t   attribR+   R   R	   R   R   R*   (   R   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR'   Ü   s    N(   R   R   R   R   R   R'   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR.   Ï   s   t   DataProcessingc           B   s    e  Z d  Z d „  Z d „  Z RS(   s2   
    Converts the text attribute to some type
    c         C   s   | |  _  | |  _ d  S(   N(   R   R*   (   R   R   R*   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   ð   s    	c         C   s#   t  | |  j |  j | j ƒ ƒ d  S(   N(   R   R   R*   R,   (   R   R   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR'   ö   s    (   R   R   R   R   R'   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR1   ë   s   	R%   R   t   programR   t   BlastOutput_programR*   t   versiont   BlastOutput_versiont	   referencet   BlastOutput_referencet   dbt   BlastOutput_dbt   query_ids   BlastOutput_query-IDt	   query_defs   BlastOutput_query-deft	   query_lens   BlastOutput_query-lent   matrixt   Parameters_matrixt   expectt   Parameters_expectt   gap_opens   Parameters_gap-opent
   gap_extends   Parameters_gap-extendt   filtert   Parameters_filterR&   t
   Parameterst
   parameterst   BlastOutput_paramt   nums   Iteration_iter-nums   Iteration_query-IDR+   t    s   Iteration_query-defs   Iteration_query-leni    t   Hit_numt
   identifiert   Hit_idt
   annotationt   Hit_deft	   accessiont   Hit_accessiont   lengtht   Hit_lent   Hsp_numt	   bit_scores   Hsp_bit-scoret   scoret	   Hsp_scoret   evaluet
   Hsp_evaluet   starts   Hsp_query-fromt   ends   Hsp_query-tot   frames   Hsp_query-framet   seqt   Hsp_qseqt   querys   Hsp_hit-froms
   Hsp_hit-tos   Hsp_hit-framet   Hsp_hseqt   hitt   identityt   Hsp_identityt   positivet   Hsp_positivet   gapst   Hsp_gapss   Hsp_align-lent   midlinet   Hsp_midlinet   hspst   Hit_hspst   hitst   Iteration_hitst   db_nums   Statistics_db-numt   db_lens   Statistics_db-lent   hsp_lens   Statistics_hsp-lent	   eff_spaces   Statistics_eff-spacet   kappat   Statistics_kappat   lambdavt   Statistics_lambdat   entropyt   Statistics_entropyt
   Statisticst
   statisticst   Iteration_statt
   iterationst   BlastOutput_iterationst   Blastc           B   s8   e  Z d  Z e j d ƒ Z d „  Z d „  Z d „  Z RS(   s.   
    Homology search by BLAST, XML output
    s$   ([A-Za-z0-9]{4})[_\-]([A-Za-z0-9]?)$c         C   s   | |  _  d  S(   N(   t   root(   R   R}   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   c  s    c         C   s7   |  j  j r3 |  j  j d j |  |  j  j d _ n  d  S(   Niÿÿÿÿ(   R}   Rz   Rk   (   R   t	   max_count(    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   restricth  s    c      
   c   s÷   |  j  j s t ‚ n  d d l m } xË |  j  j d j D]¶ } |  j j | j ƒ } | ro | j	 ƒ  \ } } 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q9 Wd  S(   Niÿÿÿÿ(   t   bioinformaticsRI   t   namest   targets   %s_%st
   alignmentsi    R2   s
   NCBI-BLASTRK   t   chainRM   t	   alignment(   RI   RI   (   R}   Rz   t   StopIterationt   iotbxR€   Rk   t   REGEXt   searchRO   t   groupst   clustal_alignmentRi   R^   R\   R`   t   homology_search_hitRM   (   R   R€   t   ht   matcht   pdbR„   R…   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyRk   n  s"    		&			(	   R   R   R   t   ret   compileRˆ   R   R   Rk   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR|   \  s
   		c         C   s   t  j j j d |  ƒ j S(   Ns   http://www.ebi.ac.uk/schema(   t   xmlt   etreet   ElementTreet   QNameR,   (   t   s(    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   ‹  s    t   nameR/   t   citationt   commandt   commandLinet   numbert	   sequencest   createdt	   databasest   scoresg        Rƒ   t   expectation_uppert   expectationUpperR‰   t   timeInfot   timet   Headert   databaset   idt   descriptiont   bitst   expectationt   probabilityt	   positivest   querySeqt   matchSeqRŽ   t   patternt   SequenceSimilaritySearchResultt
   EBIWUBlastc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   s,   
    Homology search by WU-BLAST at EBI
    c         C   s   | |  _  d  S(   N(   R}   (   R   R}   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   ý  s    c         C   s   |  j  j |  |  j  _ d  S(   N(   R}   Rk   (   R   R~   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR     s    c      
   c   s¹   d d l  m } x¢ |  j j D]” } | j d  } | j 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(   R€   i   i   R�   R‚   s   %s_%sRƒ   i    R2   s   WU-BLASTRK   R„   RM   R…   (   R‡   R€   R}   Rk   RK   R‹   Rƒ   R^   R\   RŽ   RŒ   R§   (   R   R€   R�   R�   R„   R…   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyRk     s    	&			(   R   R   R   R   R   Rk   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR°   ø  s   		c         C   s,   t  ƒ  } | j d |  d | ƒ | d | ƒ S(   NR   R   R}   (   R    R'   (   t   treet   buildert	   data_typeR}   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt
   parse_tree  s    	c         C   s.   t  j j j |  ƒ } t d | d | d | ƒ S(   NR±   R²   R³   (   R’   R“   R”   t
   fromstringR´   (   R
   R²   R³   R±   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   parse"  s    c          C   s%   d d  l  }  |  j t d t d t ƒS(   NiÿÿÿÿR²   R³   (   t	   functoolst   partialR¶   t   BLAST_BUILDERR|   (   R·   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   get_ncbi_blast_parser)  s    c          C   s%   d d  l  }  |  j t d t d t ƒS(   NiÿÿÿÿR²   R³   (   R·   R¸   R¶   t   EBI_WU_BLAST_BUILDERR°   (   R·   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   get_ebi_blast_parser/  s    t   pdb_codet
   chain_codet   domain_codet   domain_countt   cath_domain_countt	   domain_idt   pdb_idt
   dom_lengtht   dom_atom_sequencet   dom_combs_sequencet
   class_codet	   arch_codet   top_codet
   homol_codet   s35_codet   s60_codet   s95_codet	   s100_codet
   s100_countt   uni_codet	   cath_codet   seg_numt	   pdb_startt   pdb_stopt   slengtht   sseqst   segmentst   cath_domaint   domainst   cath_pdb_queryt   CathAnnotationc           B   s    e  Z d  Z d „  Z d „  Z RS(   s   
    Cath query results
    c         C   s   | |  _  d  S(   N(   R}   (   R   R}   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyR   p  s    c         C   s   |  j  j j d k S(   Ni    (   R}   R^   RÀ   (   R   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   emptyu  s    (   R   R   R   R   RÜ   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyRÛ   k  s   	c         C   sG   t  j j j |  ƒ } | j d ƒ d  k	 r. d  St d | d t d t ƒ S(   Nt   errorR±   R²   R³   (	   R’   R“   R”   Rµ   R   R   R´   t   CATH_ANNOTATION_BUILDERRÛ   (   R
   R±   (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   parse_cath_xmlz  s    c           C   s   t  S(   N(   Rß   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   get_cath_parserˆ  s    ("   t   xml.etree.ElementTreeR’   R�   t   objectR    R   t   intt   to_intt   floatt   to_floatt   noconversionR   R   R   R   R   R"   R$   R)   R.   R1   R¹   R|   t   ebi_nsR»   R°   R´   R¶   Rº   R¼   RÞ   RÛ   Rß   Rà   (    (    (    sF   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/homology.pyt   <module>   s‚  			/	$$$$$$$*!$$!!	#						