ó
šxTc           @   sŒ  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	 d e e f d „  ƒ  YZ
 d e e f d „  ƒ  YZ d e e f d „  ƒ  YZ d e e f d „  ƒ  YZ d e e e f d „  ƒ  YZ d e e e f d „  ƒ  YZ d e f d „  ƒ  YZ d  e f d! „  ƒ  YZ d" e e e f d# „  ƒ  YZ d$ e e e f d% „  ƒ  YZ d& e e e f d' „  ƒ  YZ d( e f d) „  ƒ  YZ d* e f d+ „  ƒ  YZ d, e e e f d- „  ƒ  YZ d. e f d/ „  ƒ  YZ d0 e f d1 „  ƒ  YZ d2 e e e	 f d3 „  ƒ  YZ d4 e  f d5 „  ƒ  YZ d6 S(7   t   Stagec           B   s    e  Z d  Z d „  Z d „  Z RS(   s)   
    An object with tracking ability
    c         C   s   t  ƒ  |  _ d  S(   N(   t   sett   processed_by(   t   self(    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   __init__   s    c         C   s
   |  j  ƒ  S(   N(   t   long(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   __str__   s    (   t   __name__t
   __module__t   __doc__R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR       s   	t   Childc           B   s    e  Z d  Z d „  Z d „  Z RS(   s   
    Delegating to parent
    c         C   s   |  j  ƒ  j ƒ  S(   N(   t   parentt   initial(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR      s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   t   partial(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR      s    (   R   R   R	   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR
      s   	t   Depth0c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni    (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   depth"   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR       s   t   Depth1c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   (   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   &   s   t   Depth2c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   /   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   -   s   t   Depth3c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   6   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   4   s   t   Depth4c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   =   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ;   s   t   Depth5c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   D   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   B   s   t   Depth6c           B   s   e  Z d  „  Z RS(   c         C   s   d S(   Ni   (    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   K   s    (   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   I   s   t   Initialc           B   sV   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 RS(	   s5   
    A potential partial structure for extension
    c         C   s;   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ | |  _ d  S(   N(   t   superR   R   t   caset   _partialt   missingt   index(   R   R   R   R   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   V   s
    			c         C   s   d  S(   N(   t   None(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   _   s    c         C   s   |  S(   N(    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   d   s    c         C   s   |  j  S(   N(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   i   s    c         C   s   |  j  j |  j ƒ  S(   N(   R   t	   score_forR   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   scoren   s    c         C   s   d |  j  S(   Ns   Partial structure #%d(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   shorts   s    c         C   s   d |  j  ƒ  |  j ƒ  f S(   Ns   %s, LLG = %.2f(   R   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   x   s    c         C   s   d |  j  |  S(   Ns   #%d(   R   (   R   t   width(    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   entry}   s    (   R   R   R	   R   R   R   R   R   R   R   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Q   s   								t   TemplateHitc           B   s;   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   s?   
    A homology search hit applicable for a model template
    c         C   s2   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ d  S(   N(   R   R"   R   t   _initialt   hssR   (   R   R   t   intypeR   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ‡   s    		c         C   s   |  j  S(   N(   R#   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   �   s    c         C   s&   |  j  ƒ  j ƒ  |  j j ƒ  |  j f S(   N(   R   R   R$   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ”   s    c         C   s   d |  j  ƒ  |  j |  j f S(   Ns   %s
Possible template #%d: %s(   R   R   R$   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ™   s    	c         C   s
   |  j  ƒ  S(   N(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¢   s    (   R   R   R	   R   R   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR"   ‚   s   					t   ModelTemplatec           B   s;   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   s*   
    Applicable template for ensemble
    c         C   s2   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ d  S(   N(   R   R&   R   R#   t   templateR   (   R   R   R%   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¬   s    		c         C   s   |  j  S(   N(   R#   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ´   s    c         C   s&   |  j  ƒ  j ƒ  |  j j ƒ  |  j f S(   N(   R   R   R'   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¹   s    c         C   s   d |  j  ƒ  |  j |  j f S(   Ns   %s
Model template #%d: %s(   R   R   R'   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¾   s    	c         C   s!   d |  j  ƒ  |  j j ƒ  d f S(   Ns   %s, identity = %.0f%%id   (   R   R'   t   identity(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ç   s    (   R   R   R	   R   R   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR&   §   s   					t   ModelCollectionc           B   s;   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   s/   
    Applicable models to make an ensemble
    c         C   s2   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ d  S(   N(   R   R)   R   R#   t
   collectionR   (   R   R   R%   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ñ   s    		c         C   s   |  j  S(   N(   R#   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ù   s    c         C   s&   |  j  ƒ  j ƒ  |  j j ƒ  |  j f S(   N(   R   R   R*   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Þ   s    c         C   s   d |  j  ƒ  |  j |  j f S(   Ns   %s
Model collection #%d: %s(   R   R   R*   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ã   s    	c         C   s   d |  j  ƒ  |  j j ƒ  f S(   Ns   %s, rmsd = %.2fA(   R   R*   t   rms(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ì   s    (   R   R   R	   R   R   R   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR)   Ì   s   					t   Ensemblec           B   sD   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   s   
    Applicable ensemble
    c         C   s2   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ d  S(   N(   R   R,   R   R#   t   ensembleR   (   R   R   R%   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ö   s    		c         C   s   |  j  S(   N(   R#   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   þ   s    c         C   s&   |  j  ƒ  j ƒ  |  j j ƒ  |  j f S(   N(   R   R   R-   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s   d |  j  ƒ  |  j |  j f S(   Ns   %s
Ensemble #%d: %s(   R   R   R-   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    	c         C   s   d |  j  ƒ  |  j j ƒ  f S(   Ns   %s, rmsd = %.2fA(   R   R-   R+   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s?   t  |  j ƒ } t | ƒ | k r% | Sd | t | d d ƒ S(   Ns   ...i   iÿÿÿÿ(   t   strR-   t   lent   min(   R   R    t   name(    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!     s    (	   R   R   R	   R   R   R   R   R   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR,   ñ   s   						t   Rotationc           B   sV   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 RS(	   s   
    Rotation peak
    c         C   s;   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ t |  _ d  S(   N(   R   R2   R   R-   t   peakR   t   Falset   translation_done(   R   R-   R3   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   %  s
    			c         C   s   |  j  S(   N(   R-   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   .  s    c         C   s   |  j  j ƒ  S(   N(   R3   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   3  s    c         C   s
   |  j  j S(   N(   R3   t   rfz(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   8  s    c         C   s   d |  j  S(   Ns   Rotation peak #%d(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   peakname=  s    c         C   s   d |  j  |  j ƒ  f S(   Ns   %s
%s(   R-   R7   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   B  s    c         C   s#   d |  j  ƒ  |  j j |  j j f S(   Ns   %s, RF = %.2f, RFZ = %.2f(   R   R3   t   rfR6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   G  s    c         C   s   d |  j  j |  S(   Ns   %.1f(   R3   R8   (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   L  s    (   R   R   R	   R   R   R   R6   R7   R   R   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR2      s   								t   NormalRotationc           B   s   e  Z d  Z RS(   s5   
    Rotation peak located via rotation function
    (   R   R   R	   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR9   Q  s   t   PreviouslyEstablishedRotationc           B   s    e  Z d  Z d „  Z d „  Z RS(   s@   
    A special rotation peak, for tracking and presentation
    c         C   s   d |  j  S(   Ns   Previous rotation peak #%d(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR7   \  s    c         C   s   d |  j  j |  S(   Ns   %.1fLPR(   R3   R8   (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   a  s    (   R   R   R	   R7   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR:   W  s   	t   Translationc           B   sh   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z RS(   s   
    Translation peak
    c         C   s;   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ t |  _ d  S(   N(   R   R;   R   t   rotationR3   R   R4   t   packing_done(   R   R<   R3   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   k  s
    			c         C   s   |  j  S(   N(   R<   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   t  s    c         C   s   |  j  j ƒ  S(   N(   R3   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   y  s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   R6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   ~  s    c         C   s   d |  j  S(   Ns   Translation peak #%d(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR7   ƒ  s    c         C   s   d |  j  j ƒ  |  j ƒ  f S(   Ns   %s
%s(   R<   R7   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   historyˆ  s    c         C   s   d |  j  |  j ƒ  f S(   Ns   %s
%s(   R<   R7   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   �  s    c         C   s#   d |  j  ƒ  |  j j |  j j f S(   Ns   %s, TF = %.2f, TFZ = %.2f(   R   R3   t   tft   tfz(   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ’  s    c         C   s   |  j  ƒ  |  S(   N(   t   evaluation_entry(   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   —  s    c         C   s   d |  j  j S(   Ns   %.1f(   R3   R@   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRA   œ  s    (   R   R   R	   R   R   R   R6   R7   R>   R   R   R!   RA   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR;   f  s   										t   Clashc           B   s2   e  Z d  Z d „  Z d „  Z d „  Z d „  Z RS(   s&   
    Structure failing clash test
    c         C   s    t  t |  ƒ j ƒ  | |  _ d  S(   N(   R   RB   R   t   translation(   R   RC   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¦  s    c         C   s   |  j  S(   N(   RC   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ¬  s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   R6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   ±  s    c         C   s   d |  S(   Nt   No(    (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   ¶  s    (   R   R   R	   R   R   R6   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRB   ¡  s
   			t   Packc           B   s   e  Z d  Z d „  Z RS(   s,   
    Base class for packing-type stages
    c         C   s   d |  S(   Nt   Yes(    (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   À  s    (   R   R   R	   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRE   »  s   t   Packedc           B   s_   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z RS(
   s&   
    Structure passing clash test
    c         C   s)   t  t |  ƒ j ƒ  | |  _ | |  _ d  S(   N(   R   RG   R   RC   R3   (   R   RC   R3   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ê  s    	c         C   s   |  j  S(   N(   RC   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ñ  s    c         C   s
   |  j  j S(   N(   RC   R3   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   tf_peakÖ  s    c         C   s   |  j  j ƒ  S(   N(   RC   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Û  s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   R6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   à  s    c         C   s   |  j  j ƒ  S(   N(   RC   R>   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR>   å  s    c         C   s   t  |  j ƒ S(   N(   R.   RC   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ê  s    c         C   s   d |  j  ƒ  S(   Ns   %s
Clashes: no(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ï  s    c         C   s   |  j  j ƒ  S(   N(   RC   RA   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRA   ô  s    (   R   R   R	   R   R   RH   R   R6   R>   R   R   RA   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRG   Å  s   								t   Filledc           B   s_   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z RS(
   s1   
    A peak filled in that passes clash test
    c         C   s;   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ | |  _ d  S(   N(   R   RI   R   R-   R3   R   t
   entry_code(   R   R-   R3   R   RJ   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   þ  s
    			c         C   s   |  j  S(   N(   R-   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s   |  j  S(   N(   R3   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRH     s    c         C   s   |  j  j ƒ  S(   N(   R3   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s   d  S(   N(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6     s    c         C   s   d |  j  S(   Ns   Filled peak #%d(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR>     s    c         C   s   d |  j  |  j ƒ  f S(   Ns   %s
%s(   R-   R>   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR      s    c         C   s#   d |  j  ƒ  |  j j |  j j f S(   Ns   %s, TF = %.2f, TFZ = %.2f(   R   R3   R?   R@   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   %  s    c         C   s   d |  j  j |  j f S(   Ns   %.1f%s(   R3   R@   RJ   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRA   *  s    (   R   R   R	   R   R   RH   R   R6   R>   R   R   RA   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRI   ù  s   									t	   Evaluatedc           B   s   e  Z d  Z d „  Z RS(   s1   
    Base class for identifying final stages
    c         C   s@   |  | k r t  S|  j ƒ  | j ƒ  k r, t  S|  j d | ƒ Sd  S(   Nt   other(   R4   R   t   mixable_with_stage(   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   mixable_for_amalgamation5  s
    (   R   R   R	   RN   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRK   /  s   t   Scoredc           B   s•   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   s>   
    Structure that went through identification procedure
    c         C   s)   t  t |  ƒ j ƒ  | |  _ | |  _ d  S(   N(   R   RO   R   t   packt   _significant(   R   RP   t   significant(    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   F  s    	c         C   s   |  j  S(   N(   RP   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   M  s    c         C   s
   |  j  j S(   N(   RP   R3   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR3   R  s    c         C   s   |  j  j ƒ  S(   N(   RP   RH   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRH   W  s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   R6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   \  s    c         C   s   |  j  j ƒ  S(   N(   RP   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   a  s    c         C   s   |  j  S(   N(   RQ   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRR   f  s    c         C   s   t  S(   N(   R4   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt
   is_refinedk  s    c         C   s   |  j  j ƒ  S(   N(   RP   R>   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR>   p  s    c         C   s   t  |  j ƒ S(   N(   R.   RP   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   u  s    c         C   s   d |  j  ƒ  |  j ƒ  f S(   Ns   %s
Significant: %s(   R   RR   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   z  s    c         C   s-   d |  j  j ƒ  |  j ƒ  r! d n d f |  S(   Ns   %s%st   *t    (   RP   RA   RR   (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!     s    c         C   s   | j  d |  ƒ S(   NRL   (   t   mixable_with_scored_stage(   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRM   ‰  s    c         C   s   t  S(   N(   t   True(   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRV   Ž  s    c         C   s   | j  |  k S(   N(   R'   (   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   mixable_with_templated_stage“  s    (   R   R   R	   R   R   R3   RH   R6   R   RR   RS   R>   R   R   R!   RM   RV   RX   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRO   A  s    												
		t	   Templatedc           B   s�   e  Z d  Z d d „ Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d	 „  Z
 d
 „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   sV   
    Structures that were found by matching a model to a template (superposition)
    i    c         C   sD   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ | |  _ | |  _ d  S(   N(   R   RY   R   R-   R'   t   _peakt   refinedt   llg(   R   R-   R'   R3   R[   R\   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   �  s    				c         C   s   |  j  S(   N(   R-   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   §  s    c         C   s   d  S(   N(   R   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6   ¬  s    c         C   s
   |  j  j S(   N(   RZ   R?   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ±  s    c         C   s   |  j  S(   N(   RZ   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR3   ¶  s    c         C   s   |  j  S(   N(   RZ   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRH   »  s    c         C   s   t  S(   N(   RW   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRR   À  s    c         C   s   |  j  S(   N(   R[   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRS   Å  s    c         C   s   d |  j  |  j j ƒ  f S(   Ns   %s
%s(   R-   R'   R>   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ê  s    c         C   sW   d |  j  ƒ  |  j ƒ  r d n d |  j ƒ  j |  j ƒ  j |  j rO d |  j n d f S(   Ns*   %s
Superposed: %s, TF = %.2f, TFZ = %.2f%sR[   t	   unrefineds   , LLG = %.2fRU   (   R   RS   R3   R?   R@   R[   R\   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   Ï  s    	c         C   s   d |  j  ƒ  j |  S(   Ns   %.1fS*(   R3   R@   (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!   Ú  s    c         C   s   | j  d |  ƒ S(   NRL   (   RX   (   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRM   ß  s    c         C   s   |  j  | k S(   N(   R'   (   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRV   ä  s    c         C   s   | j  |  j  k S(   N(   R'   (   R   RL   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRX   é  s    (   R   R   R	   R   R   R6   R   R3   RH   RR   RS   R   R   R!   RM   RV   RX   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRY   ˜  s   
												t   Refinedc           B   sM   e  Z d  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 RS(   s   
    Refined peak
    c         C   s2   t  t |  ƒ j ƒ  | |  _ | |  _ | |  _ d  S(   N(   R   R^   R   t	   evaluatedt	   structureR\   (   R   R_   R`   R\   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   ó  s    		c         C   s   |  j  S(   N(   R_   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   û  s    c         C   s   |  j  S(   N(   R\   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR      s    c         C   s   |  j  ƒ  j ƒ  S(   N(   R   R6   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR6     s    c         C   s   d |  j  S(   Ns
   %s
Refined(   R_   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   
  s    c         C   s   d |  j  ƒ  |  j f S(   Ns   %s, LLG = %.2f(   R   R\   (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s   d |  j  |  S(   Ns   %.2f(   R\   (   R   R    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR!     s    (
   R   R   R	   R   R   R   R6   R   R   R!   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR^   î  s   						t
   Suspensionc           B   s    e  Z d  Z d „  Z d „  Z RS(   s7   
    Suspend something until a condition gets True
    c         C   s   | |  _  d  S(   N(   t	   condition(   R   Rb   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR     s    c         C   s   d S(   Ns   rotation function suspension(    (   R   (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyR   #  s    (   R   R   R	   R   R   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyRa     s   	N(   t   objectR    R
   R   R   R   R   R   R   R   R   R"   R&   R)   R,   R2   R9   R:   R;   RB   RE   RG   RI   RK   RO   RY   R^   Ra   (    (    (    sC   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/stage.pyt   <module>   s4   1%%%/1;
46WV+