ó
šxTc           @   s€  d  d l  m Z d  d l 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 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 S(#   iÿÿÿÿ(   t	   mr_objectNt   Progressc           B   s   e  Z d  Z d „  Z RS(   s8   
    Class to indicate that a search is in progress
    c         C   s   | |  _  d  S(   N(   t   calculation(   t   selfR   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   __init__	   s    (   t   __name__t
   __module__t   __doc__R   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR      s   t   Resultc           B   s   e  Z d  Z d „  Z RS(   s'   
    Base class for identification
    c         C   s   | |  _  | |  _ | |  _ d  S(   N(   R   t   logfilet   data(   R   R   R	   R
   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR      s    		(   R   R   R   R   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR      s   t   Calculationc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   s'   
    Base class for identification
    c         C   s   | |  _  | |  _ d  S(   N(   R
   t   partial(   R   R
   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   !   s    	c         C   s   d  |  _ d  S(   N(   t   NoneR
   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   cleanup'   s    c         C   s
   |  j  j S(   N(   t	   __class__R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   __str__,   s    (   R   R   R   R   R   R   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR      s   		t   RotationSearchc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s   
    Rotation search
    c         C   s8   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ d  S(   NR
   R   (   t   superR   R   t   ensemblet   cutoff(   R   R
   R   R   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   6   s    "	i   c   
      C   sÌ  t  j ƒ  } | j | ƒ |  j j d | ƒ t |  j j ƒ  ƒ } | j |  j	 ƒ x | D] } | j
 d | ƒ qX W| j |  j j ƒ  g ƒ | j |  j	 j ƒ  d ƒ | j t ƒ | j t ƒ | j d ƒ | j |  j ƒ | j t ƒ | j t ƒ t  j | ƒ } | j ƒ  r#t | j ƒ  d  f S| j ƒ  } t | ƒ d k sGt ‚ | d } t g  | j  D] } | j! |  j	 j ƒ  k ^ q^ƒ s‹t ‚ g  | j  D] } | j" | j# | j$ f ^ q•}	 t | j ƒ  |	 f S(   Nt   inputi   t   OFFi    (%   t   phasert   InputMR_FRFt   setJOBSR
   t   applyt   setR   t	   ensemblest   addR   t   apply_ensemble_definitiont   setSOLUt   mr_sett   addSEAR_ENSE_NUMt
   identifiert   setXYZOt   Falset   setMUTEt   Truet   setMACA_PROTt   setPEAK_ROTA_CUTOR   t   setSEAR_DEEPt   setELLG_USEt   GIL_runMR_FRFt   FailedR	   R   t   getDotRlistt   lent   AssertionErrort   allt   RLISTt   MODLIDt   EULERt   RFt   RFZ(
   R   t   cpusR   R   t   enset   resultt   rawt   mst   rt	   rotations(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   run=   s0    
:.c   	      C   s�   | \ } } } | s% t  d | ‚ n  g  | D]E \ } } } t j d |  j d t j j d | ƒ d | d | ƒ ^ q, } t d |  d | d	 | ƒ S(
   Ns   Rotation calculation failed:
%sR   t   rotationt   anglest   rft   rfzR   R	   R
   (   t   RuntimeErrorR    t   RotationPeakR   t   Rotationt   EulerR   (	   R   t   resultst   successR	   t   definitionst   aR@   RA   t   peaks(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   process_   s    O(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   1   s   	"t   RestrictedRotationSearchc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s0   
    Rotation search restricted to a volume
    c         C   sA   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R   R>   t   sweep(   R   R
   R   R   R>   RM   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   x   s    "		i   c   
      C   sñ  t  j ƒ  } | j | ƒ |  j j d | ƒ t |  j j ƒ  ƒ } | j |  j	 ƒ x! t | ƒ D] } | j
 | ƒ q^ W| j t ƒ | j t ƒ | j d ƒ | j d ƒ | j |  j j ƒ  ƒ | j |  j ƒ | j |  j j ƒ  g ƒ | j |  j	 j ƒ  d ƒ | j |  j j ƒ  g ƒ t  j | ƒ } | j ƒ  rHt | j ƒ  d  f S| j ƒ  } t | ƒ d k slt  ‚ | d } t! g  | j" D] } | j# |  j	 j ƒ  k ^ qƒƒ s°t  ‚ g  | j" D] } | j$ | j% | j& f ^ qº}	 t | j ƒ  |	 f S(   NR   R   t   AROUNDi   i    ('   R   t   InputMR_BRFR   R
   R   R   R   R   R   R   R   R#   R$   R%   R&   R'   t   setROTA_VOLUt   setROTA_EULER>   t   eulert   setROTA_RANGRM   R   R    R!   R"   t   GIL_runMR_BRFR,   R	   R   R-   R.   R/   R0   R1   R2   R3   R4   R5   (
   R   R6   R   R   R7   R8   R9   R:   R;   R<   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   €   s2    
:.c   	      C   s�   | \ } } } | s% t  d | ‚ n  g  | D]E \ } } } t j d |  j d t j j d | ƒ d | d | ƒ ^ q, } t d |  d | d	 | ƒ S(
   Ns   Rotation calculation failed:
%sR   R>   R?   R@   RA   R   R	   R
   (   RB   R    RC   R   RD   RE   R   (	   R   RF   RG   R	   RH   RI   R@   RA   RJ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   ¤   s    O(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRL   s   s   	$t   TranslationSearchc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s   
    Translation search
    c         C   s/   t  |  j |  ƒ j d | d | ƒ | |  _ d  S(   NR
   R   (   R   R   R   t   rpeak(   R   R
   R   RV   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   ½   s    "i   c   	      C   s)  t  j ƒ  } | j | ƒ |  j j d | ƒ t |  j j ƒ  ƒ } | j |  j	 j
 ƒ x | D] } | j | ƒ q[ W| j |  j j d |  j	 g ƒ g ƒ | j t ƒ | j t ƒ | j d ƒ | j d ƒ | j t ƒ | j d ƒ t  j | ƒ } | j ƒ  rt | j ƒ  d  f S| j ƒ  } t g  | D]! } | j j |  j j ƒ  ƒ ^ q)ƒ sYt ‚ t g  | D] } d t  | j! ƒ k  ^ qcƒ s�t ‚ t g  | D]+ } | j! d j" ƒ  |  j	 j
 j ƒ  k ^ q—ƒ sÑt ‚ g  | D]8 } | j! d j# ƒ  | j$ | j% | j! d j& ƒ  f ^ qØ} t | j ƒ  | f S(   NR   R<   R   t   NONEt   FULLi    iÿÿÿÿ('   R   t   InputMR_FTFR   R
   R   R   R   R   R   RV   R   R   R   R    R#   R$   R%   R&   R'   t   setSGAL_SELEt   setZSCO_USEt   setSEAR_METHt   GIL_runMR_FTFR,   R	   R   t	   getDotSolR0   t
   ANNOTATIONt
   startswithR"   R/   R.   t   KNOWNt	   getModlidt   getFracTt   TFt   TFZt   getBfac(	   R   R6   R   R   R7   R8   R9   t   tRH   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   Ã   s6    74>Ec   
      C   s™   | \ } } } | s% t  d | ‚ n  g  | D]N \ } } } } t j d |  j j d |  j j d | d | d | d | ƒ ^ q, }	 t d |  d	 | d
 |	 ƒ S(   Ns"   Translation calculation failed:
%sR   R>   t   translationt   tft   tfzt   bfactorR   R	   R
   (   RB   R    t   TranslationPeakRV   R   R>   R   (
   R   RF   RG   R	   RH   Rg   Ri   Rj   t   bfacRJ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   î   s    X(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRU   ¸   s   	+t   RestrictedTranslationSearchc           B   s5   e  Z d  Z d „  Z d d „ Z d „  Z d „  Z RS(   s0   
    Rotation search restricted to a volume
    c         C   sJ   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R   R<   Rh   t   extent(   R   R
   R   R   R<   Rh   Ro   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   	  s
    "			i   c   
      C   sL  t  j ƒ  } | j | ƒ |  j j d | ƒ |  j j ƒ  } | j |  j ƒ x! t	 | ƒ D] } | j
 | ƒ qX W| j t ƒ | j t ƒ | j d ƒ | j d ƒ | j |  j ƒ | j |  j ƒ | j t ƒ | j |  j j d |  j ƒ  ƒ g ƒ t  j | ƒ } | j ƒ  r#t | j ƒ  d  f S| j ƒ  } g  } t g  | D]! } | j j  |  j j! ƒ  ƒ ^ q?ƒ sot" ‚ t g  | D] } d t# | j$ ƒ k  ^ qyƒ s£t" ‚ t g  | D]( } | j$ d j% ƒ  |  j j! ƒ  k ^ q­ƒ sät" ‚ g  | D]H } | j$ d j& ƒ  | j$ d j' ƒ  | j( | j) | j$ d j* ƒ  f ^ që}	 t | j ƒ  |	 f S(   NR   R   RN   R<   i    iÿÿÿÿ(+   R   t   InputMR_BTFR   R
   R   R   R   t   appendR   R   R   R#   R$   R%   R&   R'   t   setTRAN_VOLUt   setTRAN_POINRh   t   setTRAN_RANGRo   R[   R   R    t   rpeakst   GIL_runMR_BTFR,   R	   R   R^   R0   R_   R`   R"   R/   R.   Ra   Rb   t   getRRc   Rd   Re   Rf   (
   R   R6   R   R   R7   R8   R9   R
   Rg   RH   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=     s8    %74>Rc         C   s;   g  |  j  D]- } t j d |  j d | d d d d ƒ ^ q
 S(   NR   R>   R@   i    RA   (   R<   R    RC   R   (   R   R;   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRu   @  s    c         C   s¢   | \ } } } | s% t  d | ‚ n  g  | D]W \ } } } } }	 t j d |  j d t j j d | ƒ d | d | d | d |	 ƒ ^ q, }
 t d	 |  d
 | d |
 ƒ S(   Ns"   Translation calculation failed:
%sR   R>   t   elementsRh   Ri   Rj   Rk   R   R	   R
   (   RB   R    Rl   R   RD   t   MatrixR   (   R   RF   RG   R	   RH   R;   Rg   Ri   Rj   Rm   RJ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   H  s    a(   R   R   R   R   R=   Ru   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRn     s
   		.	t   SinglePoolPackingCheckc           B   sD   e  Z d  Z d Z d „  Z d d „ Z d „  Z d „  Z d „  Z RS(   s   
    Packing check
    i
   c         C   s=   t  | ƒ t  | ƒ k s t ‚ | |  _ | |  _ | |  _ d  S(   N(   R.   R/   R
   t   partialst   tpeaks(   R   R
   R{   R|   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   e  s    		i   c         C   s   d d  l  } t j ƒ  } | j | ƒ |  j j d | ƒ t t | j g  |  j	 D] } | j
 ƒ  ^ qN ƒ ƒ } | j g  |  j D] } | j ^ q| ƒ x | D] } | j | ƒ q™ Wg  } xs t t |  j	 |  j ƒ ƒ D]V \ }	 \ } } | j d | g ƒ }
 d |  j d |	 ƒ |
 j f |
 _ | j |
 ƒ qÒ W| j | ƒ | j d ƒ | j |  j ƒ | j t ƒ | j t ƒ t j | ƒ } | j ƒ  ržt | j ƒ  d  f St! g  | j" ƒ  D] }
 |
 j j# ƒ  d |
 f ^ q®ƒ } g  } x.t t |  j	 |  j ƒ ƒ D]\ }	 \ } } |  j d |	 ƒ } | | k r;| j g  ƒ qøn  | | }
 d t$ |
 j% ƒ k  s`t& ‚ |
 j j# ƒ  d j' | j( ƒ  ƒ sˆt& ‚ |
 j% d j) ƒ  | j j( ƒ  k sÖt& d	 |
 j% d j) ƒ  | j j( ƒ  f ƒ ‚ | j |
 j% d j* ƒ  |
 j% d j+ ƒ  |
 j, f ƒ qøWt | j ƒ  | f S(
   NiÿÿÿÿR   t   translationss   %s %st   indext   ALLOWi    i   s   %s != %s(-   t   operatorR   t   InputMR_PAKR   R
   t   apply_symmetryR   t   reduceR   R{   R   t   updateR|   R   R   t	   enumeratet   zipR    t   peakidR_   Rq   R   t   setPACK_SELEt   setPACK_CUTOt   ALLOWEDR#   R$   R%   R&   t   GIL_runMR_PAKR,   R	   R   t   dictR^   t   splitR.   Ra   R/   R`   R"   Rb   Rw   Rc   t   PAK(   R   R6   R€   R   t   pR   Rg   R7   t   mr_setst   iR:   R8   t   ms_forRH   R‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   m  sL    1&."5.
(%)1c         C   sí   | \ } } } | s% t  d | ‚ n  g  } x… t | |  j ƒ D]q \ } } | s` | j d  ƒ q> | \ } }	 }
 | j t j d | j d t j j	 d | ƒ d |	 d | j
 ƒ ƒ q> Wt | ƒ t |  j ƒ k sÔ t ‚ t d |  d | d	 | ƒ S(
   Ns   Packing calculation failed:
%sR   R>   Rx   Rh   Rk   R   R	   R
   (   RB   R†   R|   Rq   R   R    t   PeakR   RD   Ry   Rk   R.   R/   R   (   R   RF   RG   R	   RH   R
   t   dRg   t   rott   trat   clashes(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   ¬  s     		!c         C   s   d | S(   Ns   try%d(    (   R   R~   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR‡   È  s    c         C   s
   |  j  j S(   N(   R   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   Í  s    (	   R   R   R   RŠ   R   R=   RK   R‡   R   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRz   ^  s   	?		t
   Refinementc           B   s/   e  Z d  Z e d „ Z d d „ Z d „  Z RS(   s   
    Refinement
    c         C   sS   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ | |  _ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   t   peakt   significantRA   Rj   t   b_factor_refinement(   R   R
   R   R™   Rš   RA   Rj   R›   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   ×  s    "				i   c      	   C   se  t  j ƒ  } | j | ƒ |  j j d | ƒ |  j j ƒ  } |  j j ƒ  } |  j j	 d | ƒ } | j
 g  | D] } | j ^ ql ƒ x! t | ƒ D] } | j | ƒ q� W| j |  j j d | ƒ g ƒ | j t ƒ | j t ƒ | j t ƒ | j d ƒ | j d ƒ | j d t d t d |  j d	 t ƒ t  j | ƒ } | j ƒ  rYt | j ƒ  d  f S| j ƒ  }	 t |	 ƒ d
 k s}t ‚ |	 d }
 |
 j  j! |  j j" ƒ  ƒ s¨t ‚ t |
 j# ƒ t | ƒ k sÉt ‚ t$ g  t% |
 j# | ƒ D]$ \ } } | j& ƒ  | j" ƒ  k ^ qßƒ st ‚ g  |
 j# D]' } | j' ƒ  | j( ƒ  | j) ƒ  f ^ q} t | j ƒ  |
 j* | f f S(   NR   t   cellR}   R   t   CUSTOMt   ref_rotat   ref_trant   ref_bfact   ref_vrmsi   i    (+   R   t   InputMR_RNPR   R
   R   t   uctbx_unit_cellR   R   R™   t   independent_component_listt   extendR   R   R   R   R    R#   R$   t   setHKLOR%   R&   R'   t   setMACM_PROTt   addMACMR›   t   GIL_runMR_RNPR,   R	   R   R^   R.   R/   R_   R`   R"   Ra   R0   R†   Rb   Rw   Rc   Rf   t   LLG(   R   R6   R   Rœ   R   t   disassembled_peakR�   R7   R8   t   solR:   t   ndt   eRH   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   á  s@    #		
!!C7c         C   sC  | \ } } } | s% t  d | ‚ n  | \ } } |  j j ƒ  } |  j j ƒ  g  |  j j d | ƒ D] } | j ^ qb }	 t |	 ƒ t | ƒ k s– t	 ‚ t
 j d g  t |	 | ƒ D]H \ }
 \ } } } t
 j d |
 d t
 j j d | ƒ d | d | ƒ ^ q¯ d	 |  j d
 |  j d |  j d |  j ƒ } t d |  d | d | | f ƒ S(   Ns!   Refinement calculation failed:
%sRœ   RJ   R   R>   Rx   Rh   Rk   Rš   RA   Rj   t   predecessorR   R	   R
   (   RB   R
   R£   R   R   R™   R¤   R   R.   R/   R    t	   StructureR†   R“   RD   Ry   Rš   RA   Rj   R   (   R   RF   RG   R	   RH   t   llgR
   Rœ   R�   R   R®   R;   Rg   t   bt	   structure(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK     s&    ,	[			(   R   R   R   R&   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR˜   Ò  s   
-t   PeakRefinementc           B   s/   e  Z d  Z e d „ Z d d „ Z d „  Z RS(   s!   
    Refinement of peak only
    c         C   s8   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R™   R›   (   R   R
   R   R™   t   protocol(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   6  s    "	i   c      	   C   s%  t  j ƒ  } | j | ƒ |  j j d | ƒ |  j j ƒ  } t |  j j ƒ  ƒ } | j	 |  j
 j ƒ x | D] } | j | ƒ qj W| j |  j j d |  j
 g d t t t f ƒ g ƒ | j t ƒ | j t ƒ | j t ƒ | j d ƒ | j d ƒ | j d t d t d |  j d	 t ƒ t  j | ƒ } | j ƒ  rIt | j ƒ  d  f S| j ƒ  } t | ƒ d
 k smt ‚ | d } | j j  |  j j! ƒ  ƒ s˜t ‚ d t | j" ƒ k  s³t ‚ | j" d j# ƒ  |  j
 j j! ƒ  k sÞt ‚ | j" d }	 |	 j$ ƒ  |	 j% ƒ  |	 j& ƒ  | j' f }
 t | j ƒ  |
 f S(   NR   R}   t   sflagsR   R�   Rž   RŸ   R    R¡   i   i    iÿÿÿÿ((   R   R¢   R   R
   R   R£   R   R   R   R   R™   R   R   R   R    R&   R#   R$   R¦   R%   R'   R§   R¨   R›   R©   R,   R	   R   R^   R.   R/   R_   R`   R"   Ra   Rb   Rw   Rc   Rf   Rª   (   R   R6   R   Rœ   R   R7   R8   R¬   R:   R­   RH   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   =  sD    		
!+'c   
   	   C   s�   | \ } } } | s% t  d | ‚ n  | \ } } } } t j d |  j j d t j j d | ƒ d | d | ƒ }	 t d |  d | d	 | |	 f ƒ S(
   Ns!   Refinement calculation failed:
%sR   R>   Rx   Rh   Rk   R   R	   R
   (   RB   R    R“   R™   R   RD   Ry   R   (
   R   RF   RG   R	   RH   R;   Rg   R²   R±   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   q  s    		(   R   R   R   R&   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR´   1  s   4t   TFZCalculationc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s   
    TFZ calculation
    c         C   s/   t  |  j |  ƒ j d | d | ƒ | |  _ d  S(   NR
   R   (   R   R   R   R™   (   R   R
   R   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   Œ  s    "i   c   	   	   C   sö  t  j ƒ  } | j | ƒ |  j j d | ƒ |  j j ƒ  } | j |  j j	 ƒ x! t
 | ƒ D] } | j | ƒ q[ W| j t ƒ | j t ƒ | j d ƒ | j d ƒ | j |  j j ƒ | j d ƒ | j t ƒ | j t ƒ t j d |  j j	 d |  j j d d d	 d ƒ } | j |  j j d
 | g ƒ g ƒ t  j | ƒ } | j ƒ  r`t | j ƒ  d  f S| j  ƒ  } t! | ƒ d k r–d d |  j j f } nM d t! | d j" ƒ k  sµt# ‚ | d j$ | d j% | d j" d j& ƒ  f } t | j ƒ  | f S(   NR   R   RN   i   R   R>   R@   i    RA   R<   g        iÿÿÿÿ('   R   Rp   R   R
   R   R   R   Rq   R™   R   R   R   R#   R$   R%   R&   R'   Rr   Rs   Rh   Rt   t   setTRAN_FRACR[   R    RC   R>   R   R    Rv   R,   R	   R   R^   R.   Ra   R/   Rd   Re   Rc   (	   R   R6   R   R   R7   RV   R8   R¬   R
   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   ’  s<    		".c         C   s‰   | \ } } \ } } } | s. t  d | ‚ n  t j d |  j j d |  j j d | d | d | d |  j j ƒ } t d |  d	 | d
 | ƒ S(   Ns   TFZ calculation failed:
%sR   R>   Rh   Ri   Rj   Rk   R   R	   R
   (   RB   R    Rl   R™   R   R>   Rk   R   (   R   RF   RG   R	   Ri   Rj   R–   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   Ã  s    	(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR·   ‡  s   	1t
   Evaluationc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s   
    Peak evaluation
    c         C   s/   t  |  j |  ƒ j d | d | ƒ | |  _ d  S(   NR
   R   (   R   R   R   R™   (   R   R
   R   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   Û  s    "i   c         C   sö   t  d |  j d |  j g d |  j g ƒ } | j d | ƒ } y | j d | ƒ } Wn t k
 rq } t | d  f SXt	 | j ƒ d k s� t
 ‚ | j d d  k r° t | j d  f St d |  j d |  j d	 |  j ƒ } | j d | ƒ } t | j | f S(
   NR
   R{   R|   R6   RF   i   i    R   R™   (   Rz   R
   R   R™   R=   RK   RB   R$   R   R.   R/   R&   R	   R·   (   R   R6   t   packingt   pak_rawt
   pak_resultR®   t   tfzcalct   tfz_raw(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   á  s$    			c         C   s¡   | \ } } } | s! t  | ‚ n  | s6 t d  f } nR t d |  j d |  j d |  j ƒ } | j d | ƒ } t | j f } | | j	 7} t
 d |  d | d | ƒ S(   NR
   R   R™   RF   R   R	   (   RB   R$   R   R·   R
   R   R™   RK   R&   R	   R   (   R   RF   t   pak_successR	   R¾   R
   R½   R8   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK     s    		(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR¹   Ö  s   	!t   RefinedEvaluationc           B   s/   e  Z d  Z e d „ Z d d „ Z d „  Z RS(   s   
    Peak evaluation
    c         C   s8   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R™   Rµ   (   R   R
   R   R™   Rµ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR     s    "	i   c      	   C   så  t  d |  j d |  j g d |  j g ƒ } | j d | ƒ } y | j d | ƒ } Wn t k
 rq } t | d  f SXt	 | j ƒ d k s� t
 ‚ | j d d  k r° t | j d  f St d |  j d |  j d	 |  j d
 |  j ƒ } | j ƒ  } y | j d | ƒ } Wn t k
 r} t | d  f SX| j | j }	 | j \ }
 } t d |  j d |  j d	 | ƒ } | j d | ƒ } y | j d | ƒ } Wn t k
 r¦} t | d  f SX| j } t |	 | j | j | j | j | j | j |
 f f S(   NR
   R{   R|   R6   RF   i   i    R   R™   Rµ   (   Rz   R
   R   R™   R=   RK   RB   R$   R   R.   R/   R&   R	   R´   Rµ   R·   R>   Rh   Rk   Ri   Rj   (   R   R6   Rº   R»   R¼   R®   t
   refinementt   refinement_rawt
   ref_resultR	   R±   R™   R½   R¾   t
   tfz_resultt   tfz_peak(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   &  sT    								
c         C   sµ   | \ } } } | s! t  | ‚ n  | s9 t d  d  f } nc | \ } } } }	 }
 } t j d |  j j d | d | d |	 d |
 d |  j j ƒ } t | | f } t	 d |  d | d	 | ƒ S(
   NR   R>   Rh   Ri   Rj   Rk   R   R	   R
   (
   RB   R$   R   R    Rl   R™   R   Rk   R&   R   (   R   RF   RG   R	   RH   R
   R;   Rg   R²   Ri   Rj   R±   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   k  s    	(   R   R   R   R&   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRÀ     s   Et   MultiOriginEvaluationc           B   s5   e  Z d  Z d „  Z d d „ Z d „  Z d „  Z RS(   s   
    Peak evaluation
    c         C   s8   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R™   t   origins(   R   R
   R   R™   RÇ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   ‰  s    "	i   c         C   s;  |  j  ƒ  } t d |  j d |  j g t | ƒ d | ƒ } | j d | ƒ } y | j d | ƒ } Wn t k
 r� } t | d  f SXt | j ƒ t | ƒ k s£ t
 ‚ g  } x t | | j ƒ D]k \ } }	 |	 d  k rç | j d  ƒ q¼ n  t d |  j d |  j d | ƒ }
 |
 j d | ƒ } | j | ƒ q¼ Wt | j | f S(   NR
   R{   R|   R6   RF   R   R™   (   RJ   Rz   R
   R   R.   R=   RK   RB   R$   R   R/   R†   Rq   R·   R&   R	   (   R   R6   RJ   Rº   R»   R¼   R®   t   tdataR�   t   pak_pR½   R¾   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   �  s.    		!			c         C   s}   |  j  j \ } } } g  |  j D]Z \ } } } t j d |  j  j d |  j  j d | | | | | | f d |  j  j ƒ ^ q S(   NR   R>   Rh   Rk   (   R™   Rh   RÇ   R    R“   R   R>   Rk   (   R   t   mxt   myt   mzt   xt   yt   z(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRJ   µ  s    c         C   s  | \ } } } | s! t  | ‚ n  |  j ƒ  } t | ƒ t | ƒ k sK t ‚ g  } x t | | ƒ D]n \ } } | d  k r qa n  t d |  j d |  j d | ƒ }	 |	 j	 d | ƒ }
 | |
 j
 7} | j |
 j ƒ qa W| sè t d  f } n t t | d d „  ƒf } t d |  d | d | ƒ S(	   NR
   R   R™   RF   t   keyc         S   s   |  j  S(   N(   Ri   (   t   tp(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   <lambda>á  s    R   R	   (   RB   RJ   R.   R/   R†   R   R·   R
   R   RK   R	   Rq   R$   R&   t   maxR   (   R   RF   R¿   R	   RÈ   RJ   R|   R�   t   tdR½   R8   R
   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   Ä  s(    			(   R   R   R   R   R=   RJ   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRÆ   „  s
   	%	t   RestrictedSearchc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   sB   
    Rotation and translation searches restricted to a volume
    c         C   sS   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ | |  _ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R   R>   RM   Rh   Ro   (   R   R
   R   R   R>   RM   Rh   Ro   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   ë  s    "				i   c   
      C   sƒ  t  d |  j d |  j d |  j d |  j d |  j ƒ } | j d | ƒ } y | j d | ƒ } Wn t k
 r} } t	 | d  f SX| j s— t | j g  f St d |  j d |  j d |  j d g  | j D] } | j ^ qÂ d	 |  j d
 |  j ƒ } | j d | ƒ } y | j d | ƒ }	 Wn t k
 r3} t	 | d  f SXt | j d |	 j g  |	 j D]* } | j | j | j | j | j f ^ qRf S(   NR
   R   R   R>   RM   R6   RF   R<   Rh   Ro   s   
(   RL   R
   R   R   R>   RM   R=   RK   RB   R$   R   R&   R	   Rn   Rh   Ro   Ri   Rj   Rk   (
   R   R6   t   restricted_rotation_searcht   rot_tmp_resultst   rot_resultsR®   R�   t   restricted_translation_searcht   tra_tmp_resultst   tra_results(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   õ  s:    									c         C   s“   | \ } } } | s% t  d | ‚ n  g  | D]H \ } } } } }	 t j d |  j d | d | d | d | d |	 ƒ ^ q, }
 t d |  d	 | d
 |
 ƒ S(   Ns(   Restricted search calculation failed:
%sR   R>   Rh   Ri   Rj   Rk   R   R	   R
   (   RB   R    Rl   R   R   (   R   RF   RG   R	   RH   R;   Rg   Ri   Rj   Rm   RJ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   #  s    R(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRÕ   æ  s   	
.t   RestrictedSearchEvaluationc           B   s,   e  Z d  Z d „  Z d d „ Z d „  Z RS(   s1   
    Select best peak from restricted search
    c         C   sA   t  |  j |  ƒ j d | d | ƒ | |  _ | |  _ | |  _ d  S(   NR
   R   (   R   R   R   R™   RM   Ro   (   R   R
   R   R™   RM   Ro   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR   >  s    "		i   c   
      C   sÛ  t  d |  j d |  j d |  j j d |  j j d |  j d |  j j d |  j ƒ } | j	 d | ƒ } y | j
 d	 | ƒ } Wn t k
 r˜ } t | d  f SX| j sí t j d |  j j d |  j j d |  j j d
 d d d d |  j j ƒ } n t | j d d „  ƒ} t d |  j d |  j g d | g ƒ } | j	 d | ƒ } y | j
 d	 | ƒ }	 Wn t k
 rs} t | d  f SXt |	 j ƒ d k s�t ‚ t | j d |	 j |	 j d d  k	 | j | j | j | j | j f f f S(   NR
   R   R   R>   RM   Rh   Ro   R6   RF   Ri   i    Rj   Rk   RÐ   c         S   s   |  j  S(   N(   Ri   (   t   s(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRÒ   e  s    R{   R|   i   s   
(   RÕ   R
   R   R™   R   R>   RM   Rh   Ro   R=   RK   RB   R$   R   R    Rl   Rm   RÓ   Rz   R.   R/   R&   R	   Ri   Rj   Rk   (
   R   R6   t   searcht
   search_tmpt   search_resultsR®   t   bestt   pakR»   t   pak_results(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyR=   F  sH    						c         C   s•   | \ } } } | s% t  d | ‚ n  | \ } \ } } } }	 }
 t j d |  j j d | d | d | d |	 d |
 ƒ } t d |  d	 | d
 | | f ƒ S(   Ns3   Restricted search evaluation calculation failed:
%sR   R>   Rh   Ri   Rj   Rk   R   R	   R
   (   RB   R    Rl   R™   R   R   (   R   RF   RG   R	   RH   t   is_pakR;   Rg   Ri   Rj   Rm   R™   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRK   ‚  s    		(   R   R   R   R   R=   RK   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyRÜ   9  s   	<(   t   phaser.pipelineR    R   t   objectR   R   R   R   RL   RU   Rn   Rz   R˜   R´   R·   R¹   RÀ   RÆ   RÕ   RÜ   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/calculation.pyt   <module>   s"   BELZt_VODjbS