ó
šxTc           @   sÏ   d  d l  m Z d  d l  m Z d  d l  m Z d  d l Z d  d l Z	 d  d l
 m Z d  d l Z d  d l Z d  d l Z d d „ Z d „  Z d „  Z e d	 k rË e j d
 d ƒ g Z e d e ƒ n  d S(   iÿÿÿÿ(   t   process_model_new(   t   mr_object_new(   t   phaser_ai_newN(   t   bioinformaticsc         C   sx  t  j ƒ  } | j |  ƒ | j | | ƒ | j t ƒ | rL | j | ƒ n  t  j | ƒ } | j ƒ  rs t	 | ‚ n  | j
 ƒ  } | j ƒ  } t  j ƒ  } | j | j ƒ  | j ƒ  | j ƒ  ƒ | j | ƒ | j | ƒ | j t ƒ | j t ƒ t  j | ƒ } | j ƒ  rt	 | ‚ n  t j d | j ƒ  d | j ƒ  d | j ƒ  ƒ } t j d | ƒ }	 t j d | ƒ }
 | |	 |
 f S(   Nt   millert   fpt   sigfpt   space_group_hallt	   unit_cell(   t   phasert   InputMR_DATt   setHKLIt   setLABIt   setMUTEt   Truet   setHIRESt	   runMR_DATt   Failedt	   Exceptiont   getSpaceGroupHallt   getUnitCellt   InputANOt   setREFLt	   getMillert   getFt   getSIGFt   setCELL6t   setSPAC_HALLt   setHKLOt   Falset   runANOt	   mr_objectt   XrayDatat   getCorrectedFt   getCorrectedSIGFt
   SpaceGroupt   UnitCell(   t	   file_nameR   R   t   hirest   inpt   resultt   symmt   cellt	   xray_datat   spacR   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/test_jobs_new.pyt	   read_data   s6    %	c      	   C   s$  t  j j d d ƒ } t j j | d ƒ } d } t j j | d ƒ } t | d d d ƒ \ } } } t j d	 d
 d d d d ƒ } t	 j
 d d d | ƒ }	 t	 j d |	 g ƒ }
 t j d | d d d |	 ƒ } t j d | d d d |	 ƒ } t j d d d d d |	 ƒ } t j d d d d d |	 ƒ } t j d d d d d |	 ƒ } t j d d d d d |	 ƒ } t j d d d d  d |	 ƒ } | | | | | | | g } t	 j d! | d" | ƒ } t j j d# | d$ |
 d% |  d& t j ƒ } x | D] } | j d' | ƒ qæW| j ƒ  j t j ƒ | j ƒ  d  S((   NR	   t   tutorials   iod_scala-unique.mtzs(   /home/gaborb/data/lyso2001/193l_prot.pdbs   1fkq_prot.pdbt   F_Newt   SIGF_Newg      @t   namet   HEWLt   sequencet;   KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINt<   SRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDt
   VQAWIRGCRLt   mwihB  t
   componentst   pdb_filet   identityg®Gáz®ï?t	   componentgÍÌÌÌÌÌÜ?s$   /home/gaborb/data/lyso/1jhl_prot.pdbgq=
×£pí?s$   /home/gaborb/data/lyso/2gv0_prot.pdbgÃõ(\�Âå?s$   /home/gaborb/data/lyso/1gf3_prot.pdbg…ëQ¸…ã?s$   /home/gaborb/data/lyso/2z2e_prot.pdbg      à?s$   /home/gaborb/data/lyso/2h5z_prot.pdbgš™™™™™Ù?R+   R   t   problemt   compositiont
   symmetriest	   outstreamt   bbobj(   t   libtbxt   envt
   under_distt   ost   patht   joinR-   R   R3   R   t	   Componentt   Compositiont   process_modelt   SimpleEnsemblet   Problemt	   phaser_ait   PhaserAIt   MRModet   syst   stdoutt   addt   loggert   setLevelt   loggingt   INFOt   solve(   t   space_groupst   roott   mtz_filet	   pdb_file1t	   pdb_file2R+   R,   R*   t   hewl_seqR;   R=   t   mr_ensemble1t   mr_ensemble2t   mr_ensemble3t   mr_ensemble4t   mr_ensemble5t   mr_ensemble6t   mr_ensemble7t	   ensemblesR<   t   ait   ense(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/test_jobs_new.pyt   lysozyme_from_models6   sh    																	c       	   C   s–  t  j j d d ƒ }  t j j |  d ƒ } d } t j j |  d ƒ } t | d d d ƒ \ } } } t j d	 d
 d d d d ƒ } t j d	 d d d d d ƒ } t	 j
 d d d | ƒ }	 t	 j d |	 g ƒ }
 t j t d ƒ j ƒ  ƒ \ } } | sý t ‚ t j d d d |	 d d ƒ } | j | ƒ | j t	 j d t j j d d ƒ ƒ ƒ t j d | d  | ƒ } t j t d! ƒ j ƒ  ƒ \ } } | s•t ‚ t j d d" d |	 d d# ƒ } | j | ƒ | j t	 j d t j j d d$ ƒ ƒ ƒ t j d | d  | ƒ } t	 j d% | d& | ƒ } t j d' | d( |
 d) | g d* t j j ƒ  ƒ } | j d+ | ƒ | j d+ | ƒ | j d+ | ƒ | j d+ | ƒ | j ƒ  d  S(,   NR	   R.   s   iod_scala-unique.mtzs(   /home/gaborb/data/lyso2001/193l_prot.pdbs   1fkq_prot.pdbR/   R0   g      @R1   R2   R3   R4   R5   R6   t   LACTt9   MEQLTKCEVFQKLKDLKDYGGVSLPEWVCVAFHTSGYDTQAIVQNNDSTEYGLFQINt:   NKIWCKDDQNPHSRNICNISCDKFLDDDLTDDIVCAKKILDKVGINYWLAHKALCSEKt	   LDQWLCEKLR7   ihB  R8   s   ali_193l_193l.fat
   identifiert   193L_AR;   t   scoregÍÌÌÌÌÌì?R%   t   pipelines
   193L_A.pdbt	   blast_hitt	   alignments   ali_193l_1fkq.fat   1FKQ_Ag      à?s
   1FKQ_A.pdbR+   R   R<   R=   R>   t	   extensionR@   (   RA   RB   RC   RD   RE   RF   R-   R   R3   R   RG   RH   t   ali_alignment_parset   filet   readt   AssertionErrorRI   t   BlastHitt   set_sequencet   set_structuret	   Structuret	   AlignmentRK   RL   RM   t   SingleExtensiont	   AutofetchRQ   RV   (   RX   RY   RZ   R[   R+   R,   R*   R\   t   lact_seqR;   R=   t   alit   badt   b1t   a1t   b2t   a2R<   Re   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/test_jobs_new.pyt   lysozyme_from_hits~   sh    				"				"						t   __main__R   s    P 4nw 2abwRW   (   t   phaser.pipelineR    RI   R   R   R   RL   R	   t   libtbx.load_envRA   t   iotbxR   t   os.pathRD   RO   RT   t   NoneR-   Rg   R†   t   __name__R#   t   sgs(    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/test_jobs_new.pyt   <module>   s   )	H	K