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%s(RRRSR]RnR$RR#R(RRRsRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR%s   c Cs9t|_tg|jdtjD]}|j|j|jf^q"}|j }x|jdt jD]}|j d|dd||j|j|f|kr|j d|ddqknt j d|js|j d|ddqkn|j d|ddtjd |d |}tjd |qkWdS( NRERRs Testing %sspreviously exploredtothersnot in compositionsapplicable for extensionRRR(R!RnRRRRRRNRZRRt process_modelR&R^tcontainsRRSt attach_to( RRRRRtrecordsRRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's   1 (R:R;R<R%R'(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs tRotationSearchcBs)eZdZdZdZdZRS(s6 Performs rotation search for ensemble stages cCsg|jdtjD]}|js|^q}|sV|jd|ddd}nO|jd|ddt|t|dd}|jd|dd||S( NRERRsno candidates founds%s candidates foundRFcSs |jS(N(RG(RS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIJss selected %s(RRRSRRnR$RR#R(RRRsRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR%:s   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RR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR*s(R:R;R<R%R'R*(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs  t RefinementcBs)eZdZdZdZdZRS(s Refines peaks cCsg|jdtjD]}|js|^q}|sV|jd|ddd}nO|jd|ddt|t|dd}|jd|dd||S( NRERRsno candidates founds%s candidates foundRFcSs |jS(N(RG(RS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIss selected %s(RRRSRRnR$RR#R(RRRsRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR%s   cCs[t|_|jd|ddtjd|}|jj||jd|d|dS(NRRsStarting refinementRR)R(R!RnR&RStRefinementCalculationR{R5R6(RRRRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's  cCs6|jdt}|jj||jj|dS(NR (R*RR{R+R5(RRR RR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR*s(R:R;R<R%R'R*(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs  tAIcBs;eZdZdZdZdZdZdZRS(s MR solution controller cCs4d|_g|_g|_t|_t|_dS(Ni(tcpusR.t_queueRt_runningt Sequentialt_engine(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs     cCsxtrt}d|jkrx|jD]v}|jd|}|r(|jjd||jjd||jd|d||jjdt}Pq(q(W|jsPqn|j d|}|r| rt j dqqWdS(NiRs%s - action phases Candidate: %sRsAction complete i( R!RR.R%RPR&R'R"RtpollR,R-(RRtsuspendR0Rt new_results((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRxs"   c CsB|jd|d|d|d|}|jj||jdS(NR)tprotocolt executiont processing(RRRtspool(RR)RRRR1((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR6s  cCst}xt|jD]}|js.qntjdt}tj|j|j r|jjd|j |j j d|j d|d|j n0tjd|j |j jd|d|j |jj||jd7_tjdqW|S( NsPoll - job finisheds&%s - processing successful job resultsR Rtextras"%s - processing failed job resultsisProcessing complete (R"tlistt_jobstfinishedRPR&R!R$tlogfiletsuccessR)tprocess_successR Rtprocess_failureR+R(RRRR1((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR&s*        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evaluated. FinishingsALL DONEs+There were altogether %s MRCases consideredsREPORT - CAPTIONsG This partial structure is complete wrt current composition and modelssEVAL - FULL SOLUTIONsB All current models have been explored with this partial structuresEVAL - EXHAUSTEDsQ All selected partial structures are complete. This case can be considered solvedsEVAL - CASE SOLVEDs All possible extensions have been tried, but either not applicable or yield worse results than intermediate solutions. This may indicate that the solvent content is higher than expected and there are less molecules to findsEVAL - CASE EXHAUSTEDc Cstjjds"tjdntjdtjjd|_||_x?|D]7}t j d|d|d|}|j d|jqSWt dd|_ ||_||_tdd|_t|_t|_tjd d t||_|jjtj|r&tj|} n tj} | jtj d |jj!| t"|_#t"|_$t"|_%t&|_'dS( Ntpipelinet directoryRRUt space_groupRtfractiong?tnames PhaserAI.%ss %(message)s((tostpathtexiststmkdirRt Blackboardtabspatht_bbt_problemRRRtPSSelectRet_solverst _modellerstTPSelectt _tp_selectRAt_refineRt _controllertloggingt getLoggertidRbtsetLeveltINFOt StreamHandlerR t NullHandlert setFormattert Formattert addHandlerRRdRcRgR"t_all_models_present( RRURRR?RRtsymmRNthandler((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs6 !            cCs|jd|jdS(NR(RR(Rtbbobj((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR5scCs|jS(N(Rb(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRPscCsp|jjdxGtrY|j|jjdtjs|jj|jdPqqW|jjd|jj|jdt |j t |j |jjdt |j |jjdt |j |j jd|j }x||j D]q}|jjt||j jd |d |}|jjd t ||jjd |jjqWdS( NsStarting solution process...REsALL DONEsSolution process finishedsREPORT - CAPTIONs!%s were outperformed and rejecteds!%s has yielded complete solutionsRMRNROs* There are %s partials above the thresholds Best score: %s(RbR&R!RQRtread_instances_ofRRtMESSAGESR#RcRgRdReRfRhRiRjRk(RRORsRw((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRxs.         c Cs|jjd|jjdx*|jjdtjD]}|jq9W|jjd|j|jj d|jd|j|jjd|j j d|jd|j d|j|jjd|j |j j d|jd|j|jjd|jjd |js^|j jd|jd|j |_|jr^|jjd q^n|jjdtj}|jjd t|tg|jjdtjD]}|j^q}x|D]}|jjd |g|jjdtjD]}|j|kr|^q}g|jjdtjD]}|j|kr>|^q>}g|jjdtjD]}|j|kr{|^q{} |r|jjd |jjdn|s7|jjd|r|jjd|jj|n |jjd|jj||jqn|jjdt|g} x9t|D]+\} } |jjd| d|jjdt| j|jjdt| jt| jf|jjdt| jtg| D]0} | j | krt!| tj"r| ^q}g| D]} | j |krE| ^qE}g| D]'} | j#dtj"|krp| ^qp}|jjdt|t|f|jjdt|| j rd| rdtg| jD]3}tjj$d| jd| j%d|^q}|jr|j&|r|jj|j'd|j(j|| j)| qqdqdWt| t|kr|jj|j'd|jj||jqqqW|j j d|jd|j*gd|jg|jjdtj+D] }|^q*}|jjdt|xB|D]:}|jj,d|j-j%d |j-j.q]WdS(!NsStarting MR round...sClearing blackboard...REs%s - analysis startsRRPsAnalysis finished R.sEvaluating results...s All basic models are now presents!There are still %s MRCases activesTrial case: %ssC Partial structures have been selected that had already been testeds# These were not pursued any furthers) This case cannot be advanced any furthers1 All selected partial structures have been testeds) No partial structure was above thresholds1 %s initial partial structure has been identifieds" Partial structure %s - Statisticsis %s ensembles considereds %s tested for suitabilitys %s remain untesteds9 %s calculations have been done from %s tested ensembless %s calculations altogetherRNRZRsEVAL - FULL SOLUTIONsEVAL - CASE SOLVEDs! %s refined peaks have been foundRG(/RbR&R$RR Rt RoundObjecttdetach_from_blackboardRetanalyseRR2RRR t any_activeRRR#RtExhaustionRecordt identifiert InitialStageRNt RejectedStagetDescendantNodeRgR5RcRYRtuntestedRt isinstancet EnsembleStaget predecessort descriptorRZt issupersetRRdRRt RefinedStageRtfinalR(RRRMRt exhaustionsRNRStinitial_stagestrejected_stagestdescendant_stagestterminal_stagesRqtiniRtensemble_stagestimmediate_successor_stagestall_successor_stagesRtidentsRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRQs         %         ' !     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Thresholds peaks 2. Identifies ensembles that have not been tried before cCs ||_dS(N(t _fraction(RR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRasc Cs|jdtj}|s,|jddS|jdt||jd|}|jd||jdtj}|jdt|tg|jdtjD]}|j ^q}x|D]}|jd||j d|d |} |jd t| x| D]} |jd| tjj d|d | }||kr|jd tj d|d | } n+|jd tj d|d | d|} | jd|qWqWdS(NREsNo active cases availablesThere are %s cases activeRMs.Selection threshold for partial structures: %ss There are %s ensembles availables Processing %sRNROs/There are %s partial structures above thresholdRZs$This partial has already been testeds&Identified as potential starting pointRR(R RRR&R#RfRRtSelectionRecordRRiRRRR( RRRPRMRORRtpast_selectionsRNRRRS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfsB  %           cCsDtg|D]}|jj^q }|d|jt|S(Ng?(RRjRkRQR(RRMRsRl((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs+cCs5g|jD]$}||jd|kr |^q S(NRZ(RwR(RRNROR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRiscCsdS(NtPartialStructureSelect((R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR9s(R:R;R<RRRfRiR9(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRZs   4  RcBs)eZdZdZdZdZRS(s' Selects above threshold peaks cCs ||_dS(N(RQ(RR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRsc Cs |jdtj}|s,|jddS|jdt|tg|D]}|jj^qM}|d|jt |}|jd|xh|D]`}|j s||jjkr|jd|tj d|}|j d|qqWdS( NREsNo EvaluationStages availables$There are %s EvaluationStages activeg?s&Selection threshold for refinement: %ss Selected %sRR( R RtEvaluationStageR&R#RRttfRQRt is_solutiontRefinementStageR( RRRPRRRlRORt ref_stage((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs   + $cCsdS(NtMRPeakEvaluate((R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR9s(R:R;R<RRR9(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs  tKnowledgeSourcecBs;eZdZdZdZdZdZdZRS(sX Knowledge source: 1. functionality to disable if solutions have been found cCs||_||_dS(N(t _exhaustivet _selector(RtselectorR+((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs cCs|jd||jr/|jd|}ntg|jd|D]}|j^qE}|jdt|g|jd|D]}|j|kr|^q}|s|jdd}n:|jdt||jd|}|jd||jd|S( Ns%s - evaluation phasetbbs,Omitting stages belonging to %s solved casessNo candidates have been founds%s candidates has been foundtchoicess Selected %ssEvaluation finished ( R$R\tfetchRt solutionsRNR#RR](RRRPRtest solved_casesRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR%s" .   cCs8g|jd|jD]}|jd|r|^qS(NRER (R tBBOBJt acceptable(RR_R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRascCs2g|jdtjD]}|jr|^qS(NRE(R RRURW(RR_R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRbscCs |jjS(N(t __class__R:(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR9 s(R:R;R<RR%RaRbR9(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR[s     RcBs2eZdZejZdZdZdZRS(s> Analyse available ensembles for each trial structure cCs/tt|jdtdddtdS(NR^RFcSs |jS(N(tpartial_solution_score(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+(tsuperRRt SelectBestR"(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRsc Cs&|j}xt|jD]}|jd||jd|jr|jdtjd|d|}|jd|nG|jdtj d|j d |j d |}|jd||j d |qW|jd tj d|j d |j } | jd|dS( Ns Testing %sRsIt is applicable for extensionRtsearchRs It does not fit into compositionRNRZRs*Adding processing record for the candidate(R^RRR&RRRRRRRNRZR+RR( RRRRRPR^RRSRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR' s*            cCst|jS(N(tboolR(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfBs( R:R;R<RRReRR'Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs    "RcBsMeZdZejZdZdZdZdZ dZ dZ RS(s6 Performs rotation search for ensemble stages cCs8tt|jdtdddtd|_dS(NR^RFcSs|jjS(N(RkRG(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIQsR+g(RiRRRjR"RQ(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRNsc Cs|jj|tg|jdtjD]'}|jr)|jdtj^q)}||krv|j ddSt g|jdtj D]'}|j |kr|j |f^q}tj jd|} | |krW|j d|j dtj d|d|d|| jd t} |j d |jd | d |d |d|n`|j d|jd|dtjdi|jd6|jd6|jd 6di|d 6dS(NREs<Skipping search as a significant peak has already been foundR s=An equivalent search has been performed with a different casesCopying resultstexpertRSRR+s&Selecting peaks from rotation functionRkRRRPsStarting rotation searchR)RRRNRZR(t processed_byR5RR RRURWRRR&R\RRmRRRR!tevaluate_search_resultsR6Rtrotation_functionRNRZRk( RRRRRPRtsolved_ensemble_stagesR7t search_fort search_idRk((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR'WsN *  *             c Csatjjd|d|d|dt}|jdt|j|jd|d|d|dS( NRmRSt definitionsR+s+There are %s peaks in the rotation functionRkRR(RRtfrom_definitionsR!R&R#RRo(RRR RRPRk((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs   cCsdS(N((RRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCsc|jd|g|jD]}tjd|d|^q}x|D]}|jd|qEWdS(NRRR(RRRt RotationStage(RRkRRRRR7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRos + cCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<RRReRR'RRRoRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRGs  <   RcBsMeZdZejZdZdZdZdZ dZ dZ RS(s9 Performs translation search for rotation stages cCs;t|j|jdtdddtd|_dS(NR^RFcSs|jjS(N(Rtrf(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+g?(RiRgRRjR"RQ(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRsc Cs|jj|tg|jdtjD]'}|jr)|jdtj^q)}||krv|j ddS|j d|j d|dt j di|j d6|jd6|jd 6d i|d 6dS( NREs<Skipping search as a significant peak has already been foundsStarting translation searchR)RRRNRZRRR(RnR5RR RRURWRRvR&R6Rttranslation_functionRNRZR(RRRRRPRRq((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's& *      c Csatjjd|d|d|dt}|jdt|j|jd|d|d|dS(NRmRRtR+s.There are %s peaks in the translation functionRkR(RRRuR!R&R#RRo(RRR RRPRk((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs   cCsdS(N((RRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCsc|jd|g|jD]}tjd|d|^q}x|D]}|jd|qEWdS(NRRR(RRRtTranslationStage(RRkRRRRR7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRos + cCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<RRvReRR'RRRoRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs     RcBsDeZdZejZdZdZdZdZ dZ RS(s9 Performs packing analysis for translation peaks cCs2t|j|jdtdddtdS(NR^RFcSs|jjS(N(RRV(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+(RiRgRRjR!(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRsc Cst|jj||jd|jd|dtjdi|jd6|jd6|jd6di|d 6dS( NsStarting packing testR)RRRNRZRRR( RnR5R&R6Rtpacking_functionRNRZR(RRRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR'#s     c Cs|\}}|r|jdtjd|jjd|dd|dd|jjd|jj}tjd |d |}|j d |n |jd dS( NsPacking test passedRR0iR2iRVttfzRRRsPacking test fail( R&RRRRRVR{Rt PackingStageR( RRR RRPtpacksR{ttpeaktpstage((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR4s     cCsdS(N((RRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRHscCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfMs( R:R;R<RRyReRR'RRRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs     RAcBsDeZdZejZdZdZdZdZ dZ RS(s Refines structures cCs2t|j|jdtdddtdS(NR^RFcSs|jjS(N(RRV(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRI\sR+(RiRgRRjR!(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRYsc Cst|jj||jd|jd|dtjdi|jd6|jd6|jd6di|d 6dS( NsStarting refinementR)RRRNRZRRR( RnR5R&R6Rtrefinement_functionRNRZR(RRRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR'as     c Cs|\}}|jd||jj|jjg}|jdtj}|rtj d|j d|jj d|jj d|jj d|jj} n<tj d|j d|jj d|jj} tjdgt||D]!\} \} } | | | f^qd | } tjd | d |}tjd |d |}|jd|dS(NsRefined LLG: %.2fRERWRwtrfzRVR{RtRjRZRRRR(R&RZRRRRRRvRtSearchStatisticsRWRwRRVR{tPartialStructuretziptRefinedStructureRR(RRR RRPRtdefstensest rot_stagetstatsRRRRZtrefinedRY((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRrs. %     7   cCsdS(N((RRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<RRXReRR'RRRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRARs    & RcBsDeZdZejZdZdZdZdZ dZ RS(s Scores structures cCs)t|j|jdddtdS(NR^cSs|dS(Ni((R`((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+(RiRgRR!(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs c Cst|jj||jd|jd|dtjdi|jd6|jd6|jd6di|d 6dS( NsStarting LLG scoringR)RRRNRZRRR( RnR5R&R6Rtscoring_functionRNRZR(RRRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's     c Cs|}|jd||jd|r|jd|j}tjd|jd|jd|jd|d|j}t j d |d |}|j d |n |jd dS( NsLLG score: %.2fRGs,This peak conforms to expectations, acceptedRR0R2RVR{RRRs+Peak score is worse than expected, rejected( R&tacceptRRRRR0R2R{RtSpeculatedStageR( RRR RRPRtoldRRS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs      cCsdS(N((RRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<Rt ScoringStageReRR'RRRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs     RcBs5eZdZejZddZdZdZRS(s/ Identifies solutions based on Z-score g@cCs2t|j|jdddt||_dS(NR^cSs|dS(Ni((R`((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+(RiRgRR!t _z_threshold(Rt z_threshold((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs cCs|jj||j}|j|jkrGt}|jdnt}|jdtj d|d|}|j d|dS(NsThis is an outstanding peaksThis is an ordinary peakRRWR( RnR5RRR{R!R&R"RtIdentifiedStageR(RRRRRPR2RWRS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's    cCs ||jkS(N(Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<RR|ReRR'Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs   RcBs2eZdZejZdZdZdZRS(sE Superposes ensembles on solutions and creates new solutions cCs2t|j|jdtdddtdS(NR^RFcSs|jjS(N(RRV(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+(RiRgRRjR!(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCs|jj|t|tjr3|jddSt|jdtj}|sZt |j j }||ks~t |j |tj d|d|}|jd|dS(Ns/This candidate is not applicable (speculative) REttemplateRR(RnR5RRRR&RR RRaRRR+tTemplateSolveRepositoryR(RRRRRPRtusedtrepo((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR's     cCs|jo||jkS(N(RWRn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf2s( R:R;R<RRUReRR'Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR s    RcBsDeZdZejZdZdZdZdZ dZ RS(sE Superposes ensembles on solutions and creates new solutions cCs5t|j|jdddtt|_dS(NR^cSs|dS(Ni((R`((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIAsR+(RiRgRR!Rt_proxy(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR>s c Cst|j}|st|jdddt|d}|jd||jd||j}|j}|j } | j j |j s|jddSt g|j dtjD]} | j| f^q} tjjd | d |} tjjd |d | } | | krN|jd | | j}n| | kr|jd | | jj}n|jd y1|jjd | jd |j\}}Wn>tk r}|jd||jd|jdnXtjd | d |d|jd|}|jd||jd||j}|j}|jj}tjj|jj|j |j!j"f}||}t#j$d|dt#j%d|j&j'dt#j(d|j)|j*j'ddd|j+}g|j dtj,D]0}|j|kr*|j-|kr*|^q*}t.|dksxt|jd|jd|j/d|d t0j1d!i|d"6|j2d#6|d$6d%i|dd&6|d$6d'd(6dS()NRFcSs |jS(N(RG(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIKsRJiRsTrial ensemble: %ss/Template ensemble does not match trial ensembleREtfixedtmovings#Using pre-determined transformations,Using inverted pre-determined transformationsSuperposing ensemblessSuperposition error: %ssDiscarding this trialsAction completettransformationtrmsdsRMSD between ensembles: %.3fRR0telementsR2t coordinatesRVgR{isSuperposed solution generatedsStarting packing testR)RRRNRZRRRcSs d|kS(Ni((RG((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR(3RRRatsortR!R+R&RRRRRR\R Rt SuperpositionRRRtinverseRR2tpdb_fileRtrtRRNRUt unit_celltscitbxtmatrixR0t orthogonalizeR2t fractionalRRtMatrixRtelemst Fractionalt fractionalizeRR{RRkR#R6RRzRZ(RRRRRPRRRRRtsptsuperposition_fortforw_idtrev_idRttransfRRtsupRNtcelltsolutiont superposedt transformedRt ense_stages((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR'Gs       +                  !    0       c Cs|\}}|r|jdtjd|jd|dd|dd|jd|j} tjd |d | d |} | jd ||jd n|jd|jddS(NsPacking test passedRR0iR2iRVR{RRRRsSending peak for scoringsPacking test fails"Not pursuing this peak any further( R&RRRRVR{RRR( RRRRR RRPR}R{R~RS((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs"          cCsdS(N((RRRRRRP((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRscCst|jS(N(RlR(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRfs( R:R;R<RRReRR'RRRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR7s  o  t%RegularObjectCompletionInitiateExpertcBseZdZejZdejZdZ dZ dZ dZ dZ dZdZd Zd Zd Zd Zd ZdZRS(sI Finds incomplete regular assemblies in solutions completes them g@gh㈵>cCs_t|j|jdtdddtd|_d|_d|_d|_d|_dS( NR^RFcSs|jjS(N(RRV(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRIsR+i g @g333333?g+?( RiRgRRjR!t _max_foldt _spatial_sqt_angulart_axial(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs    cCs|jj|t|tjr3|jddSt|jjdkrb|jddS|jdi}|j}|j j j }xxt |j|j |jD]R\}} } |j|gjtjjd| jd|j| jqW|j} |j| jgjtjjd| jjd|j|jjg} x|jD]\} }t|dkr|jd| qng|jd |D]c}tjd | dtjd |j dtj!d |j"|j#d dd| j$^q}|jdt|qW| sj|jdn(tj%d|d| }|j&d|dS(Ns/This candidate is not applicable (speculative) is0Cannot identify operators from a single moleculesSorting candidate on ensemblesR0R2is Cannot identify operators for %stexistingRRRRVgR{s%s possible new positions foundsNo new positions foundtbaseRR('RnR5RRRR&R#RZRRNRURRR.R1RRtphaserR tOperatorRRRRRR0R2Rtpossible_further_moleculesRRRt get_rotationRRtget_translationR{t!RegularObjectCompletionRepositoryR(RRRRRPtdescription_withRRRRRRt possibilitiestensetcopiestopt identifiedR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR'sF    4     y  c s|}g|D]}|jd|^q }g}|ddxt|D]\}} | j} g||dD]}|| ^qs} dt| GHx0|jd| D]\} } d| | fGHg|jd| d | D]}|| ^q}d t|GHg|D]}|jd|^q }gt||D]@\}}tfd |jd|d |Ds9|^q9}d t|GH|j ||j g|D]}|jd|^qqWqLW|S(Ntpointg@iisConsidering %s operatorstopss Processing generator: %s-fold %sRtlengths"%s trial operators will be checkedc3s|]}|kVqdS(N((RHtd_sq(tclash_distance_square(sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pys G stotherss%s 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fractionstgcdR"RRtfloatRt length_sqRRRRR!(RRRtfold1tmult1taxis1tdisp1tp1tfold2tmult2taxis2tdisp2tp2Rtf1tf2tdiffRRttrans1ttrans2((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR s4   " c Cst|}d|ksttg|D]}|d^q(}tg|D]}||ddk^qKsttd|ttjg|D]}|d^q}d|ttjg|D]-}tjj |dddj d ^q}t ttjg|D]}|d^q}ttjg|D]}|d^q2|}t j dtjj||j|d||S( Nig?iiiiR0R2(ii(R#RaRR4R,R-R5RRRRRR RRt$r3_rotation_axis_and_angle_as_matrixR( RRtcountRRRt perpendiculartpnormtparallel((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR s  #31 ;/-  cCsF|jd|d|jd|jpE|jd|d|jd|jS(NRtangulartspatial(RRt_spatial(RRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRm s     csfd|DS(Nc3sM|]C}d|ddd|ddd|ddVqdS(iiiN((RHto(R(sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pys s((RRR((RsK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR} s cCs|jo||jkS(N(RWRn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf s(R:R;R<RRUReRtpiRtEPSILONRR'RRRRRRRRRRf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRs    @ % #   (  tModellercBs2eZdZdZdZdZdZRS(s^ Knowledge sources responsible for model generation Disabled if a solution exists cCs ||_dS(N(R](RR^((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR scCs|jr)|jjr)|jjddS|jd|j}|sX|jjddS|jjdt||j d|}|jjd||S(Ns*Disabled because solutions have been foundR_sNo candidates have been founds%s candidates has been foundR`s Selected %s( tquickRjtsolvedRPR$RRRR#R](RRRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR% s cCs8g|jd|jD]}|jd|r|^qS(NRER (R ReRf(RR_R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR scCs |jjS(N(RgR:(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR9 s(R:R;R<RR%RR9(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR! s    t FetchExpertcBs eZdZdZdZRS(s Fetches data cCs)tt|jdtdddS(NR^RFcSs |jS(N(RG(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRI s(RiR$RRj(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR scCs|jj||jjd|y|jd|d|}Wn(tk rj}|jjd|dSX|jjd|y"|jd|d|d|}Wn(tk r}|jjd|dSX|jd|d|d||jjddS( NsFetching data for %s...RRs Error: %ssParsing data for %s...trawR{sData fetch completed( RnR5RPR&Rat ValueErrortwarningtparsetpublish(RRRR%RR{((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR' s"(R:R;R<RR'(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR$ s ROcBsDeZdZejZdZdZdZdZ dZ RS(s Obtain sequence data cCs#tt|jt|_dS(N(RiRORRR(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR scCs|jjd|jS(NR(RRaR(RRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRa scCstj|\}}|r2|jjd|n|sDtdnt|dkri|jjdn|d}|j|_|S(Ns$Uninterpretable text encountered: %ssNo sequence foundis-Multiple reference sequences, keeping top onei(R tseq_sequence_parseRPR'R&R#RR(RRR%Rtseqstbadtseq((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR( s   cCs ||_dS(N(tsequence(RRR{R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR) scCs|j o||jkS(N(R.Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf s( R:R;R<RtBlastHitReRRaR(R)Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRO s     RNcBsDeZdZejZdZdZdZdZ dZ RS(s Obtain structural data cCs#tt|jt|_dS(N(RiRORRR(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR scCs|jjd|jd S(NRi(RRaR(RRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRa sc Cs|j}tjjd|dd}|j}d|d}|jj|}|j|t} | j st dt t fnt jj|jd|} |jjd| | j| tjd | S( Ntlinest source_infotPDBs chain '%s'is$No atoms selected for %s, chain '%s's%s.pdbs#Writing out selected atoms as %s...t file_name(Rtiotbxtpdbtinputtconstruct_hierarchytatom_selection_cachet selectiontselectR!tatomsR&tpdb_idtchain_idRRtjoint data_folderRPR&twrite_pdb_fileRt Structure( RRR%RRR6trootR9tasctnew_rootR3((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR( s    cCs ||_dS(N(Ry(RRR{R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR). scCs |j o|jo||jkS(N(RyR.Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf3 s( R:R;R<RR/ReRRaR(R)Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRN s     RMcBsPeZdZejZdZdZdZdZ dZ dZ dZ RS(s0 Calculates an alignment for a sequence ttargettmodelcCs,tt|jt|_d|_dS(Ntclustalw(RiRMRRRt_aligner(R((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRA s cCstjd|jd|jjj}tjd|jd|jj}|jjddjt|t|g\}}}|r|j j d|n|st dn|S(NRR.t sequencess s Warning: %ssNo alignment returned( R R.tTARGETRtMODELRR2R>RhRPR'R&(RRRtseq1tseq2talntlogterr((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRaH s     - cCstj|\}}|s+td|n|jdksCt|j|jdkr|j|jdksut|jj d|j|jg|_|j d|j dg|_ nt j |jkst|j jj |jj g|_|S(NsUnable to interpret: %siiisRearranging alignment...(R tclustal_alignment_parseR&t multiplicityRaRJtnamesRKRPR&t alignmentsRLRRR.(RRR%RRNR,((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR(` s  cCsg|jjdtjD]}|j|kr|^q}x;|D]3}|j|jjkrA|jjd|dSqAWtjd|d|j d|}|j d|jdS(NREsAlignment identical to %st blast_hittalignert alignmentR( RR Rt AlignmentRURTRWRPR&RHR(RRR{RRRTtaliR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR)x s    cCs|jo|jo||jkS(N(RyR.Rn(RR ((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf s( R:R;R<RR/ReRJRKRRaR(R)Rf(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRM8 s     RLcBsDeZdZejZdZdZdZdZ dZ RS(s Runs sculptor c Cstt|jdtddtjjf}tjdtj gdgd|tj dtj dd gd|tj j d d d|tjd tjgd|tjd gdtjjfg|_dS(NR^RFcSs |jjS(N(RURG(R7((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRI stdeletiont polishingt applicabletpruningtlevelitstartit completiontknown(RiRLRRjR tMacromoleculeSpecificstPROTEINtchiseltMainchainDeletetMDAGaptSidechainPrunetSPASchwarzenbachertResidueRenumbertTargett ResidueRenametAGACBetaUniformt CleanUnknowntUNKNOWNt _workflow(Rtmms((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR s"    c Cs|jj||jjd|jjd|j|jjd|jj|jjjf|j d|d|j d|jjj|j|j fd|jj|jj |jj fdS(NsRunning sculptor with:s Alignment: %ss Structure: %s, %sR)RRR(RnR5RPR&RWRURRyR3R6R2RVtidentity_fractionR(RRR((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR' s        cCstjjo|tjkS(N(R RURyRn(RR_((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRf sc Cs|\}}}tjj|j}tjdddtj}t}tj|}|j tj d|j |t j d|d|gd|jd|} |j||j|j|j} t} xE| jD]7} t| tjtjfr| j| jqqWx| jD]} | jq2W| jtjd |d d ||t|fd d } | j j!| t"| | | ffS(NRRR^s %(message)sRBRTtworkflowRPR3tlabels%s_%s_sculptor_%st extensionR5(#R4R5R6R7RtLoggerRRRRRRR R*Rot removeHandlertflushtclosetgetvalueRt modificationsRRdtDeleteInstructiontAttachInstructionR5t blueprinttexecutet regularizeR tautonameRRBR@R!(RR{R3RWRVRBRPt logstreamR tvrRt fingerprinttcommandtoutfile((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR2 s:              c Cs|\}}|\}}}g|jjdtjD]0} tj|kr4tjj|gkr4t^q4} x5| D]-} | j|krq|j j d| dSqqWtjd|d|d|d|d|} | j d|jdS( NREsEnsemble identical to %sRtidentityRtoriginRzR( RR RtSculptorEnsembletseRRt componentsRzRPR&R( RR RRRRzRRRRRRRF((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR s  0   ( R:R;R<RRXReRR'RfR2R(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRL s     ,RjcBs eZdZdZdZRS(s Selects best object cCs ||_dS(N(t_key(RRF((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyR& scCst|d|jS(NRF(RR(RR`((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyt__call__+ s(R:R;R<RR(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pyRj! s (Atphaser.pipelineRRRRRRtphaser.pipeline.proxiesRRRRRRRdR R R R R4R t iotbx.pdbt libtbx.utilsRt scitbx.matrixRRtsysR,R-RRttempfileRtobjectRR=RRRRRRRRRRR[RRRRRARRRRRR!R$RORNRMRLRj(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/phaser_ai_new.pytsr"         cQ)611--`#dQ'?6uX>P@*++%./\