xTc@ sddlmZddlmZddlmZddlmZddlmZddlm Z ddl Z ddl Z de fd YZ d e fd YZd e fd YZde fdYZde fdYZde fdYZde fdYZde fdYZde fdYZde fdYZde fdYZde fdYZd e fd!YZd"Zd#Zd$e fd%YZd&e fd'YZd(e fd)YZd*Zd+e fd,YZ d-e fd.YZ!d/e fd0YZ"d1e fd2YZ#d3e fd4YZ$d5e fd6YZ%d7e fd8YZ&d9e fd:YZ'd;Z(d<Z)d=Z*d>e fd?YZ+d@e fdAYZ,dBe fdCYZ-dDe fdEYZ.dFe fdGYZ/dHe fdIYZ0dJe fdKYZ1dLe fdMYZ2dNe fdOYZ3dPe fdQYZ4dRe fdSYZ5dTZ6dS(Ui(tdivision(tstage(t calculation(t mr_object(toutput(tSorryNt SelectBestcB s eZdZdZdZRS(s, Select best of possible candidates cC s||_||_dS(N(t_expertt_type(tselftexpertttype((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt__init__s cC sg|jd|jD]}|j|jkr|^q}|s\|jjddd}nx|jjddt|t|dd}|jjdd|jj |jjdt ||jj |S(NR tmsgsNo candidates founds%s candidates foundtkeycS s |jS(N(tscore(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt%ss Selected:( treadRRt processed_byRtdebugtNonetlentmaxtindenttstrtdedent(R tboardtcasetcontexttct candidatestselected((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt__call__s   (t__name__t __module__t__doc__R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs t SelectRangecB s eZdZdZdZRS(s+ Select best N possible candidates cC s||_||_||_dS(N(RRt_count(R R R tcount((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR 3s  cC sg|jd|jD]}|j|jkr|^q}|s\|jjddd}n|jjddt||jdddt ||j }|jjddx@t |d d D],\}}|jjd ||j fqW|S( NR R sNo candidates founds%s candidates foundRcS s |jS(N(R(ts((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyREstreverses Selected:tstartis%d: %s( RRRRRRRRtsorttTrueR%t enumeratetshort(R RRRRRRti((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR :s  $(R!R"R#R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR$.s t SuspendablecB s eZdZdZdZRS(s0 Suspend if certain objects are present cC s||_||_dS(N(t_markert _selection(R tmarkert selection((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR Ts cC seg|jd|jD] }|^q}|rE|jjdddS|jd|d|d|SdS(NR R sKnowledge source suspendedRRR(RR0RRRR1(R RRRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR Zs ((R!R"R#R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR/Os t FindEnsemblecB seZdZdejejfdejejfdejejfdej ej fgZ dZ dZ dZdZRS( s* Find ensembles for missing part sModels:s Collections:s Templates:sHomology search hits:cC std|dtj|_dS(NR R (RRtInitialtinspect(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR rscC s>|jj||jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt|x|j D]v\}}}|jjdtj d||jj |j d|d |d |d |d |d ||jj qW|jjdtjdddS(NR ttextsComposition analysistmessagetstatustdatasSpace group %st candidateRRRtintypetouttypesComposition analysis finished(RtaddRtverbosetsubtitletnotifytspace_group_symboltblankRtSCANStheadingRtfetch_and_identifyRt section_close(R R;RRRtcaptionR<R=((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt manipulatews(    c C sT|jjjd||jjd|}|jdddt|jjddt||jjddg}xt|dd D]q\} } |j j d | j s|jjdd | | fqn|jjdd | | f|j | qWxKt|dd D]7\} } |d |d| d| } |j d| qWdS(NR RcS s |jS(N(R(te((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRsR(R s Available: %dtR)itothers#%d: %s - not in missing compositions!%d: %s - applicable for extensiontinitialR<tindextobj(tproblemR:RR*R+RR?RR,tmissingtcontainst compositiontappendtwrite( R R;RRRR<R=t availabletacceptedRNROtst((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRFs&+   cC sdS(Nt EnsembleFind((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt__str__s(R!R"R#RtEnsembleRtModelCollectiontTemplatet ModelTemplatetHomologySearchHitt TemplateHitRDR RIRFRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR4fs   tRotationSearchcB sDeZdZdZdZdZdZdZdZRS(s6 Performs rotation search for ensemble stages cC s+tdtjd|j|_||_dS(NR2R3(R/Rt SuspensiontselectR6tcutoff(R Rd((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s c C sEtg|jjjdtjD]3}t|jtjr|jj|jj f^q}g|jdt j D]6}||j krq|j|j f|krq|^qq}|s|j jddd}nr|j jddt|t|dd}|j jdd|j j|j jd||j j|S(NR R sNo candidates founds%s candidates foundRcS s |jS(N(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRss Selected:(tsetRPR:RRtProgresst isinstanceRatpartialtensembleRR[RRRRRRRR( R RRRtprogt submittedsRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRcs"6'   c C s+|jj||jjdtjdd|jjdddd|jjdd|j|jjdtj|jjd|tj d|j d|j d |j d |j }|jjdtjdd |jjjd tjd ||jjd|d |d|dS(NR R7sRotation searchR8R9R:sSpace group %sRhRiRdsRotation job submittedRORtownertextra(RR>RR?R@RARBRCRRatcalculation_dataRhRiRdRGRPR:RURftqueuetsubmit(R R;RRRtcalc((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIs      "c C sddlm}|jjdtjdd|jjdddd |jjdd |j|jjdtj|jjdt||jjdtjg|j j j d |j D]}|j|kr|^q} t | d kst|j j j| d |jd|} |jjdd|jjd| j|j|j jkr|jjdd|j|j j jd| n|jd| d|d|d|d|dS(Ni(RR R7sRotation function processingR8R9R:sRotation function evaluationsSpace group %sR iitresultssLogfile:s4Rotation function valid for all space groups: storedROtresultRiRRR(tphaser.pipelineRRR?R@RARBRCRRPR:RRfRtAssertionErrortdeletetprocessRtlogfileRhtroottcleanupRUt place_peaks( R RRsRmRRRRqtptprogresstres((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRws8  "   c C s|jjddt|jxt|jddD]j\}}|jjdd|jjdd||ftjd|d|d |}|jd |q6W|jjdtjd d dS( NR sPeaks above threshold: %dR)iRKs%d: %sRitpeakRNROR7s%Rotation function processing finished( RR?RR:R,RtNormalRotationRURG( R RsRiRRRR.R|RX((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR{$s "   cC sdS(NRa((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ9s( R!R"R#R RcRIRwR{RZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRas   * tApplyRotationSearchResultscB s2eZdZdZdZdZdZRS(sS Reinstates existing rotation searches (only important for first molecule) cC s ||_dS(N(trotation_search_expert(R R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR Csc s|jjd|d|d|s+dSfd|jjjdtjD}y|j}Wn%t k r|j j dddSX|j j dd|fS( NRRRc3 sW|]M}t|jtjr|jjjkr|jjjkr|VqdS(N(RgRRaRhRi(t.0R~(R(sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys TsR R s*No search has been performed for this peaks+Selected rotation search has been performed( RR6RRPR:RRtResulttnextt StopIterationRR(R RRRtcalcstsearch((RsD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR6Hs  + c C s|\}}|jj|j|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjd||jj d |d |d |d |d |dS(NR R7sApply rotation search resultsR8R9R:s3Apply rotation search results for other space groupsSpace group %sRsRiRRR( RR>RRR?R@RARBRCR{(R R;RRRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIfs     cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ~s(R!R"R#R R6RIRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR>s    tTranslationSearchcB s;eZdZdZdZdZdZdZRS(s9 Performs translation search for rotation stages cC std|dtj|_dS(NR R (RRtRotationR6(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR scC s|jj||jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt|t |j j dkro|j d kro|jjdd |j d tjd |jjd |jjddd|jjd|jjddgd |d|d|d|t|_|jjdtjddnktjd|jd|j d|j}|jjdtjdd|jjd|d|d|dS(NR R7sTranslation searchR8R9R:sSpace group %siis?P1 space group with empty located part: skip translation searchtpeaksRitrotationt translationgttfttfztbfactorRRRsTranslation function finishedRhtrpeaksTranslation job submittedRlRRm(ggg(RR>RR?R@RARBRCRRRhRtspace_group_numberR{RtTranslationPeakRRiRtrftrfzR+ttranslation_doneRGRRRnRoRp(R R;RRRRq((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIs@ -               c C sR|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdtj|jd |}|jjdd |jjd|j |jjdd t |j |j d |j d |d|d|d|t |_|jjdtjdddS(NR R7sTranslation function processingR8R9R:sTranslation function evaluationsSpace group %sRrsLogfile:sPeaks above threshold: %dRRRRRs(Translation function processing finished(RR?R@RARBRCRRwRRxRR:R{R+RRG(R RRsRmRRRR~((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRws,       c C sx~t|ddD]j\}}|jjdd|jjdd||ftjd|d|d|}|jd |qWdS( NR)iR RKs%d: %sRRRNRO(R,RR?Rt TranslationRU( R RRRRRR.R|RX((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR{s  cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs(R!R"R#R RIRwR{RZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   0 tPooledPackingCheckcB s2eZdZdZdZdZdZRS(sI Performs packing check for translation stages pooling all peaks cC s%tdtjd|d||_dS(NR R R&(R$RRR6(R tpool((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s c C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjddt||jjdd |jjxJ|D]B}|jjdt||jjdd |j j |qWt j d|j d g|D]}|j^qd g|D]}|j^q3}|jj|jjdtjdd |jjd |d|d|dS(NR R7s Packing checkR8R9R:sSpace group %ss Pooled: %dRKtpartialsttpeakssPacking job submittedRlRRm(RR?R@RARBRCRRRRR>RtSinglePoolPackingCheckRnRhRRRGRoRp(R R;RRRRRq((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIs&      c C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jd |}|jjdd |jjd|jt |j t |kst xt |j |D]\}} |rd } t jd | d |} nd} t jd | } |jjdd| |jj|jjdt| |jj|jjdd|jd| t| _qW|jjdtjdddS(NR R7sPacking check processingR8R9R:sPacking check evaluationsSpace group %sRrsLogfile:tPASSRRtFAILSsPeak: %sRKROs!Packing check processing finished(RR?R@RARBRCRwRRxRR:RutzipRtPackedtClashRRRRUR+t packing_doneRG( R RRsRmRRRR~tdRtverdictRX((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRws0 !    cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ;s(R!R"R#R RIRwRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   #tSuperposeSolvecB sDeZdZdZdZdZdZdZdZRS(sV Finds ensembles that could be superposed on a solutions to get new solutions c sfd|jdtjD}y|j}Wn*tk ra|jjddd}nAX|jjdd|jj|jjd||jj |S(Nc3 s0|]&}|jr|jkr|VqdS(N(t significantR(RR(R (sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys GsR R sNo candidates founds Selected:( treaditerRtScoredRRRRRRR(R RRRRR((R sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR6Es%    c C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdd |jj||j st |jjdd |jjdd |j j }|j }g|jd tjD]-}|j |kr|j |kr|^q}g} xf|D]^}|jjd |j jszqSn|jjd |j j} | jrS| j|qSqSW|jjdd t| |jjdd x| D]} |jjdd| j | j |ks!t |jjzy@|jjd|j d| j d|jd|jj} Wn@tk r}|jjdd||jjddwnXWd|jjX|j j j| j jkr<|jjddtjd|j d|j!d| d|j"} |j#}nF|jjddtj$d|j d|j!d| } |j%}|jjdd|jjdd |j&j'd|d| d|| |fqW|jjdtj(dddS(NR R7sTemplate structure solutionR8R9R:sSuperpose solutionsSpace group %sRKs*This peak is significant and could be usedR RLsApplicable: %s casessReplacement ensemble: %sRRitcelltstreamsSuperposition error: %ssAlternative rejecteds1Different ensembles: do refinement before scoringRhtprotocols>Ensembles have the same template: no refinement before scoringsEvaluation job submittedRlRRms$Template structure solution finished()RR?R@RARBRCRRR>RRuRRiRMRRR[RSRRtoverlapt superposableRTRRt superpositiont substitutetuctbx_unit_cellt RuntimeErrorRtsuperpose_templateRtRefinedEvaluationRnRhtb_factor_refinementtprocess_refinedt Evaluationtprocess_unrefinedRoRpRG(R R;RRRRiRMRJtestagest applicableRtesRRqtmethod((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIZs   -         $              c C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|\}}} |jjdt||jjdtjdd |j|j d |} | j d | j d } } | s|jjdd |jjdddS|jjdd| d| d| j d|d|d|} |j d| |jjdtj dddS(NR R7s(Template structure evaluation processingR8R9R:sSuperpose solution evaluationsSpace group %ssReplacement ensemble: %sRriis!Generated peak fails packing testsDiscarding this solutionsAccepting this solutionRRittemplateRROs1Template structure evaluation processing finished( RR?R@RARBRCRRERiRwR:RURG(R RRsRmRRRRRRR~tis_pakRRX((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRws8       c C sE|jjdd|j|jftjd|d|d|dtS(NR s&Peak statistics: tf = %.3f, tfz = %.2fRiRRtrefined(RR?RRRt TemplatedtFalse(R RR:RiRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  c C sX|d}|jjdd|j|j|ftjd|d|d|dtd|S( NiR s2Peak statistics: tf = %.3f, tfz = %.2f, llg = %.2fRiRRRtllg(RR?RRRRR+(R RR:RiRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs( R!R"R#R6RIRwRRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR@s  ] ( tRotationPeakSalvagecB s2eZdZdZdZdZdZRS(s} Transfer good rotation peaks to the next round (if there is one) in order to save rotation function calculation cC std|dtj|_dS(NR R (RRR[R6(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s&|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdd |jj|g|j j d t j D]6}|j |jkr|jj|jkr|^q}|s(|jjdtjdd dS|jd d g}xqt|ddD]]\}}tjd|d|jd|} |jd| |j| |j jd|qTW|jjddt|tjdtd|d|} |jd| |jjdtjdddS(NR R7s-Previously located significant rotation peaksR8R9R:s8Reinstate significant rotation peaks found in last cyclesSpace group %sRKR s!No previously located peaks foundRcS s |jjS(N(RR(tr((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR&sR)iRiRRNROsReinstating: %d peakst conditionRt rotationss?Rotation searches are suspended until these peaks are processed(RR?R@RARBRCRRR>R:RRtHistoricRotationt structureRhRRiRGR*R,RtPreviouslyEstablishedRotationRURTRvRRbtRotationsExplored( R R;RRRthrtrelatedRRNtrpt suspension((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRI sD  !        cC s|jjdtjdd|jjddddtg|jdtjD]}|j^qQ}g|jdtj D]*}d |j j kr||kr|^q} |jjdd t | g} x|D]}|j } g| D]} | | j kr| ^q} | s"qn|jjdtjdd |jj|jjdtjdd |jj|jjdt||jj|jjdtjdd |jj| jdddtx~t| ddD]j\}} |jjdd|| j f|jjddtjd|jd| j }| j|qW|jj|jjqW|jjdtjdd| S(NR R7s&Rotation peak salvage - identificationR8R9R:s.Search for untested significant rotation peaksR g@s)Unexplored significant rotation peaks: %ds Associations:s Structure:sPeaks:RcS s |jS(N(R(R'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyResR(R)is%d: %sRKRRsRotation peak salvage finished(RR?R@RAReRRRRRRRRRMRERRRR*R+R,RtGenuineRotationRRTRG(R RRRt solutionstpostprocessingsR'tusedsRtunusedsRRMRtfoundR.throt((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR ?sL  .*   +          cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ{s(R!R"R#R RIR RZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   4 sc3 s*|] }|jjkr|jVqdS(N(RRR(RR'(R (sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys sR (tallRRRRRR(R ((R sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s(R!R"R#R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs t PeakEvaluatecB s2eZdZdZdZdZdZRS(sN Evaluate potential peaks that have been associated with a structure cC std|dtj|_dS(NR R (RRR[R6(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjd||jjdtj|jj||j}|j }g|j j d t j D]'}|jd |d |jr|^q}|s1|jjdtjdd dSx)t|d dD]\} } | jd |d| } |jjd| |jj|jjd| j|jj| jd|d|} |jjdd| jjtjdd} |jd| |jjd|d| d|| | f|j jd| |jjdtjqDW|jjdd|jjdtjdddS(NR R7sPeak evaluationR8R9R:sEvaluate potential peakssSpace group %sR RhRis!No previously located peaks foundR)iRNRsEvaluation job (%s) submittedRcS stS(N(R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRsRORlRRms;Rotation searches suspended until these peaks are processedsPeak evaluation finished(RR?R@RARBRCRR>RhRnR:RRt PotentialPeakt is_relatedRiRGR,tget_handler_forRRRRt __class__R!RRbRURoRpRv(R R;RRRRhR:tppRRNRthandlerRqR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIsH  '       c C s |jjdtjdd|jjdddd|jjdd|j|jjdtj|\}}} |jd | |jjd||jjdtj|jjd||jjdd |j|jjdtj|jd |jd |} | j s|jjdd |jjddt j d|j d|j} |j jd | ni|jjdd| j|jjdd| j|jjdd|jd |jd|d | |jjdtjdddS(NR R7sPeak evaluation processingR8R9R:sEvaluate peak rescoring resultssSpace group %sROs %s (trial)RsRrs!Generated peak fails packing testsDiscarding this solutionRRs %s (final)sPeak statistics: %ssAccepting this solutiontparents#Peak evaluation processing finished(RR?R@RARBRCRvRRwRRtFillFailureRecordRR:RUt statisticsRRG( R RRsRmRRRRiRRR~tfailure((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRws8      " cC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs(R!R"R#R RIRwRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   4 (t AmalgamationcB szeZdZdZedZedZedZedZedZ edZ dZ RS( s> Mix solutions if coming from the same starting point c C s|jjdtjdd|jjdddd|jd|r|jjdd d d lm}|j|j}|j d |r|jjdd |j }|j } q|jjdd|j }|j } nd.g}|j }|j } g|D]} | jjr| ^q} g|D]} | jjr+| ^q+} |jjddt| |jjdtjddg} d dlm}x| D]}|jjdd|jj|jjdt||jj|j}g| | D]$} |jjd| jr| ^q}|jjdd|jjdt|g}|jjd }|jdtjd|gdt}|jjx|D]}|jjdd|jjdt|j|jjd }|j|jkr*|jjdd|j|qn|jj |jj krh|jjdd|j|qn|jjdd|j|jf|jjzjy:|j!j"d|d|jd|j#d |jj$}Wn)t%k r}|jjdd!wnXWd|jjX|jdtjd|g}|j&d"|d#|sr|jjdd$|j|qn|jjdd%qW|jj|jjdd|jjdd&t||s|jjdd'|jjdd(qn|jjdd)t|| j'|d|jd*|d+|qW|jjdd| d,| d |d+|}|jjdtj(dd-|S(/NR R7sAmalgamation - identificationR8R9R:s&Find solutions that can be amalgamatedRs*Initial structure empty - undefined origini(tAlterOriginSymmatetoriginss4Floating origin - extracting rotation component onlys/Discrete origin - adding possible origin shiftsisSignificant peaks: %ds Processing:(tmatchings Structure:RLRKsPotential peaks: %dRRtcacheds%ACCEPTED: unique peak with same models)ACCEPTED: peak with non-alternative modelsRelating %s to %s:RRiRRsREJECTED: no 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||f|jjd d tj d |d |}|j |qW|S(NR)iiRiRRgRR s%d: %sRKRR( R,RRRt RotationPeakRiRRR?tExtractedRotationRT( RRRRR.RRRtexrp((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs      cC s!|jjddt||S(NR s!Number of extracted rotations: %d(RR?R(RRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs cC sg}xyt|ddD]e\}}|j}|jjdd||jdf|jjdd|jt||gqW|S(NR)iR s%d: %siRK(R,RRR?RRTt frozenset(RRRt associationsR.Rtcurrent((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  cC sRt|}|jjddt|g|D]}tjd|d|^q0S(NR s@Number of possibilities found (taking symmetry into account): %dt structuresR(ReRR?RRR(RRRtuniquestfs((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   cC s7tttj|d}t|jdddgS(Ntxtytz((RetreducetoperatorR>tboolt intersection(Rttokens((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRscC sdS(NR((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs( R!R"R#R t staticmethodRRRRRRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs    c C sl|jjd|s!tdny(|jd|d|d|d|}Wntk rg}tdnX|S(NRLsdifferent compositionRRiRRsno superposition(Ritsubstituteable_withRR(RRiRRRtspeakRJ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytsubstitute_peaks    cC sc|jd|stdny"|jd|d|d|}Wntk r^}tdnX|S(NRLsdifferent compositiont referencetmovingRsno superposition(RRt superpose(RRRRtsupRJ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytget_superpositions    tGeneratorSearchcB sMeZdZdZdZdZdZdZdZdZ RS(sb Recognizes generators (pure rotations around an axis) Only active in post-processing cC s ||_dS(N(t tolerances(R R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR scC sp|jjdtjdd|jjddddg|jdtjD] }|^qN}|jd d |jjdd t|x|D]}|jjdd |j |j d |j d|d|}|jjddt||r6|j dtj d |j d||jjddn|jjddqW|jjdtjdddS(NR R7sGenerator searchR8R9R:sFind generatorsR RcS s|jS(N(RN(R'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR/ssAnalysing %s structuress %d. structureRRRs"Total %s geometric relations foundROt relationss$Saved relations for further analysisRKsGenerator search finished(RR?t underlinedRARRtForSymmetryAnalysisR*RRNtfind_assemblies_inRRUtStructureRelationsRG(R RRRtlRtlabelR!((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR "s6  (             c C s?|j}g}x&t|jd D]\}}|jjdd|jjdd|d|f|jjdtj|jjdd|jj|jd|j }|j j } xHt|j|dd|dD]%\} } |jjdd| d| fy7t d | d |j d|d |j d |jj} WnFtk r} |jjdd | |jjdtjqnX|jjdd|jd|d| d|}|jjddt|x't|ddD]\}}|jjdd||jjdd|||jd|}y|jd|d | }Wn-tk r} |jjdd | qnX|jjdd|jjdd|jjdd||jtjdtjd |j d|d|| fqWqW|jj|jjdtjq&W|S(NiR sReference peak:s%s: %sisComparing with other peaks:RR)RRiRRs REJECTED: %ss ACCEPTEDRRLRs9 Testing %s symmetry equivalents for assembly memberships %s. potential mate:s %stops Generator:tsettingt generatortrelating(RR,RRR?RCRRtas_scitbx_rt_operatortinverseRitmatching_ensemble_infoRRRtpotential_assembly_members_forRtto_generator_formRTRt ModelRelationtGeneratorSettingR(R RRRRR!ti_refRR-teinfoti_otherRLRRJtmembersR.tmttransftgen((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR$Ssf  ! .!          c C s|j|jkst|jd|j}|jd|j}g}ddl}ddl}|jjj} |j} xs|j d|D]_\} } |j j | j |j } |j j g|j | D]}t|^q}tjjd| j|j j|jj j}|j j | j |j}x|jdddgddD]}||j j |}|j j | j| ||j }|jd |d | r`|jtjd |jd |d ||jddq`q`WqW|S(NRiRLtelementsiitrepeatitdeltatextentRiRRR(RiRutcreate_matching_mr_peakt positionalt scitbx.matrixt itertoolsR.R=Rtorthogonal_differences_betweentmatrixtcoltsgoptcentretroundRRtMatrixt orth_rotationtsqrRtelemsRtproductt orthogonalizetsufficiently_closeRTtPeak(R RRLRttmf_reft tmf_othert potentialstscitbxRAR=RtsymopR<t transformedtntshiftRRt neighbourtishifttnpos((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR/s6    ) (%    c C sy=tjjd|d|jjd|jjd|jj}Wntk r[}t|nXxU|j D]G}||j }|j |}|j d|d|j sitdqiqiW|S(NR(tmax_foldtangulartspatialR<R=s&Generated assembly larger than allowed( Rt Generatortfrom_scitbx_rt_operatorR R[tmax_angular_errortmax_spatial_errort ValueErrorRtnontrivial_seriesRFRNR=(R R(RiR*RJtoR R<((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR0s      cC s|j||jjkS(N(tlengthR tmax_relative_assembly_size(R R<R=((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRNscC sdS(NsGenerator search((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs( R!R"R#R R R$R/R0RNRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  1 K )  tGeneratorClassifyAveragecB s;eZdZdZdZdZdZdZRS(sO Averages near-identical generators Only active in post-processing cC s ||_dS(N(R (R R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjddddtg|jdtjD]}|j|j f^qQ}|jjdd t |tt t j g|jD]+\}}g|D]}||f^q^qg}|jjdd t ||jd |jd |} |jjdd t | xg| jD]Y\} } tjd| } x(| D] } | j d|| d| qlW|jd| qGW|jjdtjdddS(NR R7s&Generator classification and averagingR8R9R:sClassify and average generatorsR s4Analysing geometric relations data for %s structuress%s relations foundR!Rs%s clusters formedtaverageRtrelationROs!Generator classification finished(RR?R"RAtdictRRR%RR!RRRR>titemstmerge_equivalent_assembliestkeystGeneratorClusterRURG(R RRRRt analysis_forR'trelst origin_oft components_ofRhR6tgclusttrel((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s6  4 ;      c  s6t|}i}x|r1|j}|jjdd|jjd|j|jjdd|jjtjdfd}|jd|jj |fxt |D]}|jjdd|jjd|jy:t d|jj d |jj d |j d |jj}WnFtk re} |jjdd | |jjdtjqnX|jj jd |j} |jjdd| |jd| |f|j|qW|jjx_t|jddD]E\} } |jjdd| t| fdt| ks,tttjg| D]\} }| j^q<j}dt| ttjg| D]\} }| j^q}}tg| D]\} }| j^q}xc|r)t|}|j|i}g| D]!\} }| j|kr|^q||R*tlistRRiRRRRCRUttransformationtremoveRR,tclassesRRuRRR|t normalizeRFRzRR2R^tnewtdetermine_generator_foldtvalues(R R!Rt remainingt members_ofRRttrialRRJttrRNtclusterR(RtR|RFtunmerged_foldsthighestR{toftaverR6((R sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRl#s~          % +,(   2 9       cC s|s ttg|jD]}t|^q}x>t|dtD]*}|jjt|||krJ|SqJWtddS(NR(s$This statement should not be reached( RuRRRtsortedR+R tmin_fold_fractionR(R R{tvt highest_countR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  + cC sdS(Ns&Generator classification and averaging((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs(R!R"R#R R RlRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRgs   0 c tPointGroupDeterminecB sHeZdZdZdZdZdZdZied6ZRS(si Analyzes averaged generators and turn them into point groups Only active in post-processing cC s ||_dS(N(R (R R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjdddd|jdtj}|jjdd t|g}x_|jj D]N\}}||d |}|jjdd t||f|j |qW|jjdd t||jjdd |j d|d|} xA| D]9} |jjddt | j j|jd| q!W|jjdtjdddS(NR R7sPoint group determinationR8R9R:sDetermine point group symmetryR s%s generators foundtclusterss %s %s founds%s point groups founds"Merging subgroups into supergroupstanalysesRsSymmetry id: %sROs"Point group determination finished(RR?R"RARRRnRt METHOD_FORRkRtfind_supergroupstidR)t point_groupRURG( R RRRt averagedsRtnameRt symmetriesthighestsRO((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s*    # c C spg}xc|D][}|jtjdtjd|jjdtjd|jjd|jd|gq W|S(NR)RiRR|trelations_fromt formed_by( RTRtSymmetryAnalysistSymmetrySettingRhRit RotationAxisR*R(R RRtclust((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytfind_rotation_axess      cC st|}g}x|rt|dd}|jjdd|j|j||j|xvt|D]h}|jjdd|j|jd|r|jjdd|j|qq|jjddqqWqW|S( NRcS st|jjjS(N(RR)Rtseries(R'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRsR sHighest symmetry: %ss Testing: %sRLs CONTAINEDs NOT contained( ReRRR?R)RTRRRR(R RRRt supergroupsRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs    cC sdS(NsPoint group determination((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZss rotation axes( R!R"R#R R RRRZR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  $   cC s7tj}x!|D]}|jd|jqW|jS(sG Determines which molecules are related by a specific symnetry Ri(RtEquivalenceRelationChainR>R+R(R!tecR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt find_symmetry_related_assembliess  tSymmetryComparecB s)eZdZdZdZdZRS(sC Compares new symmetries with that has been located before cC s ||_dS(N(R (R R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjdddd|jjdtj}|jjdd t||jdtj }xpt |d d D]\\}}|jjdd ||jjdd |jj g}g} x|D]} |jjdd| y+|j d| d|j d|\} } Wn*tk r_} |jjdd| nX| r|jjdd| j| n| r|jjdd|j| qqW|jjtjd|d| d|}|jd|qW|jjdtjdddS(NR R7sSymmetry comparisonR8R9R:s1Compare found and existing point group symmetriesR s%s symmetries knownR)is %s. symmetrys#Compare with existing point groups:s Compare: %stexistingRRs REJECTED: %ss KNOWN CONTAINS NOVELs NOVEL CONTAINS KNOWNtanalysist contained_byRRROsSymmetry comparison finished(RR?R"RAR:RRRRRR,Rt"determine_containment_relationshipR)RRTRtSymmetrySetRelationAnalysisRURG(R RRRtknownRRNRttrial_containsttrial_contained_byRRRRRJR!((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sJ          c C std|jd|jd|jd|jj}|jjd|j}|jjd|d|j j d|j j }|jd|jd|j j d|j j }||fS( NRRRRRyRLt min_cos_angletmax_spatial_disp( RRiRRRRRURtapprox_containsR RwRa(R RRRRRRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRMs        (R!R"R#R R R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s  9tSymmetryCreationPolicycB seZdZdZRS(s$ Creates novel point groups c C s_|jjdtjdd|jjdddd|jjddg|jd tjD]}|jsa|^qa}|jjdd t|x|D]}|j j d |j j t g|j jjD]!\}}|td |f^q} |j d tjd |d| |jjdd|qW|jjdtjdddS(NR R7sSymmetry creationR8R9R:sRationalise point groupssCreate novel point groupsR s %s novel point groups identifiedROR!Rt assemblies_ins %s: SAVEDsSymmetry creation finished(RR?R"RARRRRRR:RURR)RjRRkRt NewSymmetryRG( R RRRtsrRtsratstructRpR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR ks,    :    (R!R"R#R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRfstSymmetrySubgroupPolicycB s&eZdZdZedZRS(sR Controls what to do with point groups that are not the highest available c C s|jjdtjdd|jjdddd|jjdd|jd tj}|jjdd t|xyt|d d D]e\}}|jjdd ||f|jj |j d|d|d|d||jj qW|jjdtj dddS(NR R7sSymmetry updateR8R9R:sRationalise point groupss Remove subgroups of new symmetryR s%s new symmetries createdR)is%s. %stsymmetryRRRsSymmetry update finished( RR?R"RARRRRR,RRRRG(R RRRRRNtns((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s     " cC st|jj}tg|jjdtjD]}||kr.|^q.}xx|jjD]j}||kr|jjd|n|jdtj d|d|jjj |j j dd|q\WdS(NR ROR)t supersymmetryR s DELETED: %s( ReRRRR:RRRRvRUtObsoletedBySuperSymmetryR)RR?(RRRRt moribundstsstpresents((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   (R!R"R#R RR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs tSymmetryUnsupportedPolicycB seZdZdZRS(sl Controls what to do with point groups that are too high, i.e. not found in current best models cC sB|jjdtjdd|jjdddd|jjdd|jd tj}ttt j g|D]}|j ^qsg}i}x>|D]6}x-|j D]"} |j | tj |qWqWg|jjd tjD]} | |kr| ^q} |jjdd t| xt| d d D]\} } |jjd | |jjdd| | |krtg|| D]} | jj^qdd}|jjdd||jjd |nd}|jjdd|jd tjd| d|q?W|jjdtjdddS(NR R7sSymmetry removal - unsupportedR8R9R:s@Remove point groups with symmetry not found in current solutionss(Remove supergroups not supported by dataR s%s symmetries not detectedR)iROs %s: REMOVEDRcS st|jjS(N(RRR(R'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRssHighest subgroup symmetry: %ssNo subgroup symmetry detectedR)RsSymmetry removal finished(RR?R"RARRRReRRR>RRRt setdefaultR:RRR,RvRRR)RURtSymmetryDowngradeRG(R RRRtssrasR't subgroupst supergroup_ofRttsymmRRRNtraR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sB  . $  #     (R!R"R#R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRstSymmetryUpdatecB s)eZdZdZdZdZRS(s0 Handles updates to existing symmetries cC s||_d|_d|_dS(Ng?gGz?(R RaRu(R R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s  c C s|jjdtjdd|jjddddi}xW|jdtjD]@}x7|j|jD]%}|j |t j |j qkWqTW|jjdd t |xt|jjdtjd d D]\}}|jjd ||f||kr%|jjdd qn|jjttjg||D]} | j^qFt } |jd|d| d|} |jj| |jkr|jjddqn|jjddi} xK||D]?} x6| jjD]%\}}| j |gj|qWqWtg| jD]!\}}|td|f^q.}|j}|jdtjd|d|jd|| |_qW|jjdtj dddS(NR R7sSymmetry updateR8R9R:sUpdate existing symmetriesR s%Up to %s symmetries could be affectedR)is%s. %ssNo updateable elementsRRRsSkipping this symmetrys(Replacing original with updated symmetryR!ROR)tpreviousRsSymmetry update finished(!RR?R"RARRRRRRRReR>RRR,R:RRRRtor_Rtupdated_point_groupRRRRkRRjRRUtSymmetryUpdateRecordRG(R RRRt analyses_fortssraRRNRtaRtupdatedRRRR!RRpRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s^  ' 1       !4       c  s|jjddt||jjddg}x|D]x}y7td|jd|jjd|jd|jj}Wntk r}q=nX|j |jj j d|j q=W|jjdd t||jjdd g}xt |jjd d D]\} } |jjdd | g} xv|D]nfdt| j| jD} y| j} Wntk rq;nX| j j d| q;W|jjddt| | rb|jjddtjd| jjdttjg| D]}|j^qjddt| ttjg| D]}|j^qC}n|jjdd| j}|j |q W|g|jjD]} | j^qkr|jjdd|jS|jjdd|jjd|S(NR s%s related generators founds Transforming to common referenceRRRRRys%s generators transformeds+Matching with point group generator classesR)is %s. classc3 s?|]5\}}jd|djdjr|VqdS(RLRuRaN(RvRuRa(RtgR((R9R (sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys ~s    s%s generators matchsAveraging spatial componentsRzR|RFg?sUsing original operators2No generator updated, keeping original point groupsForming point group from basest generators( RR?RRRiRhRRRRTR*RURR,Rtgenerator_classesRRt operationsRRRR^tstandardRzRRR>R|RRFtfrom_generators(R RRRt transformedsRRRJtbasesRNtgcR t searchgentstdopR(Rh((R9R sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR]s\     ( (   %, + (R!R"R#R R R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s  HtSpatiallyEquivalentMatchingPeakcB s#eZdZedZdZRS(sR A matching-compatible class that takes care of superpose transformations c C sddlm}||_||_||_||_|rO|j} |j} n|j} |j } |j j d|jj j d|jjd|jd|jjjd|d|d | d | |_||_||_dS( Ni(RRRtcrystalRitdmint multipliertdetail_positiontdetail_orientation(RRRRRRtcached_rotation_differencestcached_position_differencestsimple_rotation_differencestsimple_position_differencestMRPeakPOt phaser_styleRRCRRiR.R]RR( R RRRRRRRRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s*              c c sy7td|jjd|jjd|jd|j}Wntk rR}tnXddlm}|jj d|j j |j }|j jd|jjd |j j j|jjd |j d |jjjd |jd |j}x"|jjd|D] }|VqWdS(NRRRRi(RRRRRRiRRRL(RRRiRRRRRRR,RRRRRRRKt fractionalizettR.RRR]toperations_between(R RLRRJRt superposedRUR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs(          (R!R"R#RR R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs tSymmetryTolerancescB s)eZdZdddddddZRS(s6 Small container class to hold all tolerances i g333333?g?gGz?g@g333333?cC s:||_||_||_||_||_||_dS(N(R[R`RaRwRfR(R R[R`RaRwRfR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s     (R!R"R#R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRstLocalSymmetryExpertcB s,eZdZeeeedZdZRS(sP A wrapper class to contain all symmetry-related experts for scheduling cC st|_td|jtd|jtd|jtd|jg|_|rm|jjtn|r|jjt d|jn|r|jjt n|r|jjt ndS(NR ( RR RRgRRtactionsRTRRRR(R tadd_new_symmetrytremove_subgroup_symmetrytremove_unsupported_symmetrytupdate_known_symmetry((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR  s c C sb|jjdtjdd|jjdddd|jjdtjddg||D]}|jjrb|^qb}xt|d d D]{\}} |jjdd ||jj|jjdt | |jj |j d t j d | jd|qWx*|jD]} | d|d|d|qW|jjdtjddgS(NR R7sLocal symmetry analysisR8R9R:s.Analyse solutions to identify local symmetriessStructure selectionR)is%d. Structure:RORRNRRRs Local symmetry analysis finished(RR?R@RAR"RRR,RRRRURR#RRG( R RRRRRR'RRNtsoltaction((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR 2 s,   )      (R!R"R#R+R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s  c!C sddlm}|j}|j}g|jD]K}td|d|jd|jjd|d|j j j d|d t ^q2} t |j} tt| |j} tt|j| } g} x| re| j}gg}xt|jd d D]\}}|jjd d |y4td|jd|jd|jd|jj}Wn-tk r}|jjd d|qnX|jd||j}g}x|jD]\}}||}tjd|dtjjd|jjd|j|j d|j!}td|d|jd|jjd|d|j j j d|}|j"|qW|j#dg| D]}| |^qjd|}g|j$d|D]\}}|^q}|jjd dt%|d |j"|qWgt&|dt%D]}| |^q} |jjd dt%| d x| D]}| j'|q7W| j"|g| qW|jjd dt%| | S(Ni(RRRRRRRRR)iR s Anchor %sRRs REJECTED: %sRRiRR:RRRRtoverlapss members: %sRs"Largest association has %s memberss Number of associations found: %s((RRRtmatching_crystal_infoRRRRRRPt xray_datat resolutionR+ReRjRR}R,tanchorsR?RRiRR,RRRORRHRRKRRRRTRtpairsRRR(!RtassemblyRRRRRRRttmfsRtpeak_forttmf_forR theadt alternativesRNtanchorRRJRttrialstenseR(tfinaltptmfR|RR&RtassocRtlargest((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyt.partition_structure_according_to_membership_inZ sn   X   "           +!)   cC s|jjddtS(s1 Accepts any assembly without any checks R s+Accepting assembly (no condition specified)(RR?R+(RR RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytAcceptAssemblyStrategy scC s|jjddtS(s1 Rejects any assembly without any checks R s+Rejecting assembly (no condition specified)(RR?R(RR RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytRejectAssemblyStrategy stAcceptObservedAssemblyStrategycB s#eZdZddZdZRS(sF Accepts if the assembly has been observed in any structures g@cC s ||_dS(N(R(R R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjddt|j}|jjdd||jjddt|xt|ddD]\}}td|d|d |d |d |j}tg|D]} t| ^q} |jjdd || f|| kri|jjdd tSqiW|jjddt S(NR s+Accepting symmetry if full assembly presentsFull assembly has %s memberss#Testing membership in %s structuresR)iRRRRRs-Structure %s: largest assembly has %s memberssFull assembly foundsFull assembly NOT found( RR?Rt descriptionR,R RRR+R( R RR RRt member_countRNRR RR ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s0     %   (R!R"R#R R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s tAssemblyCreatecB sMeZdZdZdZedZedZedZRS(s( Creates models with symmetries cC s ||_dS(N(tis_valid(R R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR  sc C s|jjdtjdd|jjddddtg|jjdtjD]}|j ^qT}|jjdd t |g|jjdtj D]}|j |kr|^q} |jjdd t | g||D]}|j jr|j ^q} xt| d d D]\} } |jjdd | | ftjjd| jd| j dtj} |jd| d| d|d|r|jjdd|jjd| |jdtjd| q|jjddqW|jjdtjddgS(NR R7sAssembly creationR8R9R:s,Create assemblies from identified symmetriesR s$Current assemblies use %s symmetriess0%s symmetries not used in assemblies are presentR)is%s. %sRiRtstrategyRR RRs ACCEPTEDROs REJECTEDsAssembly creation finished(RR?R@RAReR:RRtAssemblyRRRRRRR,tSimpleRitRefineStrategyRRUtNewAssemblyRecordRG(R RRRRRRRR'RR RNR)R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR  sB  1  ,       cC s |dtS(NR(R(tcls((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytAlwaysB scC s|dtS(NR(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytObservedH scC s |dtS(NR(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytNeverN s( R!R"R#R R t classmethodRRR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s   <tAssemblyRemovecB s)eZdZdZdZdZRS(s2 Removes models with obsoleted symmetries cC s|jjdtjdd|jjdddd|jjdtjdd|jd |d |d ||jjdtjdd |jd |d |d ||jjdtjdd gS(NR R7sAssembly removalR8R9R:s+Remove assemblies with obsoleted symmetriessSubgroup symmetriesRRRsSupergroup symmetriessAssembly removal finished(RR?R@RAR"tremove_subgroup_symmetriestremove_supergroup_symmetriesRG(R RRRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR Y s(       cC stg|jdtjD]}|jj^q}|jjddt|xx|j jdtj D]^}|j |krj|jjdd||j j d||j dtjd|qjqjWdS(NR R s%s symmetries obsoleteds%s: symmetry obsoleted, removeROR(ReRRRR)RRR?RR:RRRvRUtAssemblyRemovalRecord(R RRRRVt obsoletestassem((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR z s.   c C sbtg|jdtjD]}|jj|jf^q}|jjddt |x|j jdtj D]}|j |krs|jjdd||j j d||jdtjd|||j }|dk rZ|jjdd|tj d|jd |jd |j}|j jd||jdtjd|qZqsqsWdS( NR R s%s symmetries downgradeds%s: symmetry obsoleted, removeRORsReinstating subgroup: %st definitionsRR(RjRRRR)RRRR?RR:RRRvRUR"RR%RR( R RRRtdgt downgraded_toR$t replacementtr_assem((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR! s.7             (R!R"R#R R R!(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRT s ! tAssemblyUpdatecB seZdZdZRS(s( Updates models with symmetries c C s$|jjdtjdd|jjdddd|jjddtg|jd tjD]}|j|j j f^qd}|jjdd t |xY|j jd tj D]?}|j|kr|jjdd |||j|_qqW|jjdtjdd gS( NR R7sAssembly updateR8R9R:sUpdate symmetry for assembliess9Update assemblies according to changes made to symmetriesR s%s updates availables %s: UPDATEDsAssembly update finished(RR?R@RARjRRRRR)RRR:RRRG( R RRRRRRt update_forR$((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s$   7 (R!R"R#R (((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR* stSearchModelMaintenancecB s_eZdZdZdZdZdZedZedZ edZ RS(sE Creates/removes AssemblyEnsembles as dictated by Assemblies cC s ||_dS(N(R(R R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjdddd|jjdtjddg||D]}|jjrb|j^qb}|jd |d |d |d ||jjdtjdd |jd |d |d ||jjdtj ddgS(NR R7s%Search model assembly and maintenanceR8R9R:s)Creates and search models from assembliessNew assembliesR RRRsObsoleted assembliess!Search model maintenance finished( RR?R@RAR"RRtadd_new_assembliestremove_deleted_assembliesRG(R RRRRRR'R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s,   ,    c C sUtg|jjdtjD]}|j^q}|jjddt|g|jjdtj D]}||krj|^qj}|jjddt|xt |ddD]\} } |jjdd| | f|j d| d |d |d |r:|jjdd |jj d tjd| q|jjddqWdS(NR R s Current models use %s assembliess,%s assemblies not used as models are presentR)is%s. %sRR RRs ACCEPTEDROs REJECTED( ReR:RRtAssemblyEnsembleRRR?RRR,RRU( R R RRRRJRRRRNR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR- s&1     cC std|jdtjD}|jjddt|x\|jjdtjD]B}|j |kr[|jjdd||jj d|q[q[WdS(Ncs s|]}|jVqdS(N(R(RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys * sR R s%s assemblies deleteds%s: removed search modelRO( ReRRR"RR?RR:R/RRv(R RRRtdeletedsR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR.' s"cC s |dtS(NR(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR4 scC s|dtS(NR(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR: scC s |dtS(NR(R(R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR@ s( R!R"R#R R R-R.RRRR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR, s  % # tAssemblyModelCreatecB sheZdZdZdZdZdZdZdZdZ dZ d Z d Z RS( sU Creates aggregate models from assemblies Only active in post-processing cC s7|r|j|_n |j|_d|_d|_dS(NgGz?g?(taccept_if_observedtacceptt accept_anywayRR(R t observe_first((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR L s   c C s|jjdtjdd|jjdddd|jjdtj}|jjdtj}|jjdd t |x|D]}|jjdd ||jjdtj dd x|D]p} |jjdd |jjd| |j d |d| j d|s"qn|jjdd|| _ PqW|j d|d|rtjd|} |jjd| n|jjdtjqW|jjdtjddgS(NR R7sModel assemblyR8R9R:s%Create models according to assembliesR sAssemblies: %ssProcessing: %ssComparing with existing modelssTrial:RRRs*There is a model for this assembly: UPDATERROsModel assembly finished(RR?R@RAR:RRtRegularEnsembleRRR"RRR3RURCRG( R RRRRRRt assembliesR$tregtreg_ense((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR X s8     !   cC s|jjddtS(NR sNovel assembly: CREATE model(RR?R+(R RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR4 scC s;|jr |jjddtS|jjddtSdS(NR s'Novel assembly (observed): CREATE models$Novel assembly (unobserved): DISCARD(tpresentRR?R+R(R RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR2 s  c C s|j}|j}t|t|krA|jjddtS|jjdd|d\}}xt|ddD]x\}\} } y1|jd|d| d |jd |jj} Wnt k r} qwnX|jjdd |||f| | ff|dg|D]} | | | fkr | ^q | j f}x|j d |d |D]\}}}|jjdd|r|j |dnd|r|j |dndf|dkrS|jjddPqSqSW|jjddtSqwWtS(NR sContaining assembly smallers Finding seed:iR)iRRRRs Seed: 1 vs %stmatchRsMatch: %s vs %ssn/as5Unmatched component in larger assembly, dropping seedsAll components match(RRRR?RR,tensemble_relationRRRRtassignRNRR+(R RRRt left_desct right_desctl_ensetl_optr_indextr_ensetr_opRRJtriR;R&RR'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sB  %  ( ( $  cC s%tjjd|d|jd|jS(NRyRR(Rt PointGrouptapprox_identity_operationRR(R R(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRG s  cC s:|jd|stdn|jd|d|d|S(NRLsdifferent compositionRRR(RRR(R RRRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR< s   cc s|\\\}}\}}}}} ||f||f| fV||| j} g|D]\} } | | | f^qY} xq|jd|d| d|D]Q\}}}|dk r|| kst|| j|}n|||fVqWdS(NRRR(R-RRRuRN(R R;RR@RARCRDRRRR8RJR(tr_transfR&Rts_op((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR= s$). c c st|}x|D]\}}|j}x|D]\}} y1|jd|d|d|jd|jj} Wntk r} q2nX|jd|| | jr2|j || f||f|| f| jfVPq2q2W||fddfVqWx|D]} d| dfVqWdS(NRRRRR(( ReR-R<RRRRRGRRR( R RRRtcopytref_ensetref_opR-t trial_ensettrial_opRRJR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s&     cC sdS(NsModel assembly((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ s( R!R"R#R R R4R2RRGR<R=RRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR1F s /  6  !tObjectCompletioncB sDeZdZdZdZdZdZdZdZRS(s1 Adds molecules to incomplete assemblies cC s d|_dS(Ng@(R(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR  sc C s|jjdtjdd|jjdddd|jjdtj|jjjdtj}g|D]}|j j rp|^qp}|jjdd t ||jjdtj dd g|jjdtj D]B} | jj|jd | jd |j|jd | j f^q} g} x[|D]S} |jd | j d|d|d|} |jd | j dt}g}xz| D]r\}}|jd |d |d| d|d|s|j||fq|jjd||jjddqW|jjddt |xU|D]M\}}tjd | j d |d|}|jjd|| j|q'W|jjddq8W|jjdtjdd| S(NR R7s"Object completion - identificationR8R9R:s%Find assemblies that can be completedR sSignificant peaks: %ds Processing:RRRR7RRRtfailuress REJECT: know failures%s missing molecules filled inRRKsObject completion finished(RR?R@RAR:RRRRPRRRRERRRiR>RRtcomplete_assemblies_inR+tis_known_failureRTRORG(R RRRRRR7R'RtrecRPRrRt generatedsttrial_structure_tmfRRtstratRtroc((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR $ s\  %^              c C sg}x|jD]}|jjd||jjd|jss|jjdd|jjdtjqny1|jjd|jd|jd|jj}WnBt k r}|jjdd|jjdtjqnX|jjdd|j d ||j } g} xy|j D]n\} } | | } | j tjd | d tjjd | jjd |j| jd|j|jfq%W|jjddt| |jjdtj|j| qW|jjddt||S(NR RLs! REJECTED: different compositionRRRs REJECTED: no superpositions2Generating possible molecules using current anchorRRiRR:RRs %s peak generateds+Total %s peaks generated from this assembly(RRR?RiRRCRRRRR,RRRTRRORRHRRKRRRRRR(R RRRRRTRRRJRtcurrentsRR(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytprocess_assemblyu sF        c)  s|jjdd|jj|jjd||jj|jjdtjtjdd}x|jD]}|jjdd|jj|jjd||jj|jjdtj|jjdd|jjdtjg}xt|ddD]\}} |jjdd || f|jj|j |j d |d | d |j d ||jjdtj|jjqW|jjddt ||jjdtjxK|D]C\} } |j d | d|j} |jd| | f| fqWqxW|jjddt |j|jjdtjg} |jd|dtd|j}tg|jD]} | j^q}ddlddlddlm}|jjddxt|jddD]\}}|s&t|jjdd|t |f|j\\}}}|j}|jj}|jj g}j j!|j"g}|j#g}|g}x'|D]\\} } } t$|j%d| jdfd\}}t&|j'd| jjdfd\}}|j(|j)j j*| jj |j+j j!|j,| j"}|j(|j j!g|d|D]} t-| ^q|j(| j#|j(| qWj.j/|}!dt |t0t1j|}"dt |t2|}#t&|dd}$tj3d|jd tj4j5d!|!d"|"j6d#|#}%|jjdd$|jjd|%x.|D]}&|%jj7d|&sqny7|j8j9d |%d|&d |j d%|jj:}'Wnt;k rqnX|j<d&|d'|j d |'d|jg}(t=|j>d(|(r|jjdd)|jjdtjPqqW|jjdd*|jjdtj| j(|%|$fqW|jjddt | | S(+NR s Structure:RicS st|djd|dS(NiRL(RR(RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR ss Trial peak:sProcessing assemblies:R)is%d: %sRRRRs'Total %s peaks generated for trial peakRRxs+Total %s peaks generated for this structureRRi(RsMerging quasi-equivalent peakssCluster %d: %d elementsRLRc sjj|djS(Ni(RCRDt length_sq(R|(RS(sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc sjj|dS(Ni(tmatht*r3_rotation_cos_rotation_angle_from_matrix(R|(RS(sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sig?cS s |jS(N(tcoverage(R'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sRiRR:RRsAveraged peak:RRRRs"REJECT: present in known structuretACCEPT(?RR?RRRCRR~RR,RRYRRR>RR>RRR+ReRit scitbx.mathR@RRRRuR}R?R]t orientationRRCRDRRtminRBRtrotation_differences_betweenRTRIRJRRERGR[t1r3_rotation_average_rotation_matrix_from_matricesRRtsumRORRHRKRRRRRRRR()R RR7RRRRRXRNR$R|R'RRRtstructure_ensemblesRRtrefRVtrtmftref_positref_oritrotsttrastbfacststratsRTR<tpgoptrotmatRRVtrotttratbfacRRRtsub_peakR((RSsD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRQ s           $   %  %      *8            c C sddlm}x|D]\}}} |jjd|sAqny7|jjd|d|d|jd|jj} Wnt k rqnX|j d| d|j } t | j d|sqn|jd |jd |d | } tt| t| krtSqWtS( Ni(RRLRRiRRRRRR(RRRiRRRRRRRR>RRRRRRRR+R( R RRRPRRRRtp_tmfts_tmfRsRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRRJ s,      cC sdS(NsObject completion((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZo s( R!R"R#R R RYRQRRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRO s  Q 9 %t CoordinatorcB s)eZdZdZdZdZRS(s Manages suspensions cC s2g|jdtjD]}|jr|^qS(NR (RRRbR(R RRRR'((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR6y scC s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdtjddxJt|d d D]6\}}|jjd ||f|jd |qW|jjdtj dd dS(NR R7sProcess coordinationR8R9R:sSpace group %ssExpired suspensions:R)is%s: %sROsProcess coordination finished( RR?R@RARBRCRER,RvRG(R R;RRRRNR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRI s   cC sdS(NRv((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZ s(R!R"R#R6RIRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRvt s  t EnsemblercB s2eZdZdZdZdZdZRS(s Runs ensembler cC sAtd|dtj|_ddlm}|jj|_dS(NR R i(t ensembler( RRR\R6RRxt PHIL_MASTERtextracttparams(R Rx((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jj||jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdd|j d |j d |d |}||j _ |jjdd |j j |j }g|jd tjD]}|j |kr|^q}tjd|d|dt|d}|jd||jjdtjdddS(NR R7sModel generation - ensemblerR8R9R:sSpace group %sRKRRRsEnsemble #%d generatedR RMR<RNiROsEnsembler finished(RR>RR?R@RARBRCRRwRRiRNRMRRR[RRURG( R R;RRRRiRMRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRI s4         c  s|jdk r)|jjdd|jS|jjjd|tjd|jj}|j }|j |j j _ ddl m}y+|jd|dgd |j d |}Wn7tk r}|jjdd |td |nXg|D]} | jj^q} xSt|| D]B\} } | jj| jj| j} | jj| qW|j j j rtd |Dst|jdd|jdtj|jd|d| d |ny/|j dd|j!d|d| d |} Wnt"k r}t|nXt#| t#|ks>tt$t|j%|j&tfd|Ds{tg|D]} | j'j(^q}t)j*d| d|d|j+}|jjj,d||S(NR sThis entry has been processedRORi(Rxtpdbst alignmentsR{tloggersEnsembler error: %ss Ensembler: %scs s|]}t|dVqdS(tensembler_trimming_maskN(thasattr(Rtinfo((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys ssTrimming chainstinfostchainsRys ensembler_%dc3 s!|]}|jjkVqdS(N(tpdbR(RR(trmsd_for(sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pys strmsdsRS(-RiRRR?RPR:Rvt SingleStreamRt pdb_objectsttrimR{t configurationRRxRwRRtchaint detached_copyRtensembler_rotationRKtatomst extract_xyztensembler_translationtset_xyzRRuRRCt trim_chainst)write_chain_and_model_sorted_output_filesRNtIOErrorRRjR|RRRRtMultifileEnsembleRSRU(R RRRR~R|RxRRJRRRtsitest file_namest chain_rmsdsRi((RsD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRw sZ    "     "#  cC sdS(NsModelGeneration (ensembler)((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs(R!R"R#R RIRwRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRw s   ( FtSculptorcB sAeZdZdgdZdZdZdZdZRS(s Runs sculptor RcC std|dtj|_ddlm}|jj|_||jj _ |j d|jdt j |_|jdd|_dS(NR R i(tsculptorR{R~(RRR^R6RRtPHIL_MULTIPROTOCOL_MASTERRzR{t macromoleculet protocolstprocess_multiprotocol_philRRt sculptorstget_discarder_objectRt discarder(R RR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR s  c C s|jj||jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdd|jjdd t |j |j d |j d |d |}||j _ |jjdd |jj|j}g|jdtjD]}|j|kr9|^q9}xkt|dt |dD]M\} } |jjd| tjd|d| d| }|jd|qzW|jj|jjdtjdddS(NR R7sModel generation - sculptorR8R9R:sSpace group %sRKsNumber of active protocols: %sRRRsUnique models generated:R R)iRMR<RNROsSculptor finished(RR>RR?R@RARBRCRRRtprocess_and_uniqueifyRt ensemblesRRMRRR[R,RURRG( R R;RRRRRMRRR.Ri((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRI,s@         )    cC s0|jdk r)|jjdd|jS|jjjd|tjd|jj}ddl m }ddl m }|j }|j }|jd||jd |jd |jd |jgd id |jjd|jjd|\} } |jd|} |jd| d| d|} |jd| d| d|jd|} |jd| d| d|}g}ddl}x|D]\}}x!| jD]}|jd|qW|jd|d|d| dddd|j|fd|}|jj |j!}|j" s#|j# rW|jjdd||jjdd|qn|jjdd|t$t%|j"dj&}|j'd|j(d |}|jjdd!|j(d"||ft)j*d#|gd$|gd%|j+d&|}|jjj,d||j-|qW|S('NR sThis entry has been processedRORi(R(tchiselRytfactoryt chain_infosR}t sequence_fort min_lengtht min_fractionR~tindexerRtsamplest processortdatumt blueprintt identitiest file_roottsculpttsuffixs%s%ss%s: model emptys %s: discardeds%s: model generateditidentityt num_residuess'Identity=%.2f%%, length=%d => rmsd=%.3fidR|RRSR(.RRRR?RPR:RvRRRRRt pdb_objecttobjecttsanitize_occupanciest chain_samplestaligned_chain_sampletget_chain_infost alignmentR{tmin_hssp_lengthtmin_matching_fractiontForwardIndexertidentity_processtsample_processRt unique_modification_instructionst iotbx.pdbR>twrite_pdb_outputRRtinputtconstruct_hierarchytmodelsRRRtresidue_groupstidentity_to_rmsRRtSculptorEnsembleRSRURT(R RRRR~RRRRyRtunknownRRt bp_unknownt unique_mist outensemblestiotbxttagtbpRtoutfilet outfile_rootRetrmsdRi((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR[s                  "           c C sddlm}g}t}x|jD]\}}} |jd|d|d| d|} tg| jD]$\} } | jri| | f^qi} | |krq)n|j| |j || fq)W|S(Ni(RRRRR~( RRReRRRR:tis_structural_changeR>RT(R RRR~Rt blueprintsR RRR'RR.Rtmods((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs"   !  cC sdS(NsModelGeneration (sculptor)((R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZs(R!R"R#R RIRRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs  / ] t DataFetchcB s2eZdZdZdZdZdZRS(s Fetches models cC s(td|dtj|_||_dS(NR R (RRR`R6tsite(R R((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyR sc C s|jjdtjdd|jjdddd|jjdd|j|jjdtj|jjdt||jjdd |jj||j d |j d |d |}||j _ t |t jr&|jjdd |j|jjdtjdddS|j}g|jdtjD]}|j|krH|^qH}tjd|d|dt|d}|jd||jjdtjdddS(NR R7sHomology search - fetchR8R9R:s Data fetchsSpace group %sRKthssRRsThis entry cannot be used: %ssFetch finishedR RMR<RNiRO(RR?R@RARBRCRRR>tfetchRtfetchedRgRtBadHomologySearchEntrytreasonRGRMRRR^RRU( R R;RRRRRMttsR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRIs4 !      c C s7|jr#|jjdd|jS|jjjd||j}ddl}ddl}yR|j j j d|j d|j }|j j d|jd|j j}Wn=tk r}|jjdd |tjd |d |SX|js!|jjdd tjd |d d S|jjdd|j|jjd|j} |j| t} | js|jjddtjd |d d|jSd|j |jf} |jjdd| | j| tjd| d|jd|j} |jjdd| |jjjd| | S(NR sThis entry has been fetchedROiRtmirrortlinest source_infos Error: %sRRsError: PDB file emptys Empty filesSelecting reference chain %ss chain '%s's%Error: No atoms after chain selections No chain '%s's %s_%s.pdbsWriting out file: %stpdb_fileRRSsSaving template: %s(RRR?RPR:Rvthittiotbx.pdb.fetchRRRt identifierRRRRRRRRRtatom_selection_cacheR3RcR+twrite_pdb_fileR]talignment_objectRSRU( R RRRRRRRyRJtasctcroott file_nameR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRsF    $         cC s d|jS(NsDataFetch (%s)(R(R ((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRZCs(R!R"R#R RIRRZ(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pyRs   ) 4cC sN|jd|jr5|jd|jtdn|jd|jr|jd|jd|j}|sxt|jd|||_n|jd|jd|j}|js|jdtdn|jd |j |j j d |j }|j |t }|jsJ|jd td |j n|S( NRsEntry %s has been retracted t retractedsThis entry has been obsoleted sReplacement entry: %s sRetrieving file... sError: PDB file empty temptysSelecting reference chain %s s chain '%s's&Error: No atoms after chain selection s no chain '%s'(RRRURt obsoletedtreplacement_forRut fetch_entryRRRR3RcR+(RRt redirectionsRtreplRyRR((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytdownload_homology_hit_modelHs*          (7t __future__RRtRRRRRt libtbx.utilsRRR[RRR$R/R4RaRRRRRRRRRRRRgRRRRRRRRRRR RRRRRR*R,R1RORvRwRRR(((sD/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/pipeline/expert.pytsd  !PElQk  f \,9>KJ a /X]$q['m