%Tc@sdZddlmZmZmZmZmZmZmZm Z m Z m Z m Z m Z mZe ZdZddlZddlZddlmZddlmZddlmZmZmZmZddlmZmZdd lmZm Z m!Z!dd l"m#Z#dd l$m%Z%m&Z&m'Z'm(Z(m)Z)dd l*m+Z+dd l,m,Z,ddl-m.Z.ddl*m/Z/ddl0m1Z1ej2j3ej2j4e5Z6dZ7dZ8dZ9dZ:dZ;dZ<dZ=dZ>dZ?dZ@dZAdddYZBdS(sCA class for the graphical interface used to trace the RNA backbone.i( timol_refinement_maptnew_generic_object_numbertset_display_generic_objecttclose_generic_objectt graphics_drawtset_rotation_centretto_generic_object_add_linetrotation_centre_positiontis_closed_generic_object_ptshow_select_map_dialogt zoom_factortscreen_vectors_pytadd_status_bar_textcCstdtdtdgS(Niii(R(((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pytrotation_centresN(tdeepcopy(tNextPhos(tplustminust rotateAtomstdist(tdetermineRotamerSeqtdeterminePucker(t calcCoordst recalcCoordstbuildOnlyPhosOxy(tReviewSuitesGui(tbuttonWithIcont HBOX_SPACINGt VBOX_SPACINGtBUTTON_SPACINGtcreateRCraneWindowObject(tPseudoMolecule(tselectMapDialog(tcreateCitationPopup(tCONNECTED_DISTANCE_CUTOFF(tSTANDARD_BASESg333333?tgreeng?tcyansCandidate phosphate positionssCandidate C1' positionstorangesCurrently Selected Peaks$Manually adjusted phosphate positiong?tTraceGuicBseZdZdeeedZdZeeeedZdZedZeeeedZ dZ d Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZ dZ!d Z"d!Z#d"Z$d#Z%d$Z&d%Z'd&Z(d'Z)d(Z*d)Z+d*Z,d+Z-d,Z.d-Z/d.Z0d/Z1d0Z2d1Z3d2Z4d3Z5d4Z6RS(5sCA class for the graphical interface used to trace the RNA backbone.ic Cs|d k rtn|d kr.t}n|rI||_||_nt|_d |_||_tdtj j t ddtj j t ddtj j t ddtj j t dd tj j t d |_ d |_ d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d |_d d d g|_d d d g|_ d d d g|_!d |_"d |_#t$|_%|d kr|j&|n |j'd S(sInitialize a TraceGui object and create a GUI for tracing a molecule OPTIONAL ARGUMENTS: direction - which direction to trace the chain: 3 implies 5'->3' 5 implies 3'->5' defaults to 3 (5'->3') curCoords - the current (x,y,z) coordinates for where to start building if not given, the screen center is used existingMolecule - an existing molecule to extend if given, must also give resToExtend resIndexToExtend - the residue of existingMolecule to extend from if given, must also give existingMolecule RETURNS: an initialized gui object EFFECTS: Creates and displays an RCrane dialog box tphosDistFilenamesdata/phosDistSmoothed.csvtphosAngleFilenamesdata/phosAngleSmoothed.csvtsugarPhosSugarAngleFilenames$data/sugarPhosSugarAngleSmoothed.csvt basesFilenamesdata/bases.pdbtpseudoChiFilenamesdata/pseudoChiSmoothed.csvitCN((tNoneR!R t_TraceGui__pseudoMoleculet_TraceGui__resIndexToExtendRt_TraceGui__directionRtostpathtjointsrcPatht_TraceGui__nextPhost_TraceGui__candidatePhosphatest _TraceGui__currentPhosphateIndext_TraceGui__candidateC1st_TraceGui__currentC1Indext_TraceGui__candidateBasest_TraceGui__baseTypet_TraceGui__candidatePhosObjectt_TraceGui__candidateC1Objectt_TraceGui__batonObjectt_TraceGui__customPhosphatet_TraceGui__customBaset_TraceGui__customPhosObjectt_TraceGui__adjustPhosOrigt_TraceGui__adjustPhosWindowt_TraceGui__adjustBaseOrigt_TraceGui__adjustBaseWindowt_TraceGui__translatedPhosCoordst_TraceGui__adjustedBaseCoordst%_TraceGui__previousPhosTranslateValuet%_TraceGui__previousBaseTranslateValuet"_TraceGui__previousBaseRotateValuet%_TraceGui__previousBaseRotateValueChit_TraceGui__deleteHandlerIDtFalset_TraceGui__tracedInitialPhostselectInitialPhost_TraceGui__extendChainSetup(tselft directiont curCoordstexistingMoleculetresIndexToExtend((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__init__=sT                               csJt}|dkr1dGHtfddSt}|jd|j|_tjd}|jtj |j ||j xtj rtj tqW|jj||_|j|j|jdtjd}td d }td d }tjd }tdd} tdd} |jd|j|jd|j|jd|j|| jd|j|| jd|j|tjtd} |j||j | |jddtj} | j| ttdtjtd} | j | | j|ttt tj!t"t }|j|t"t"t#|j|t"t"t#| j|ttt#tj!td}|j|t"tt#| j|ttt#tj$}| j|tj!tt }|j| t"tt#|j| t"tt#| j|ttt#| j%|j dS(sCreate a GUI for building the initial phosphate ARGUMENTS: curCoords - the current (x,y,z) coordinates for where to start building RETURNS: none EFFECTS: creates a GUI for building the initial phosphate for a chain trace REQUIREMENTS: a refinement map must be selected (i.e. imol_refinement_map must return a valid map ID) otherwise this function will display a map selection dialog and then return is)No refinement map set for RCrane buildingcs tS(N(R'((RT(sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pytsNt delete_eventsH Calculating potential phosphate coordinates... Please wait... is& Select starting phophate location: s Next sgtk-media-nexts Previous sgtk-media-previouss Manually Adjust s Accept sgtk-oks Cancel s gtk-canceltclickediii(&RR Rtconnectt_TraceGui__initialPhosCloseWinRMtgtktLabelt set_justifytJUSTIFY_CENTERtaddtshow_alltevents_pendingtmain_iterationRNR6t firstPhosR7t_TraceGui__drawPhosPeakst_TraceGui__drawBoxRtButtont_TraceGui__initialPhosNextt_TraceGui__initialPhosPrevioust(_TraceGui__createAdjustInitialPhosDialogt_TraceGui__initialPhosAcceptt_TraceGui__initialPhosCanceltVBoxtremovetresizetFramet pack_startRtHBoxtTrueRt HSeparatort grab_focus(RRRTtmapNumtwindowt waitLabelttopLabelt nextButtontpreviousButtont adjustButtont acceptButtont cancelButtont windowBoxtframetframeBoxt nextPrevBoxt adjustBoxt separatortacceptCancelBox((RTsV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyRPsf             c;Cs t}|d3kr!t}n)|j}|j||j|j|jd|j|_t j d}|j t j |j ||jxt jrt jtqW|jd3kr|jdkr|jjd}qd}n |jj}d3} d3} d3} |jdkr|jj|} |jj|sX|jdkr|jj|d} |jj|d} qna|jj|} |jj|s|jdkr|jj|} |jj|d} n| d3kr!|jj|| |j\|_|_n-|jj || | | |j\|_|_dgt!|j|_"g|_#x.|jD]#} |j#j$d3gt!| qzW|j%d3|_&d3|_'|d3k r||_(nd|_)|d3k s|d3k r|d3k r |} n |d} xt*|jD]U\}}|d| dkr%|d| dkr%|d| dkr%||_)Pq%q%W| |_&|j(t+|g|_'|j'dd=|d3kr|j&d3kr|d}xt*|j|j)D]\\}}|d|dkr|d|dkr|d|dkr||j"|j)||$jd"|j?||jd#|j@| jd"|jA|jdkrd$}%nd%}%|j}&|&dkr|jd3krt j d&|%}'t1d'd(}(|(jd"|jB| |n2t j d)|&d|&dkr d*nd+|%f}'t jCttD})|j||j |)|jEddt jCtd}*|)jF|*ttd,|*jF|ttdt jGttH}+|*jF|+tttD|jjdkrR t jId-dd.d/},|,j |'t jId-dd.d/}-|-j |(|+jF|,tJtJtK|+jF|-tJtJtKnA|+jF|'tJtdy|+jLd0|jMWntNk r nXt jOd1}.|.jPd/d/|)jF|.ttdt jCttD}/|.j |/t jGtJtH}0|0jF|tJtJtK|0jF|tJtJtK|/jF|0tttKt jGtd}1|1jF|tJttK|/jF|1tttKt jOd2}2|2jPd/d/|)jF|2ttdt jCttD}3|2j |3t jGtJtH}4|4jF|tJtJtK|4jF|tJtJtK|3jF|4tttKt jGtd}5|5jF|tJtJtK|5jF| tJtJtK|3jF|5tttKt jGtd}6|6jF|tJttK|3jF|6tttKt jQ}7|)jF|7t jGtJtH}8|8jF|!tJtJtK|8jF|"tJtJtK|)jF|8tttKt jGtJtD}9|)jF|9tttKt jCtJtD}:|9jF|:tttK|:jF|#tJttK|:jF|$tJttK|!jR|j|+jSd|_Md3S(4sBCreate a GUI for building the next nucleotide OPTIONAL ARGUMENTS: window - a pyGTK+ window object (from the previous iteration of selectNextNt, if there was one) initialNtCoords - a dictionary of atom coordinates indicating what the initially selected nucleotide should be This is typically used if the user has just clicked "Previous Nt" If not given, the the most likely predicted base location is used initialNtType - what type of base (i.e. A, C, G, or T) should be initially selected this is typically used if the user has just clicked "Previous Nt" If not given, then self.__baseType is used. If initialNtCoords is given, then this argument MUST match the base type described by initialNtCoords. initialPhos - the coordinates for the initially selected phosphate should be If this is given, then initialNtCoords and must *NOT* be given RETURNS: none EFFECTS: creates a GUI for building the next nucleotide of a chain trace REQUIREMENTS: a refinement map must be selected (i.e. imol_refinement_map must return a valid map ID) RYsH Calculating potential phosphate coordinates... Please wait... iiitPisC1'sTrace the next nucleotide:s Next Phos sgtk-media-nexts Previous Phos sgtk-media-previouss Manually Adjust u Next C1′ u Previous C1′ s Adenine (A)s Cytosine (C)s Guanine (G)s Uracil (U)tAR-tGtUs Anti/Syn Flip s Accept Nt sgtk-oks Previous Nt s gtk-cancels Build Backbone s gtk-applys Delete Trace s gtk-closeRZtchangeds5' -> 3's3' -> 5'sTracing s Switch s gtk-refreshs%i nucleotide%s traced (%s)tstitxaligntyaligng?it PhosphatetBaseN(TRR.Rt get_childRot disconnectRMR[t_TraceGui__nextNtCloseWinR]R^R_R`RaRbRcRdRNR0R1R/t getNumNtstresInsertionPointtgetPhosCoordsFromIndextconnectedToPrevFromIndext_TraceGui__numNtsTracedtgetSugarCoordsFromIndextconnectedToNextFromIndexR6t secondPhosR7R9tnextPhostlenR:R;tappendRfR@RAR<R8t enumerateRt_TraceGui__drawC1PeakstfindBaset iteritemst_TraceGui__drawAdjustPhosCrosst_TraceGui__drawNtRRhtcombo_box_new_textt append_textt set_activet_TraceGui__nextNtNextPhost_TraceGui__nextNtPrevPhost!_TraceGui__createAdjustPhosDialogt_TraceGui__nextNtNextC1t_TraceGui__nextNtPrevC1t!_TraceGui__createAdjustBaseDialogt_TraceGui__nextNtAcceptt_TraceGui__nextNtPrevNtt_TraceGui__nextNtBuildBackbonet_TraceGui__nextNtCloset_TraceGui__nextNtBaseSelectt_TraceGui__flipBaset_TraceGui__switchDirectionRnRRpRrRsRt AlignmentRtRtset_size_requestt_TraceGui__directionBoxHeighttAttributeErrorRqtset_label_alignRuRvt size_request(;RRRxtinitialNtCoordst initialNtTypet initialPhosRwt windowChildRyRVtprevPhost prevSugart prevPrevPhostcurC1stinitialPhosCoordstindextcoordstinitialC1Coordst phosIndextc1indextatomNamet curPhosCoordst curC1Coordst curBaseCoordsRztnextPhosButtontprevPhosButtontadjustPhosButtont nextC1Buttont prevC1ButtontadjustBaseButtont baseSelectt baseTypeNumtflipBaseButtonR~t prevNtButtontbuildBackboneButtont closeButtontdirectionStringtnumNtstdirectionLabeltswitchDirectionButtonRttopBoxt directionBoxtdirectionLabelAligntswitchDirectionAlignt phosFramet phosFrameBoxtphosPrevNextBoxt adjustPhosBoxtC1Framet C1FrameBoxt C1PrevNextBoxtbaseBoxt adjustC1BoxRRtbuildCloseHboxt buildCloseBox((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt selectNextNts|         $$ *-  !         <    #<  D(H         )   2           cCsc|jdk r%|jd|jn|jdk rJ|jd|jn|j}|j|}d}d}|jdk r|j}|jdd}n"|j||}|j ||}|d|j krdS|j j ||j }|jdk r||_n||j||RRR.RD(RRRRx((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__adjustPhosAccepts   c CsA|jdk r%|jd|jntd}|j||jd|jtjt t }|j |tj d}|j |t t dtjddddd }tj|}|jt |j |tj d }|j |t t dtjddddd } tj| } | jt |j | tj d } |j | t t dtjddddd } tj| } | jt | j | tj d }|j |t t dtjddddd }tj|}|jt |j |tj d }|j |t t dtjddddd }tj|}|jt |j |tj d}|j |t t dtjddddd }tj|}|jt |j |tj d}|j |t t dtjddddd }tj|}|jt |j |tj}|j |tdd}tdd}tjtt}|j |ttt|j |ttt|j |t t t|jd|jd| jd|jd| jd|jd|jd|jd|jd|jd|jd|jd|jd|j|jd|j||jd|j||jdk rt|j|_n*|j}|j|}|j |||_t|j|_!dddg|_"dddg|_#d|_$||_%|j&dS(sCreates a dialog that allows the user to manually change the base position. ARGUMENTS: widget ARGUMENTS: widget - the widget that called this function. Ignored. parentWindow - the RCrane window. The newly created dialog box is set as a transient for parentWindow RETURNS: None EFFECTS: Creates and displays a dialog box for adjusting the base location s Adjust BaseRYs X translationiiiLihg?g?s Y translations Z translations X Rotations Y Rotations Z Rotations Chi Rotations OK sgtk-oks Cancel s gtk-cancelRiRZN('RDR.RRRR[t_TraceGui__adjustBaseCancelR]RnRNRRaRqRrRRRRuRRsRtRRt_TraceGui__translateBaset_TraceGui__rotateBaset_TraceGui__rotateBaseChiRRARRER8R:R;RHRJRKRLRFRb( RRRRRRRR R R R R RRRt xRotFrametxRotAdjustmentt xRotScalet yRotFrametyRotAdjustmentt yRotScalet zRotFrametzRotAdjustmentt zRotScalet chiRotFrametchiRotAdjustmentt chiRotScaleRRRRRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__createAdjustBaseDialogs                       c Cs[|j|j|}|j|j|s$      c Cs|j|j|}|j|j||j|j}n |j}|j|j|jdd||j|jd|_ dS(sJRespond to the user clicking Cancel in the adjust base dialog box ARUGMENTS: widget - the cancel button window - the dialog box window RETURNS: None EFFECTS: Closes the adjust base dialog box and reverts the base to its original coordinates isC1'N( R8R:R.R@R7RRRERRF(RRRRxRRR6((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__adjustBaseCancels   * cCs#|j|_|jd|_dS(sGRespond to the user clicking OK in the adjust base dialog box ARUGMENTS: widget - the OK button window - the dialog box window RETURNS: None EFFECTS: Closes the adjust base dialog box and stores the coordinates that the user has selected N(RHRARR.RF(RRRRx((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__adjustBaseAccepts  cCs|jdkrE|jd7_|jt|jkr[d|_q[nd|_t|j|jdk rz|jjnd|_|j |j|jdS(sSelect the next phosphate in the initial phosphate GUI. ARGUMENTS: widget - the button used to call this function. Ignored. RETURNS: None EFFECTS: Highlights the next phosphate iiN( R@R.R8RR7RRBRDRRg(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__initialPhosNexts    cCs|jdkrI|jd8_|jdkr_t|jd|_q_nd|_t|j|jdk r~|jjnd|_|j |j|jdS(sSelect the previous phosphate in the initial phosphate GUI. ARGUMENTS: widget - the button used to call this function. Ignored. RETURNS: None EFFECTS: Highlights the previous phosphate iiN( R@R.R8RR7RRBRDRRg(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__initialPhosPreviouss    cCs,|j|||j|j|j|jdS(sBCreates a dialog to adjusting the initial phosphate coordinates. ARGUMENTS: widget - the button used to call this function. Ignored. window - the RCrane window RETURNS: None EFFECTS: Creates and displays the adjust phosphate dialog N(Rt_TraceGui__adjustInitialPhost"_TraceGui__adjustInitialPhosAcceptt"_TraceGui__adjustInitialPhosCancelt$_TraceGui__adjustInitialPhosCloseWin(RRRRx((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__createAdjustInitialPhosDialog<s cCs|j|j|}|j|j|R?RBRR8R:R@R7RAR;R1R/taddBaseAndPhostaddBaseAndPhos5pRR(RRRRxRRR6tbaseTypet baseCoords((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtAccepts6           cCs=|jjr|jjn |jj|j|dS(s:Close the next nucleotide dialog and delete the molecule ARGUMENTS: widget - the button used to invoke this function window - the RCrane window RETURNS: None EFFECTS: Destroys the next nucleotide dialog and the Coot molecule N(R/thasSavedMoleculeStatetrestoreMoleculeStatetdeleteMoleculet_TraceGui__nextNtFinished(RRRRx((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt __nextNtCloses  cCst|jt|jt|j|jdk rFt|jn|jjt|j dk ry|j j n|j dk r|j j n|j dS(sKClose the next nucleotide window without deleting the molecule ARGUMENTS: window - the RCrane window RETURNS: None EFFECTS: Destroys the next nucleotide dialog NOTE: This function is called by __nextNtClose and __nextNtBuildBackbone. N( RR=R>R?RBR.R/RNRRDRRF(RRRx((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtFinished-s    c Csd }|jd k r%|jjn|jd k rD|jjn|jdkr|jd kru|j|q|jrt|j |j|j |j|qdGHt dt Sn#|jdkrS|jd krSt |jt |jt |j|j j}t|jdj}t|||j ||j|nt |jt |jt |j|jd kr|j j}n|j dkr|jd}|j j}|j|}|dkrQ|d7}qQnc|j j}|j j}|j|}|dkr8|d8}|d8}n|dkrQ|d8}n|j j||dt\}} } t|} t|\} } ddj| GH|jd krt|| |j |\}}n| d krd g| }d }n|j j|}|g| }| d kr8|d g}d }n|j j| }||g}|j j |}|j j!|r|j j |d}n|j j |}|j j"| p|| p||j dkr|j j#||j j |jn"|j j#|j j |j||rz|j dkrU|j j#|j j |j|qz|j j#||j j |jnt$|||||j |\}}|j j%|j&|j't(| | |j | |||d |d S( siFinish tracing the backbone and calculate all-atom backbone coordinates. ARGUMENTS: widget - the button used to invoke this function window - the RCrane window RETURNS: None EFFECTS: Calculates an initial set of backbone coordinates and creates a review suites GUI dialog is4No nucleotides traced, so there is nothing to build.iiitaddFlankingAtomssSuite string: Rt prevTorsionsN()R.RDRRFRR0RdRORR/R1R RNRR=R>R?tcreateChainObjectRt nucleotidestpperpRRt_TraceGui__extendChainJoinedRSt!createPartialChainObjectFromIndexRtRRR4tcalcSuiteTorsionsFromIndextcalcSuiteTorsionst resNumFulltisOnlyPhosGroupFromIndextsetExtraBondRanget resetNucsRRNRRMR(RRRRxRht builtChaintpuckertstartingResIndextendingResIndextjoinedtresNum5ptresNum3ptbuiltChainOrigtbestPathtpredictedProbstintermediateAtomLocstminimizationScorest rebuildRotst nextTorsionst startResNumt endResNum((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtBuildBackboneMs   !                $  !        %"%%$ cCs|j||dS(s Respond to the user closing the next nucleotide window ARUGMENTS: window - the window to close widget - the widget used to close the window NOTES: This function simply calls __nextNtClose with a reversed argument list N(R(RRRxR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtCloseWins cCs9|j}ddddg|}||_|jdS(s<Mutate the base in response to the user selecting a base type from the drop-down ARGUMENTS: combobox - the drop down object used to select the new base type RETURNS: None EFFECTS: the current base is mutated to self.__baseType and redrawn RR-RRN(t get_activeR<RW(RRtcomboboxt selectionNumR^((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtBaseSelects  cCs,|jdk r:|jj|jjkr:dGHtddS|jdkra|jj\}}n|jj\}}|dkrdGHtddSt |j t |j t |j |j dk rt |j nd|_d|_|j}t|d|d|d|j|||dS(sdCancels building the current nucleotide and moves back one nucleotide ARGUMENTS: widget - the button used to invoke this function window - the RCrane window RETURNS: None EFFECTS: Undraws the current nucleotide and prompts the user to rebuild the previous nucleotide sCan't go back any further.Niiii(R0R.R/RSRR R1tremoveLastBaseAndPhostremoveFirstBaseAndPhosRR=R>R?RBR@RARRR(RRRRxt prevNtTypet prevNtCoordsR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__nextNtPrevNts* '         c Cst||d|d||d|d|d||d|d t||d|d|d||d|d|d||d t||d|d|d|d||d|d|d| dS(sDraw a cross of the specified size and color ARGUMENTS: coords - the coordinates for the center of the cross crossLength - the size of one "arm" of the cross (i.e. the distance from the center to the end, not end-to-end) crossColor - the color of the cross object - the Coot drawing object to add this cross to RETURNS: None EFFECTS: Adds the specified cross to object iiiiN(R(RRRt crossLengtht crossColortobject((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt __drawCrossSsBBcCs|j|tt|jdS(sEDraw a cross for a phosphate candidate ARGUMENTS: coords - the coordinates for the center of the cross RETURNS: None EFFECTS: Adds the cross to self.__candidatePhosObject Note that this function does not issue a graphics_draw() command N(t_TraceGui__drawCrosstCROSS_LENGTH_PHOStCROSS_COLOR_PHOSR=(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__drawPhosCrosses cCs|j|tt|jdS(s=Draw a cross for a C1' candidate ARGUMENTS: coords - the coordinates for the center of the cross RETURNS: None EFFECTS: Adds the cross to self.__candidateC1Object Note that this function does not issue a graphics_draw() command N(RtCROSS_LENGTH_C1tCROSS_COLOR_C1R>(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt __drawC1Crossrs cCsU|jrt|jntt|_t|jd|j|tt|jdS(sDraw a cross for the manually adjusted phosphate ARGUMENTS: coords - the coordinates for the center of the cross RETURNS: None EFFECTS: Deletes the current manually adjusted phosphate cross if one is present and creates a new cross Note that this function does not issue a graphics_draw() command iN(RBRRtADJUST_PHOS_TITLERRRR(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__drawAdjustPhosCrosss c Cs?|jrt|jntt|_t|jdt|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt t|jtd|dt|dt|dt|dt|dt|dt tdS(s>Draw a new box around the specified point ARGUMENTS: coords - the coordinates for the center of the box RETURNS: None EFFECTS: Deletes the current box if one is present and creates a new box Then issues a graphics_draw() command iiiiN( R?RRt BATON_TITLERRt BATON_COLORt BOX_LENGTHR(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt __drawBoxs" UUUUUUUUUUUUc Cs|jrt|jntt|_t|jdt|jtd|d|d|d|d|d|d t|jtd|d|d|d|d|d|d |\}}d}|dkr*ddgddgdd gd d gd d gd d gd dgdd gd dgg }nq|dkrddgddgdd gd d gd d gd d gd dgdd gd dgg }n |dkrddgddgddgdd gd d gd d gd dgddgdd gd d gd dgddgd dgg }n|dkrddgddgddgdd gd d gd d gd dgddgdd gd d gd dgd dgg }nxk|D]c}|\} } || } || } t|jtd| d| d| d| d| d| d qWtdS(sDraw batons for a new nucleotide candidate ARGUMENTS: phos5 - the coordinates of the 5' phosphate c1 - the coordinates of the C1' phos3 - the coordinates of the 3' phosphate base - a 2 item list consisting of (baseType, baseCoords) baseType is either C, U, G, or A baseCoords is a dictionary of atom type => coordinates EFFECTS: Draws the specified nucleotide Issues a graphics_draw() command iiiiR-sC1'R=tC2tN3tC4tC5tC6tO2tN4RtO4RR<tC8tN7tN2tO6RtN6N( R?RRRRRRR.R( RRtphos5tc1tphos3tbaseR^R_tbondListt bondAtomstatom1tatom2t atom1Coordst atom2Coords((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__drawNts, ==  Z Z ~ u    AcCsDtt|_t|jdx|jD]}|j|q)WdS(s&Draw crosses for all phosphate candidates ARGUMENTS: None RETURNS: None EFFECTS: Draws crosses for each point in self.__candidatePhosphates Note that this function does not issue a graphics_draw() command iN(RtCANDIDATE_PHOS_TITLER=RR7t_TraceGui__drawPhosCross(RRtcurPeak((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__drawPhosPeakss cCsz|jdk r/t|j r/t|jntt|_t|jdx%|j|jD]}|j |q_WdS(sXDraw crosses for all C1' candidates for the currently selected phosphate ARGUMENTS: None RETURNS: None EFFECTS: Draws crosses for each point in self.__candidateC1s for the current phosphate Note that this function does not issue a graphics_draw() command iN( R>R.RRRtCANDIDATE_C1_TITLERR9R8t_TraceGui__drawC1Cross(RRR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt __drawC1Peakss cCs|jdkrd|_n d|_d}|jdkrL|j|j}n |j}|jdk rz|jd|jn|jdk r|jd|jnt |j t |j t |j |j dk rt |j nt|j|d|dS(s3Switch the direction of the trace ( from 3'->5' to 5'->3', or vice-versa) ARGUMENTS: widget - the button used to call this function prevPhos - the coordinates of the previous phosphate atom window - the RCrane window RETURNS: None iiRN(R1R.R@R7R8RDRRFRRR=R>R?RBRR(RRRRRxR6((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__switchDirection s$       cCsg|jdkr0|jdkr'd}qWd}n'|jdkrN|jj}n |j}|jj|S(sGet the coordinates of the previous phosphate ARGUMENTS: None RETURNS: the coordinates of the previous phosphate (phosphate -1 if tracing 5'->3', phosphate 1 if tracing 3'->5') iiiN(R0R.R1R/RR(RRt prevResIndex((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__getPrevPhosCoordsG s    cCs|jdkr*|jj|jd k sN|jdkr[|jj|jr[|jn|jdkrdddddg}ndd d d dg}d }x?|D].}|jj||j}|d k rPqqWd GHtS|j |d S(sStart an extend chain call ARGUMENTS: None RETURNS: False if we could not find any atoms to use for starting coordinates (if this happens, something has gone very wrong) iisO3'sC3'sC2'sO2'sC1'sO5'sC5'sC4'sO4's2No suitable atoms found to start phosphate search.N( R1R/RR0R.RqRtgetAtomCoordsFromIndexRNRP(RRt atomOrdert startCoordsR4((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__extendChainSetup^ s *$   cCs>|jdkr|jjSt|jj|jjdSdS(sCalculate the number of nucleotides that have been traced thus far ARGUMENTS: None RETURNS: The number of nucleotides traced iN(R0R.R/RtabsRRS(RR((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__numNtsTraced s  c Cs|jj|}d }d }|jdkr||d|jjkrJtS|jj|d}|jjd|d}n?|dkrtS|jj|d}|jjd|d}|d k rt||tkrt }nt}|d k rt||t krt }nt}d }|s-|r.|jdkrI|d}n |d}|jj |s|jj |d krt }n|jj |} | tkrt }qn|jj|ddkrtS|jdkr|jj|d krt }q.|jdkr.|jj| r.t }q.n|r{|jdkrV|jj|n|jj|d|rttSdSnX|r|jdkr|jj||d|rtSdSn|r|rtSdSntSd S( sIf we're doing an extend chain, figure out if we've joined up to the next segment of the molecule. (i.e. if we're tracing 5'->3', has the 3' end of the newly traced segment met up with the next residue) If we are, then set up the molecule to prepare for the join (i.e. remove redundant phosphates) ARGUMENTS: endingResIndex - the residue index of the last residue of the newly traced segment we could determine this ourselves, but __nextNtBuildBackbone will have just finished determining it when this function is called RETURNS: False if the new segment was not joined 1 if the segment was joined and a residue containing only a phosphate was deleted or merged into another residue (i.e. the residue numbering has changed by 1 2 if the segment was joined no residues were deleted iisO5'isO3'RiiN(R/RR.R1RRNRRtCONNECTED_DISTANCE_CUTOFF_PHOSRtR"RqRtresTypeFromIndexR#tresNumRtdeleteResFromIndextmergeRes( RRRwtnewSegmentPhosCoordRtnextOxytnextPhosIsClosetnextOxyIsClosetcantCalcPseudoTorst nextResIndext nextResType((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyt__extendChainJoined sh ! !       ' " (7t__name__t __module__t__doc__R.RWRPRRWRRRRRRRR$R%R&t_TraceGui__adjustBaseCloseWinR#RRiRjRkRERHRGRFRmR\RlRRRRRRRdRRRRRRRRRgRRfRRRRQRRl(((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyR':sj^ fu 4 5i , %  } 1 ' '      ( "    9 7 7 . . :   :   ( 0   0  % ((CRtcootRRRRRRRRRR R R R RR R]R2tcopyRRRt strucCalcRRRRt rotamerSeqRRRRRtreviewSuitesGuiRtguiUtilsRRRRRtpseudoMoleculeRR t citationPopupR!R"treportInputErrorsR#R3tdirnametabspatht__file__R5RRRRRRRRRRRR'(((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/traceGui.pyts<X   "(