%Tc@sdZddlZddlZddlmZddlZddlmZddlm Z m Z m Z m Z m Z mZddlmZmZddlmZmZddlmZmZmZmZmZdd lmZd Zd ZejZd dd YZdS(sLA class for the graphical interface used to review the predicted conformers.iN(tdeepcopy(tsleep(tset_rotation_centretadd_atom_labeltremove_atom_labelt graphics_drawtclose_generic_objecttset_display_generic_object(tpuckerListFullNamet puckerList(t calcCoordst recalcCoords(tbuttonWithIcont HBOX_SPACINGt VBOX_SPACINGtBUTTON_SPACINGtcreateRCraneWindowObject(tdetermineAlternateConftpinkt palegreentReviewSuitesGuicBseZdZdededddZdZdZdZ dZ dZ dZ dZ d Zd Zd Zd Zd ZdZdZdZddZddZdZdZdZdZRS(sLA class for the graphical interface used to review the predicted conformers.c Cs||_||_||_||_||_||_||_| |_||_| |_ | |_ | |_ t ||_ d|_t|jd|_d|_|jdjdrd|_n d|_|j|jdS(s Initialize a ReviewSuitesGui object and create a GUI for reviewing the predicted suites ARGUMENTS: predictedProbs - the probabilities for each rotamer calculated for each suite formatted as a list of suites, where each suite is represented as a dictionary of rotamer => probability bestPath - a list of the most likely rotamers for each suite This is typically calculed by rotamerSeq using an HMM, so it may differ slightly from simply taking all the maxima from predictedProbs pseudoMol - a PseudoMolecule object for the built molecule origCoords - a copy of the coordinates contained in pseudoMol as a Chain object intermediateAtomLocs - phosphate, O3', and C3' coordinates for each nucleotide immediately before minimization of that nucleotide was started minimizationScores - the minimization scores for each nucleotide OPTIONAL ARGUMENTS: window - a window to put the GUI into If not provided, a new window will be created. useResNums - whether or not to display the rotamer numbers (as opposed to just the indices) in the GUI Defaults to True oldCoordsObj - a Coot generic object for drawing the coordinates we are potentially replacing when running rotamerize If not provided, then the toggle checkbox will not be displayed and the generic object will not be destroyed when closing the window. ignoreDensity - ignore the density when performing the minimization defaults to False prevTorsions - the pre-rotamerize torsions for the suite before the start of origCoords. These torsions will be used as restraints when rebuilding the first suite defaults to None nextTorsions - the pre-rotamerize torsions for the suite after the end of origCoords. These torsions will be used as restraints when rebuilding the first suite defaults to None RETURNS: an initialized ReviewSuitesGui object EFFECTS: Displays an RCrane dialog box for reviewing the predicted suites NOTE: If the pseudoMol object has savedCoordinates, then an an "Accept New Coordinates" and a "Restore Original Coordinates" will be displayed. Otherwise, only a "Done" button will be displayed iiisC1'N(t _ReviewSuitesGui__predictedProbst_ReviewSuitesGui__bestPatht _ReviewSuitesGui__pseudoMoleculet_ReviewSuitesGui__origCoordst&_ReviewSuitesGui__intermediateAtomLocst_ReviewSuitesGui__windowt_ReviewSuitesGui__useResNumst_ReviewSuitesGui__oldCoordsObjt$_ReviewSuitesGui__minimizationScorest_ReviewSuitesGui__ignoreDensityt_ReviewSuitesGui__prevTorsionst_ReviewSuitesGui__nextTorsionsRt_ReviewSuitesGui__curPatht_ReviewSuitesGui__curSuitetlent_ReviewSuitesGui__numNucstNonet*_ReviewSuitesGui__treeViewChangedHandlerIDtnucsthasAtomt_ReviewSuitesGui__skipFirstNuct_ReviewSuitesGui__clearCachet_ReviewSuitesGui__reviewSuites( tselftpredictedProbstbestPatht pseudoMolt origCoordstintermediateAtomLocstminimizationScorestwindowt useResNumst oldCoordsObjt ignoreDensityt prevTorsionst nextTorsions((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__init__*s*%                 c#Cs|jdkrt|_nS|jdk rq|jj}|dk r[|jj|n|jjddn|jjd|jtdd}tdd}tdd}td d }|j j rtd d }td d}ntdd }|j j d|j j}|jrGdt|t|jf} ndt|j} tj| } |jd\} } |j| | \} }}t|jdkr|j| | }nd}|jd|j||_|j| |\}}t|jdkr/|j|||\}}n|jd|j||jd|j|t|jdkr|jd|j| | ||jd|j | | |n|jd|j!|j j r|jd|j"ntj#t$t%}t|jdkrgtjd}tj&t'd}|j(|t'|d|j)||j(|t$t't*ntj&t$t+}tj#t$t%}| j)||j(|t't't*|j(| t't't*tj#t't%}tj,dddd}|j)||j(|t$t$t*|j(|t't't*|j(|t't't*|j-dk rtj.d}|j/t'|jd|j0tj,dd}|j)||j(|t't't*n|j(|t't$t*t|jdkr|tj&t't+}tj,dd}|j)||j(|t't't*|j(|t't't*|j j rc|j(|t$t$t*q||j(|t$t$t*n|j j rtj&t't+} tj,dd}!|!j)| |j(|!t$t$t*| j(|t't't*| j(|t't't*n5tj,dd}!|!j)||j(|!t$t$t*|j1d|_2|j j3|}"t4|"t5|j j6|j j7t8|dt9|jj)||jj:t|jdkr|j;n |j;dS(sCreate the review suites GUI ARGUMENTS: None RETURNS: None EFFECTS: Displays an RCrane dialog box for reviewing the predicted suites it delete_events Previous Conformer s gtk-go-ups Next Conformer s gtk-go-downs Previous Suite sgtk-media-previouss Next Suite sgtk-media-nexts Accept New Coordinates sgtk-oks Restore Original Coordinates s gtk-cancels Done sSuite %s (1 of %i)s Suite 1 of %itchangedtclickedtOverviewitxaligng?tyalignsDisplay old coordinatesttoggleds P N(<RR%Rt get_childtremovetresizetconnectt_ReviewSuitesGui__closeWinR RthasSavedCoordinatesRR'R)tresNumRtstrR#RtgtktFramet%_ReviewSuitesGui__createConfListStoret$_ReviewSuitesGui__createConfTreeViewRt(_ReviewSuitesGui__createOverviewTreeViewt_ReviewSuitesGui__changedR&t*_ReviewSuitesGui__createConfScrolledWindowt._ReviewSuitesGui__createOverviewScrolledWindowt_ReviewSuitesGui__prevConft_ReviewSuitesGui__nextConft_ReviewSuitesGui__prevSuitet_ReviewSuitesGui__nextSuitet_ReviewSuitesGui__acceptt"_ReviewSuitesGui__restoreOldCoordstVBoxtFalseRtHBoxtTruet pack_starttaddRR t AlignmentRt CheckButtont set_activet!_ReviewSuitesGui__toggleOldCoordsR!t_ReviewSuitesGui__selectedConft getPhosCoordsRRtmolNumtchaintintRtshow_allt grab_focus(#R,t windowChildtprevConfButtontnextConfButtontprevSuiteButtontnextSuiteButtont doneButtont cancelButtontsuiteNumt frameTitlet suiteFramet confListStoretinitialConfNumt confTreeViewtconfTreeSelectiont rowHeighttoverviewTreeViewttreeViewScrollttreeViewScrollWidthtoverviewScrollt wideOverviewt windowBoxt overviewFramet overviewBoxtsuiteFrameHBoxtsuiteFrameVBoxtprevNextConfBoxtprevNextConfAlignmenttoldCoordsCheckButtontoldCoordsAlignmenttprevNextSuiteBoxtprevNextSuiteAlignmenttdoneBoxt doneAlignmentt firstPhos((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__reviewSuitesws   "         (  cCs|j|jd}|dkr/d}t}nt}|j|jd}|jj|j}|jj|j}|j}|dkr|jj|dj} n|} |jj |s|j j | ||j|Hstreverseis%4.2f( RIt ListStoreRHReRtitemstsortRZR RRRR!( R,tcurSuiteRrt conformerListtdefaultLeadingPuckertdefaultEndingPuckertitconftscoreRs((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__createConfListStore9s $\ cCs(tj|}|jttj}|jdd|jd|jjjtj tj d|dd}|j |tj}|jdd|jdt tj d|dd d d }|j |tj}|jdd|jdt tj d |dd d d } |j | tj} | jddtj d| dd} | j | |jd|j | tj} | jddtj d| dd} | j | |jd|j | |j}|j|j|| jd|jd}|||fS(sBCreate the TreeView object for the list of conformers ARGUMENTS: confListStore - the ListStore object to attach to the TreeView initialConfNum - the most likely suite (i.e. the row of confListStore to initially highlight) RETURNS: confTreeView - the newly created TreeView object confTreeSelection - the TreeSelection object associated with the TreeView rowHeight - the height of a single row in the TreeView (used to determine how high to size the ScrolledWindow) R>g?scell-background-gdktRankttextiscell-backgroundt Conformeritcell_background_setitScoreisLeading Puckeriis Ending Puckeriisvertical-separator(ii(ii(RItTreeViewtset_enable_searchRXtCellRendererTextt set_propertyRt get_styletbgt STATE_NORMALtTreeViewColumnt append_columntBEST_PATH_COLORtset_cell_data_funct_ReviewSuitesGui__setPuckerBgt get_selectionRRt cell_get_sizetstyle_get_property(R,RrRsRtt renderRankt columnRankt renderConft columnConft renderScoret columnScoretrenderLeadingPuckertcolumnLeadingPuckertrenderEndingPuckertcolumnEndingPuckerRuRv((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__createConfTreeViewSs>   #          c Cstj}|jtjtj|jtj|j||j\}}y|j jd}Wn't k rtj jd}nX|j d}|t t|}|||d} |j| ||dd|| fS(sCreate a ScrolledWindow object to display the conformer TreeView ARGUMENTS: confTreeView - the TreeView object used to display the list of conformers rowHeight - the height of a row in confTreeView RETURNS: treeViewScroll - the newly created ScrolledWindow object treeViewScrollWidth - the width of treeViewScroll (used to figure out how wide to make the overview ScrolledWindow) isscrollbar-spacingii(RItScrolledWindowt set_policyt POLICY_NEVERtPOLICY_AUTOMATICtset_shadow_typetSHADOW_ETCHED_INR\t size_requesttget_vscrollbartAttributeErrort VScrollbarRR#R tset_size_request( R,RtRvRxt tableWidthReqttableHeightReqtvScrollWidthReqtscrollbarSpacingt headerHeightRy((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__createConfScrolledWindows   cCs<tgt|j}tj|}|jjd|jd!}|j||jg|jD]}|j dd^q_t g|D]}t|^qdg}tj |} | j t | jt | jjtjy| jtjWntk rnXt|j} xt|jD]\} }tj} | jdd| jd|d| d kr| jd tnt|j| jd td d!\} }y| |}Wntk rtd }nX| d krt |jd |jd}n|j| d}|d ks:|dkrM| jddnV|dkse|dkrx| jddn+|dks|dkr| jddntj t| d| d| }|j!t| j"|| d kr |j#d|j$d}n| jd|q0W| j%d|j&||| S(sVCreate a TreeView object for the suite overview ARGUMENTS: confTreeView - the TreeView object for the list of conformers suiteFrame - the Frame object containing information about the current suite RETURNS: overviewTreeView - the newly created TreeView object iit&s&iR>g?s width-charsitweightRtinfg333333?iscell-backgroundtredg?itorangeg@i tyellowtmarkupisvertical-separatortheightsbutton-press-event('RHR#R!RIRRt resNumListR)RtreplacetmaxRRRXtset_headers_visibleRtset_modetSELECTION_NONEtset_grid_linestTREE_VIEW_GRID_LINES_VERTICALRt enumerateRRt BOLD_WEIGHTtsortedRtvaluesRZtZeroDivisionErrortfloatRRt set_expandRRRRDt_ReviewSuitesGui__overviewClick(R,RtRqttypeListtoverviewListStoreR RRGtcolumnWidthCharsRwt setColumntcolNumtrenderertbestProbtsecondBestProbtratiotminimizationScoretcolumnt colHeight((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__createOverviewTreeViewsV  /,     ,   "    cCstj}|jtj|j||j\}}|j}tg|jD]}|jd^qW} | d|j |jddd|j |jdd7} || t dt } || kr|j tj tj |j|d|dt} ny|jjd} Wn'tk rVtjjd} nX|jd} |j tjtj |j| | | |dt} || fS(s@Create a ScrolledWindow object to display the suite overview TreeView ARGUMENTS: overviewTreeView - the TreeView object used to display the suite overview prevConfButton - the previous conformer button (so we can calculate its width) treeViewScrollWidth - the width of the TreeView used to display the conformer list RETURNS: overviewScroll - the newly created ScrolledWindow object wideOverview - whether or not the ScrolledWindow takes up the full window width iiiiisscrollbar-spacing(RIRRRR\RRAtsumt get_childrentquery_child_packingRR RRRRXtget_hscrollbarRt HScrollbarRt POLICY_ALWAYSRZ(R,RwRiRyRztoverviewTableWidthReqtoverviewTableHeightReqtprevConfButtonHBoxtchildtprevConfButtonWidthtsuiteFrameWidthR{thScrollHeightReqR((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__createOverviewScrolledWindows*   /D   c Csv|\}}|j||}|r7|jdtn;|j||} | rb|jdtn|jdddS(s4Appropriately set the background of a cell listing sugar pucker ARGUMENTS: column - the TreeViewColumn to be changed renderer - the CellRenderer for the column confListStore - the ListStore containing the displayed data iter - a TreeIter pointing to the specified row of the TreeView columnList - a list of (the number of the column to be changed, the number of the column containing the best conformer) RETURNS: None EFFECTS: Sets the background color for the specified cell to: DIFFERENT_PUCKER_COLOR if it's different than the pucker for the best path BEST_PATH_COLOR is it's the best conformer None otherwise scell-backgroundN(RRtDIFFERENT_PUCKER_COLORRR%( R,R$RRrtitert columnListt puckerColumntbestPathColumntisDifferentPuckert isBestPath((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt __setPuckerBgDs cCs9|jdkr5|j||||j|jdndS(s4Select the previous suite ARGUMENTS: widget - the button used to invoke this function. Ignored. confTreeView - the TreeView used to display data about conformers for the current suite suiteFrame - the GTK frame containing the "Suite X of Y" label overviewTreeView - the TreeView used to display the suite overview RETURNS: None EFFECTS: Recenters the screen on the previous suite and updates the RCrane GUI to reflect that suite. iN(R"t!_ReviewSuitesGui__prevOrNextSuite(R,RRtRqRw((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt __prevSuitebs cCsB|jt|jkr>|j||||j|jdndS(s,Select the next suite ARGUMENTS: widget - the button used to invoke this function. Ignored. confTreeView - the TreeView used to display data about conformers for the current suite suiteFrame - the GTK frame containing the "Suite X of Y" label overviewTreeView - the TreeView used to display the suite overview RETURNS: None EFFECTS: Recenters the screen on the next suite and updates the RCrane GUI to reflect that suite. iN(R"R#RR=(R,RRtRqRw((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt __nextSuitess cCs|j|j|dsN(i(i(RIRt set_valueRR (R,RwRotnewConfR((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyt__changeOverviewConformerMs  +N(t__name__t __module__t__doc__R%RZRXR9R+RNRQRRRKRLRORMRPRRSRTR=R*RER]RUR`RVRR(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyR's.M    8 # ` 6    K    (( RoRIRGtcopyRtosttimeRtcootRRRRRRR RR R tguiUtilsR R RRRt rotamerSeqRR5Rt WEIGHT_HEAVYRR(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.pyts   .(