%Tc@sdZddlmZddlZddlZddlmZmZm Z m Z m Z m Z m Z ddlmZddlmZmZddlmZddlmZdd lmZmZdd lmZdd lmZdd lmZdd lm Z ddl!Z!ddl"m#Z#m$Z$m%Z%m&Z&dZ'da)da*e+a,da-e+dZ.e+dZ/dZ0e+e+dZ1dZ2dZ3dZ4dZ5dZ6dS(sDRecalculate coordinates for an already-built stretch of nucleotides.i(tdeepcopyN(tadd_status_bar_texttnew_generic_object_numbertset_display_generic_objecttto_generic_object_add_linet graphics_drawtclear_pending_pickstimol_refinement_map(tuser_defined_click_py(tPseudoMoleculetPseudoMoleculeError(tdetermineRotamerSeq(t recalcCoords(tcreateRCraneWindowObjecttcreateRCraneErrorDialog(tReviewSuitesGui(tBOND_LIST_FULL(tselectMapDialog(tcreateCitationPopup(treportPDB2ErrortreportInsCodeErrortSTANDARD_BASEStreportModifiedNucErrort yellowtinticsttjtr=dGHtdtttan[ rftdkrfdGHt t dSdGHtdt t at dfddS( sPrompt the user to pick two atoms to rotamerize a stretch of nucleotides. Alternatively, if we're already waiting for the user to pick atoms, then cancel the pending picks. ARGUMENTS: None OPTIONAL ARGUMENTS: ignoreDensity - ignore the density when performing the minimization defaults to False RETURNS: None sRotamerize cancelledis+No refinement map set for RCrane rotamerizeNs'Click on 2 atoms (in the same molecule)s2Pick 2 atoms [Ctrl Left-mouse rotates the view]...icst||S(N(trotamerizeFromAtomSpecs(t atomSpec1t atomSpec2(t ignoreDensity(sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pytcs(Rt extendChaintclearPendingExtendChaintwaitingForClicksRRt__setMenuToRotamerizetFalseRRt pickAtomst__setMenuToCanceltTruetuser_defined_click(R((RsX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyR"9s"     c'Csatta|d\}}}}}}|d\} } } } } }|| krddGHtdtS|| krdGHtdtS|}|}t|t|}t| t| }ytd|d|dt}Wn-tk r }|GHtt|dtSX|j|}|j|}||kr^||}}||}}|| }} n|j |r{t |tS|dkr|j t d d d d d gkr|j |r|d8}|j|}n|d|jkr,| j dkr,|j|r,|d7}|j|}n||krKdGHtdtSxt||D]t}|j|s[d|j|d|j|ddGHtd|j|d|j|ddtSq[Wxt||dD]}|j|}|tkr"t|j||tS|j|}|d&k rd|j|d|dGHtd|j|d|dtSqW|d|jks|j| r|d8}|j|}||krdGHtdtSnxKt||dD]6}|j|ddkrt|j|tSqW||d}tdkr|tkrdGHdG|GdGtGHdGHdt|dGHdGHtd t|d!tttS|j||t\}}}t|\}}d"dj|GHd&} |d&krd&g|}!n|j|} | g|}!d&}"|d&krV|!d&g}!n|j|}"|!|"g}!|j|||j |p||p|t!|}#t"}$|j#|||j$|p||p|t%|||!|||$|\}%}&|d&k rd&g|%}%n|j&t'|||||%|&|$t|#d#|d$| d%|" d&S('sRotamerize a stretch of nucleotides ARGUMENTS: atomSpec1 - an atom spec specifying the start of the stretch atomSpec2 - an atom spec specifying the end of the stretch OPTIONAL ARGUMENTS: ignoreDensity - ignore the density when performing the minimization defaults to False RETURNS: False if there is a problem with the selected nucleotides None otherwise is-Rotamerize atoms are not in the same molecules*Rotamerize atoms are not in the same chaintcreateFromMoleculetchaintbatonss Rotamerization canceled.itPtOP1tOP2sO5'sC5'sO3's@You must select at least one suite (two residues) to rotamerize.s Nucleotides s and s' are not connected. Cannot rotamerize.s Nucleotide s is missing sL atom. Cannot rotamerize without phosphate and glycosidic bond coordinates.s4Cannot rotamerize this suite without a 3' phosphate.its-Warning: Too many nucleotides to rotamerize.s Trying to rotamerizes'nucleotides and your current maximum issB To increase the maximum, go to Calculate -> Scripting -> Pythons/ and type rcrane.setRotamerizeMaxNucleotides(t)sF or type rcrane.setRotamerizeMaxNucleotides(-1) to remove the limit.s<Warning: Too many nts to rotamerize. Trying to rotamerize s nts and your current max is sSuite string: Rt prevTorsionst nextTorsionsN((R R!RRtstrR R RtresIndextcheckPDB2FromIndexRtstript frozensettconnectedToPrevFromIndext resNumFullt getNumNtstconnectedToNextFromIndextrangetresTypeFromIndexRRtcheckPhosAndGlycosidicFromIndextNonetresNumRtMAX_NUCLEOTIDES_TO_ROTAMERIZEtcreatePartialChainObjectR$R tjointcalcSuiteTorsionst saveBfacstsaveCoordinatest__drawOrigCoordsR t resetNucstsetExtraBondRangeR trestoreSavedBfacsR('RRRtmol1tchain1t startResNumt startInsCodet startAtomtalt1tmol2tchain2t endResNumt endInsCodetendAtomtalt2tmolNumR't startResFullt endResFullt pseudoMolterrt startIndextendIndextcurIndext curResTypet missingAtomtnumNucsToRotamerizetchainObjtresNum5ptresNum3ptbestPathtpredictedProbsR.t rebuildRotsR/t oldCoordsObjtwindowtintermediateAtomLocstminimizationScores((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyRfs         '    +0  #&   "       $  c Cs5td}t|dg}d}x|jD]}xotdt|jD]X\}}|j|rK|j|rK|j|}|j|}|j||qKqKW|dk r|jdr|j||jdn|jdr|jd}q/d}q/Wx!|D]} t |t d| q Wt |S(sDisplay the original pre-rotamerize coordinates as a generic object ARGUMENTS: origCoords - a chain object containing the atoms to be drawn RETURNS: drawNum - the generic object number EFFECTS: creates and displays a new Coot generic object sPre-rotamerize coordinatesitbackboneR)sO3'iN( RRR<tnucsRttypethasAtomtatomstappendRtORIG_COORDS_COLORR( t origCoordstdrawNumtlineListtprevO3tcurNuctatom1tatom2t atom1Coordst atom2CoordstcurLine((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyRDKs&  "    cCs6|r|an|a|r2tattndS(sStore the "Rotamerize existing structure..." and "Rotamerize without density..." menu entries so that we can later change them to "Cancel current rotamerize..." ARGUMENTS: menuItem - the gtk MenuItem to store OPTIONAL ARGUMENTS: resetLabel - whether we should reset the menu label to "Rotamerize existing structure..." (and also clear all pending atom picks in Coot) This is intended for use when we're reloading RCrane Defaults to False ignoreDensity - whether this is the menu entry for "Rotamerize without density..." RETURNS: None EFFECTS: stores menuItem in the module-level variable __menuItem N(t__menuItemNoDensityt __menuItemR!RR R(tmenuItemt resetLabelR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyt storeMenuItemys cCsHtdk r"tjjdntdk rDtjjdndS(sSet the menu entry labels to "Rotamerize existing structure..." and "Rotamerize without density..." ARGUMENTS: None RETURNS: None s Rotamerize existing structure...sRotamerize without density...N(R{R<t get_childtset_textRz(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyR s  cCsHtdk r"tjjdntdk rDtjjdndS(szSet the menu entry label to "Cancel current rotamerize..." ARGUMENTS: None RETURNS: None sCancel current rotamerize...N(R{R<RRRz(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyR#s  cCst|adS(s Set the maximum number of nucleotides that can be rotamerized at once ARGUMENTS: newVal - the new maximum number of nucleotides to rotamerize at once if this value is <= 0, then there will be no limit RETURNS: None N(tintR>(tnewVal((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pytsetRotamerizeMaxNucleotidess cCstS(sGet the maximum number of nucleotides that can be rotamerized at once ARGUMENTS: None RETURNS MAX_NUCLEOTIDES_TO_ROTAMERIZE - the maximum number of nucleotides that can be rotamerized at once (R>(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pytgetRotamerizeMaxNucleotidess cCs+tr#dGHtttatStSdS(sCancel any pending rotamerize call (intended to be called by extendChain) ARGUMENTS: None RETURNS: True if there was a pending rotamerize call False otherwise sRotamerize cancelledN(RRR R!R$(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pytclearPendingRotamerizes (7t__doc__tcopyRtgtktos.pathtostcootRRRRRRRRR%tpseudoMoleculeR R t rotamerSeqR t calcCoordsR tguiUtilsR RtreviewSuitesGuiRt bondLengthRRt citationPopupRRtreportInputErrorsRRRRRoR<R{RzR!RR>R"RRDR~R R#RRR(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerize.pyts:  4 " - .!