ó Ñ%Tc@s%dZddlmZmZmZddlmZddlmZddlm Z ddl m Z ddl Z ddl mZdd lmZmZmZmZdaead „Zd „Zed d gƒZedddddddgƒZd„Zed„Zd„Zd„Z d„Z!dS(s(Extend an existing chain of nucleotides.iÿÿÿÿ(tadd_status_bar_texttclear_pending_pickstimol_refinement_map(tuser_defined_click_py(tselectMapDialog(tcreateCitationPopup(tPseudoMoleculeN(tTraceGui(treportPDB2ErrortreportInsCodeErrortSTANDARD_BASEStreportModifiedNucErrorcCsŒtƒtjƒtr=dGHtdƒtƒtƒtanKtƒdkr_dGHt t ƒdSdGHtdƒt ƒt at dtƒdS( síPrompt the user to pick an atoms to extend a stretch of nucleotides. Alternatively, if we're already waiting for the user to pick an atom, then cancel the pending pick. ARGUMENTS: None RETURNS: None sRotamerize cancelledsExtend chain cancellediÿÿÿÿs-No refinement map set for RCrane extend chainNsClick on a nucleotide to extends7Pick a nucleotide [Ctrl Left-mouse rotates the view]...i(Rt rotamerizetclearPendingRotamerizetwaitingForClicksRRt__setMenuToExtendChaintFalseRRt pickAtomst__setMenuToCanceltTruetuser_defined_clicktextendChainFromAtomSpec(((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyR"s"      cCs‘tƒta|d\}}}}}}|jƒ}ytd|d|ƒ}Wn-tk r}}|GHtt|ƒdƒtSXt|ƒt|ƒ} |j|ƒ} |j | ƒ} |j | ƒ} |j | ƒ} t}| rò|j | dƒ}nd}| r3| r d}qéd| dGHt d| dƒtSn¶|rƒ| rgd}| d7} t} |j| ƒ} qét|| ƒ}|sétSnf| r²| r²d| dGHt d| dƒtS| rÁd }n(| rÐd}nt|| ƒ}|sétS|j| ƒdd krt| ƒtS| rN|j| dƒdd krNt|j| dƒƒtS| rŒ|j| dƒdd krŒt|j| dƒƒtS| r²| d}|j| dƒ}n | }| }|j|ƒ}|tkrêt||ƒtS|j|ƒrt|ƒtS|j|ƒ}|d ks.|d kr7d }nd}|jd|ƒdkrxd|dGHt d|dƒtS|j||ƒdkrÃd|d|dGHt d|d|dƒtS|j| ƒ}| r| r|dkrd| dGHt d| dƒtS|d krJ| rJd| dGHdGHt d| dƒtSdt|ƒdGH|j| ƒ|jƒtd|d|d| ƒdS(síRotamerize a stretch of nucleotides ARGUMENTS: atomSpec - an atom spec specifying the start of the chain extension RETURNS: False if there is a problem with the selected nucleotide None otherwise itcreateFromMoleculetchains Rotamerization canceled.is Nucleotide s0 is an isolated phosphate group. Cannot extend.s is not at the end of a chainittAtGtN9tN1sC1's0 does not have a C1' atom. Cannot extend chain.s does not have an s atom. Cannot extend chain.sHis an isolated nucleotides without any phosphates. Cannot extend chain.sCannot extend nucleotide s, in the 5' direction without a 3' phosphate.sG Please add a 3' phosphate by extending the chain in the 3' direction.s!About to extend the chain in the s ' directiont directiontexistingMoleculetresIndexToExtendN(RRRtstripRtPseudoMoleculeErrortcreateRCraneErrorDialogtstrtresIndextconnectedToNextFromIndextconnectedToPrevFromIndextisOnlyPhosGroupFromIndextNoneRRt resNumFullt__decideDirectionFromAtomtresNumR tresTypeFromIndexR R tcheckPDB2FromIndexRtgetAtomCoordsFromIndextgetPhosCoordsFromIndextsetResInsertionPointtsaveMoleculeStateR(tatomSpectmolRR+tinsCodetatomtaltt pseudoMolterrR)R$tconnectedToNexttconnectedToPrevtcurResIsPhosOnlytnextResIsPhosOnlyt extendDirtresIndexToChecktresNumFullToChecktresTypetbaseTypetglyNt curPhosCoords((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyRLs¸          ##          sC3'sO3'tPtOP1tOP2tOP3sO5'sC5'sC4'cCsD|tkrdS|tkr dSd|dGHdGHtdƒtSdS(sDetermine the direction to extend the chain based on the atom name (for use with isolated nuclotides) ARGUMENTS: atomName - the atom name resNum - the residue number of the current nucleotide (used in reporting errors) RETURNS: False if the direction cannot be determined from the atom name 3 or 5 otherwise EFFECTS: if the direction cannot be determined from the atom name, an error will be reported to the user (and False will be returned) iis Nucleotide s< is an isolated nucleotide. Please select either the O5' ors;O3' atom to extend in the 5' or 3' direction, respectively.s6Must select either O5' or O3' of isolated nucleotides.N(tATOMS3PtATOMS5PRR(tatomNameR+((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyR*õs    cCs'|a|r#tatƒtƒndS(sÐARGUMENTS: menuItem - the gtk MenuItem to store OPTIONAL ARGUMENTS: resetLabel - whether we should reset the menu label to "Extend chain..." (and also clear all pending atom picks in Coot) This is intended for use when we're reloading RCrane Defaults to False RETURNS: None EFFECTS: stores menuItem in the module-level variable __menuItem N(t __menuItemRRRR(tmenuItemt resetLabel((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyt storeMenuItems cCs&tdk r"tjƒjdƒndS(snSet the menu entry labels to "Extend chain..." ARGUMENTS: None RETURNS: None sExtend chain...N(RKR(t get_childtset_text(((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyR(s cCs&tdk r"tjƒjdƒndS(stSet the menu entry label to "Cancel extend chain..." ARGUMENTS: None RETURNS: None sCancel extend chain...N(RKR(RORP(((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyR5s cCs+tr#dGHtƒtƒtatStSdS(sËCancel any pending extend chain call (intended to be called by rotamerize) ARGUMENTS: None RETURNS: True if there was a pending extend chain call False otherwise sExtend chain cancelledN(RRRRR(((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pytclearPendingExtendChainBs ("t__doc__tcootRRRRRRt citationPopupRtpseudoMoleculeRR ttraceGuiRtreportInputErrorsRR R R R(RKRRRRt frozensetRHRIR*RNRRRQ(((sY/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/extendChain.pyts& " * ¥!