%Tc@sdZddlZddlZddlZddlmZddlmZm Z m Z m Z m Z m Z mZmZmZmZmZmZmZddlmZddlmZddlmZddlmZdd lmZdd lmZydd lm Z!Wne"k rnXydd lm#Z#Wne"k rJd Z#nXddl$m%Z%m&Z&ddl'm'Z'ddl(m(Z(m)Z)ddl*m+Z+ddl'm'Z'ddl,m-Z-m.Z.m/Z/ddl0Z0ej1j2ej1j3e4Z5ej1j6e5dZ7e%dej1j6e7ddej1j6e7dZ8e+ej1j6e7dZ*dZ9dZ:dZ;dZ<dZ=dZ>dZ?dZ@d ZAd!ZBd"ZCd#ZDd$ZEd%ZFd&ZGd'ZHd(ZIeJZKeLd)gZMeLd*jNd+ZOeLd,jNd+ZPeJaQeLd-jNd+ZRd.ZSeJd/ZTeJeJeUeUeJd0ZVd1ZWd2ZXeJd3ZYeJd4ZZd5Z[ej\d6Z]d7Z^d8Z_d9Z`d:Zad;ZbeJeUd<Zcd=Zdd>Zed?Zfd@Zgd&dAZhdBfdCYZidS(Ds0Functions for calculating nucleotide coordinatesiN(tdeepcopy( t&refinement_immediate_replacement_statet$set_refinement_immediate_replacementtaccept_regularizementtclear_all_fixed_atomstadd_extra_torsion_restraintt"set_refine_with_torsion_restraintst$refine_with_torsion_restraints_statet matrix_statet set_matrixtdelete_all_extra_restraintstadd_extra_start_pos_restraintt refine_zonet2set_use_only_extra_torsion_restraints_for_torsions(t svn_revision(tmonomer_restraints_py(tset_monomer_restraints_py(trefine_residues_py(trefine_zone_with_score_py(tmark_multiple_atoms_as_fixed_py(tregularize_zone_with_score_py(t4use_only_extra_torsion_restraints_for_torsions_statecCsdS(Ni((((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyR2s(tBuildInitSugart rotateSugar(t puckerList(t buildPhosOxytbuildInitOrTerminalPhosOxy(t RotDataLoader(t HBOX_SPACINGt VBOX_SPACINGtcreateRCraneWindowObjecttdatatc3pStrucsc3p.pdbtc2pStrucsc2p.pdbs dihedData.csvg?ig?g@gt@g b@g0u@gA@g^@g^gL8@ii iiisO3's!P C2' O2' C3' O3' C4' O4' C5' O5't s P O5' OP1 OP2s3N1 N9 C1' C2' O2' C3' O3' C4' O4' C5' O5' P OP1 OP2c Cst||jd}t}d}d}zc|jdkrGdS|jdkrt|ddddddd|jdjd|jdjd|d|jdj ndg}g}t|ddddd|dd|jdj|jdj|jdj \}} |\|jd_|jd_|j |jdjd|jdjd|jdjd g|j | |j t } x7t dt |D] } t|| dpd| | d| d|| d|| |j| dj|j| j|j| dj|j| jd | \}} |\|j| d_|j| _|j| d_|j |j| djd|j| jd|j| jd g|j | |j t} qWt |} t|| dpd| | d| d|| dd|j| dj|j| jd|j| jd | \}} |\|j| d_|j| _|j| d_|j | |j Wdt|X|jdkr|jn||fS( s\Calculate coordinates for a chain of nucleotides ARGUMENTS: builtChain - a chain object containing phosphate and base coordinates for all nucleotides to be built bestPath - a list of the desired conformers to be built pseudoMol - a pseudoMolecule object currently being used to display the chain window - the window contianing the GUI RETURNS: intermediateAtomLocs - phosphate and O3' coordinates for each nucleotide immediately before minimization of that nucleotide was started minimizationScores - a list of the minimization scores for each nucleotide NOTE: If only a single nucleotide is being built, then we don't have a full suite, so there are no confmers In this case, bestPath should be a scalar containing the intended pucker of the nucleotide to be built iNiitpuckert nextResAtomstPsO3'sC3'tfixPrevPhosOxy(tProgressDialogObjecttnumNucst__changeCootSettingstNonet __minCoordst nucleotidesttypetatomstnucstappendtprogresstTruetxrangetlentFalset__restoreCootSettingstdrawExtraBonds( t builtChaintbestPatht pseudoMoltwindowtprogressDialogtorigCootSettingstintermediateAtomLocstminimizationScorest newCoordstscoreR&tresNum((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyt calcCoords|sh      @  /5D    !5   cCss|j|}|j|}t|||d} xtjrTtjtq8Wt} t|} dG|GdG|GHd g} g} z|dkrdGHt |d d || j dj d |dd | j dj | j dj | j djd| \}}|\| j d_| j d_| j| j djd| j djd| j djd g| j||d7}d }| jnd}t}x{t||D]j}t ||dkr| j |d j nd | j |dj | j |j | j |dj ||d||| j |dj | j |j | j |dj | j |jd |d| \}}|\| j |d_| j |_| j |d_| j| j |djd| j |jd| j |jd g| j|| j|d7}t}t}qW|}|dt| j kr<t ||dkrY| j |d j nd | j |dj | j |j | j |dj ||d||| j |dj | j |j | j |dj | j |jd td |d| \}}|\| j |d_| j |_| j |d_| j|n| jWd t| | jX|j| | fS(sRecalculate coordinates (using different rotamers) for part of a chain of nucleotides starting with a chain built by calcCoords ARGUMENTS: startingRes - the first residue to rebuild endingRes - the last residue to rebuilt rots - what rotamers to use for the rebuild origCoords - a chain object containing the current coordinates pseudoMol - a pseudoMolecule object currently being used to display the chain window - the window contianing the GUI OPTIONAL ARGUMENTS: ignoreDensity - ignore the density when performing the minimization defaults to False RETURNS: intermediateAtomLocs - phosphate and O3' coordinates for each nucleotide immediately before minimization of that nucleotide was started minimizationScores - a list of the minimization scores for each nucleotide NOTE: Currently, the return values from this function are only used for initial rotamerize minimization. They are ignored for all other calls to this function isRecalculating t-isRebuilding initial nucleotidet ignoreDensityR%sO3'sC3'iR&tnextResAlreadyBuiltN(tresIndexR'tgtktevents_pendingtmain_iterationR5R)RR*R+R/RBR,R-R.R0R1R2R3R4R6t restoreWindowR7(t startingRest endingRestrotst origCoordsR:R;REtstartingResIndextendingResIndexR<R=R8R>R?R@RAt rotsIndexR&RGtfirstRes((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyt recalcCoordssr      @   R/5D    R/5   c' Cs~|j}d}d}d}d}ts0d}nt|trPt|d}n#|dk rmt|d}n| }tj| |}|j|||dk rt | j |j }t |}|j ||t ||}|j ||n|j |p ||}|j}t||||| t||||||||| trt|||||||||| |dk rt||||j|dtqnt|||p|p|||}|}d}|tkr|j|p||}|j |p||}|j|p1|||tt|| d}|j||t|||px|px|||}||kr|j|p|||q|j|p||}|}d}n|j|p||}|tkr|j |p||} |j|p|||tt|| d}!|j||!t|||pe|pe|||}||kr|j|p||| q|j|p||}|}d}ntr.dGHdGHdGHd t|GHd t|GHd t|GHdGHd |d dt|dGHdGHn|dkrj|j|}"|dkr|\}#}$t |#}%|%dk rg|j ||%qgqj|j |"ddkr*|j!|"d r*|\}&}#}$t"|#|&}|dk r|j ||nt |$|#}|dk rg|j ||qgqj|\}&}#}$t"|#|&}%|%dk rj|j ||%qjnt#|||fS(s Build a single nucleotide and minimize its coordinates. ARGUMENTS: pseudoMol - the pseudoMolecule object currently being used to display the chain prevPrevResNum - the residue number of residue i-2 only used if we're using Phenix's pucker-specific restraints, in which case it's needed to restrain the non-bridging oxygens of residue prevResNum prevResNum - the residue number of the previous residue using Coot numbering (i.e. starting at 1, not 0) curResNum - the residue number to build using Coot numbering (i.e. starting at 1, not 0) nextResNum - the residue number of the next residue using Coot numbering (i.e. starting at 1, not 0) curRot - the rotamer to use when building the current residue nextRot - the rotamer to use when building the next residue prevResType - the residue type (i.e. A, G, C, or U) of the previous residue curResType - the residue type (i.e. A, G, C, or U) of the current residue nextResType - the residue type (i.e. A, G, C, or U) of the next residue curResAtoms - a hash of atom coordinates for the current residue OPTIONAL ARGUMENTS: nextResAlreadyBuilt - should be True if the next residue is already built (i.e. if we are being called from recalcCoords instead of calcCoords) Defaults to False. fixPrevPhosOxy - whether to fix the phosphoryl oxygens of the previous nucleotide during minimization pucker - the sugar pucker for this nucleotide. Only necessary when both curRot and nextRot are None (i.e. when we're building the only nucleotide of the chain) Defaults to None nextResAtoms - a hash of atoms containing coordinates for the next phosphate. Should only be provided if we are building the only nucleotide of the chain Defaults to None ignoreDensity - ignore the density when performing the minimization defaults to False RETURNS: newCoords - new atomic coordinates calculated by the minimization procedure, formatted as a list of dictionaries score - the score received from Coot's minimization iitstriptantitsyns high-antis ********************************s * Starting struc * Score *s* Anti * %s *s* Syn * %s *s* High-anti * %s *s* Using %s minimizationR"i s *N($tchainR*tUSE_PHENIX_RESTRAINTSt isinstancetstrRt sugarBuildert buildSugartaddSugartdicttitemsRt addPhosOxyt getCootNucstmolNumt __fixAtomst__setTorsionRestraintst__addPhenixRestraintst__fixEntireResiduet getAtomNamesR5t__runRefinementtSYN_REBUILDING_CUTOFFt updateRest setCootNucsRt replaceSugartHIGH_ANTI_REBUILDING_CUTOFFtPRINT_SUMMARY_TABLEt__stringifyScoreR4RGtnumAtomsFromIndextconnectedToNextFromIndexRt__clearResRestraints('R:tprevPrevResNumt prevResNumt curResNumt nextResNumtcurRottnextRott prevResTypet curResTypet nextResTypet curResAtomsRFR&R#R$RERXtantiRefinementScoretsynRefinementScorethighAntiRefinementScoretselectedStartingStruct curPuckertinitSugarCoordst sugarAndPtphosOxyCoords5tphosOxyCoords3tpreMinimizationStrucRcRAR@tantiRefinementStructsynSugarCoordstprevRefinementStructhighAntiSugarCoordst curResIndextnewCurResAtomstnewNextResAtomst phosOxyCoordstnewPrevResAtoms((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyR+}s+      "% ($  $   $       -    cCs,|tkrdS|dk r$d|SdSdS(sFormat a refinement score for printing in the summary table ARGUMENTS: score - the refinement RETURNS: score formatted as a fixed length string or "Not run" if score is None s Faileds%7.3fsNot runN(tREFINEMENT_FAIL_SCORER*(RA((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRp\s   c Cs|j}|j}t|\}}t|\} } t|\} } g} |dk r|rlt}ntjddg}xQ|j|dtD]7}|j|kr| j ||||dgqqWnt ||| | ddt t ||| | ddt xN|j| dtD]7}|jt kr#t ||| | |dt q#q#W| dk rxQ|j| dtD]7}|jtkr| j || | |dgqqWnt|| ddS(s$Fix and restrain the appropriate atoms for minimization ARGUMENTS: pseudoMol - the PseudoMolecule object representing the molecule to fix atoms in prevResNumFull - the residue number of the previous residue using Coot numbering (i.e. starting at 1, not 0) including insertion code curResNumFull - the residue number using Coot numbering (i.e. starting at 1, not 0) including insertion code nextResNumFull - the residue number of the next residue using Coot numbering (i.e. starting at 1, not 0) including insertion code OPTIONAL ARGUMENTS: fixPrevPhosOxy - whether to fix the phosphoryl oxygens of the previous nucleotide during minimization Defaults to False RETURNS: None tOP1tOP2RUts P iN(RcRXt __splitResNumR*tPREV_RES_MOBILE_ATOMStunionRhR5RUR0R tHARMONIC_STD_DEV_PHOSPHATEtCUR_RES_MOBILE_ATOMStHARMONIC_STD_DEV_BASEtNEXT_RES_MOBILE_ATOMStmark_multiple_atoms_as_fixed(R:tprevResNumFullt curResNumFulltnextResNumFullR&RcRXRutprevResInsCodeRvt curResInsCodeRwtnextResInsCodetfixListtprevResMobileAtomstcurAtom((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRdls.    &# &c #Csf t|\} } t|\} } t|\} }|dk rt|tr tj|}tj|}tj|}tj|}tj |}tj |}tj |t }tj |t }tj|t }tj|t }tj|t }tj|t }n`|d}|d}|d}|d}|d}|d}t}t}t}t}t}t}|dk rt||| | dd|| | d d|| | d d|| | d d||dn|dk r<t||| | d d|| | d d|| | d d|| | d d||dn|dk rt||| | d d|| | d d|| | d d|| | d d||dn|dk rt||| | dd|| | d d|| | d d|| | d d||dn|dk rVt||| | d d|| | d d|| | dd|| | d d||dn|dk rt||| | d d|| | dd|| | d d|| | d d||dqnd}d}t|trt|d}tj|}tj|t }nBt|trGt|d}tj|}tj |t }n|dk rt||| | dd|| | d d|| | d d|| | d d||dn|dk r|dkrt}t}t} nt}t}t} t||| | d d|| | dd|| | dd|| | dd|tdt||| | dd|| | dd|| | dd|| | d d|tdt||| | dd|| | d d|| | dd|| | dd| tdn|dks|dkrd}!d}"n d}!d}"t||| | dd|| | dd|| | |!d|| | |"dttd|dk rb t|tr'tj|}tj |t }|rtj|}tj|}tj |}tj |}tj|t }tj|t }tj|t }tj|t }qnY|d}t}|r|d}|d}|d}|d}t}t}t}t}n|dk rt||| | d d|| | d d|| | d d|| |d d||dn|rb |dk rBt||| | d d|| | d d|| |d d|| |d d||dn|dk rt||| |dd|| |d d|| |d d|| | d d||dn|dk rt||| |d d|| |d d|| |dd|| |d d||dn|dk r_ t||| |d d|| |dd|| |d d|| |d d||dq_ qb ndS(sSet the appropriate torsional restraints for the minimization ARGUMENTS: molNum - the Coot molecule number chain - the chain name prevResNumFull - the residue number of the previous residue including insertion codes curResNumFull - the residue number to build including insertion codes nextResNumFull - the residue number of the next residue including insertion codes curRot - the rotamer to use when building the current residue nextRot - the rotamer to use when building the next residue curResType - the residue type (i.e. A, G, C, or U) of the current residue OPTIONAL ARGUMENTS: nextResAlreadyBuilt - should be True if the next residue is already built (i.e. if we are being called from recalcCoords instead of calcCoords) Defaults to False. RETURNS: None iiiiiis C5'Rs C4's C3's O3's P s O5's O4's C1's C2'tGtAs N9 s C4 s N1 s C2 N( RR*RZR[trotDatat prevDeltaMeantepMeantzetaMeant alphaMeantbetaMeant gammaMeant prevDeltaSDtTORSION_STD_DEV_MODtepSDtzetaSDtalphaSDtbetaSDtgammaSDtMANUAL_TORSION_STD_DEVRRt curDeltaMeant curDeltaSDtNU0_C2tNU1_C2tNU4_C2tNU0_C3tNU1_C3tNU4_C3t NU_STD_DEVtCHI_MEANt CHI_STD_DEV(#RcRXRRRRxRyR{RFRuRRvRRwRt prevDeltateptzetatalphatbetatgammaRRRRRRRtdeltatdeltaSDtcurNu0tcurNu1tcurNu4t baseAtom1t baseAtom2((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyResR                                 c CsdGHdG|GdG|GHdGHt|\}}t|\}}|r`t||||d} nt||||d} tt| S(sORun the minimization using Coot's built-in refinement functions ARGUMENTS: molNum - the Coot molecule number chain - the chain name startingResNumFull - the residue number (including insertion code) of the first nucleotide to refine endingResNumFull - the residue number (including insertion code) of the last nucleotide to refine OPTIONAL ARGUMENTS: ignoreDensity - ignore the density when performing the minimization defaults to False RETURNS: the refinement score s*************************sAbout to refine residuesRDR(Rtregularize_zone_with_scoretrefine_zone_with_scoreRt__calcRefinementScore( RcRXtstartingResNumFulltendingResNumFullREtstartingResNumtstartingResInsCodet endingResNumtendingResInsCodetrefinementResults((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRiscCst|t|dS(sClear the torsional restraints and fixed atoms that applied to the residues we were just minimizing ARGUMENTS: molNum - the Coot molecule number RETURNS: None N(RR (Rc((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRss s(-?\d+)([A-Za-z]?)$cCsK|dkrdStjt|j\}}t|}||fSdS(s!Split a residue number into number and insertion code ARGUMENTS: resNumFull - a residue number potentially contianing an insertion code RETURNS: resNum - the residue number without the insertion code (as an int) insCode - the insertion code N(NN(R*t__splitResNumREtmatchR[tgroupstint(t resNumFullRBtinsCode((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRs ! c Csi}xd#D]}t|||| d kr|ddkrd} qd} n|d dkr5d}q>d}n| d k r_| d kr_| } nt|\}}t|\}}t|\}}t|\}}tj||||||| | | || tj|||||| | | || d S( sAdd angle and bond restraints for the specified nucleotides using the Phenix pucker-specific restraint values ARGUMENTS molNum - the Coot molecule number chain - the chain name prevPrevResNumFull - the residue number of residue i-2 (needed to restrain the non-bridging oxygens of residue prevResNum) prevResNumFull - the residue number of the previous residue using Coot numbering (i.e. starting at 1, not 0) curResNumFull - the residue number to build using Coot numbering (i.e. starting at 1, not 0) nextResNumFull - the residue number of the next residue using Coot numbering (i.e. starting at 1, not 0) curRot - the rotamer to use when building the current residue nextRot - the rotamer to use when building the next residue curResType - the residue type (i.e. A, G, C, or U) of the current residue OPTIONAL ARGUMENTS: nextResAlreadyBuilt - should be True if the next residue is already built (i.e. if we are being called from recalcCoords instead of calcCoords) Defaults to False. onlyPucker - should only be provided if curRot and nextRot are None. This is used when we're only building a single nucleotide, so we don't have a full suite and therefore can't predict a conformer RETURNS: None RRs N9 s N1 ig\@iiiN( R*RZt basestringRtlistRtphenixRestraintstsetAngleRestraintstsetBondRestraints(RcRXtprevPrevResNumFullRRRRxRyR{RFt onlyPuckertglycosidicBaseAtomt prevPuckerRt nextPuckerRttprevPrevResInsCodeRuRRvRRwR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRfsD          +cCs+tdkrtadGHtSdGHtSdS(s Enable Phenix's pucker-specific restraints for minimization ARGUMENTS: None RETURNS: True if enabling the restraints succceeded, False otherwise NOTE: Phenix restraints are only available in versions of Coot newer than 3926 iVsUsing Phenix restraintss\Coot must be newer than 0.7-pre r3926 to use Phenix restraints. Using Coot/CCP4 restraints.N(RR2RYR5(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pytenablePhenixRestraintss cCstadGHtS(sDisable Phenix's pucker-specific restraints for minimization and use the Coot/CCP4 restraints instead ARGUMENTS: None RETURNS: True (for consistancy with enablePhenixRestraints()) sUsing Coot/CCP4 restraints(R5RYR2(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pytdisablePhenixRestraintss cCstS(sCheck if we are using Phenix's pucker-specific restraints for minimization ARGUMENTS: None RETURNS: True if we are using Phenix restraints False if we are using Coot/CCP4 restraints (RY(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pytusingPhenixRestraintss cCsNt|\}}g|D]}||d|dg^q}t||ddS(s^Fix all atoms in a residue ARGUMENTS: molNum - the molecule number of the residue to fix chain - the chain of the residue to fix resNumFull - the residue number of the residue to fix including insertion code atomList - a list of all atoms in the specified residue RETURNS: None RiN(RR(RcRXRtatomListRBRRR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRgs (cCs|dkrE|j|d|}|jdj}|jdj}n(|j||}|jdj}d}t||}|j||dS(sBuild the non-bridging oxygens onto a terminal nucleotide ARGUMENTS: resIndex - the index of the residue to build the phosphates onto OPTIONAL ARGUMENTS: direction - which side of the residue to add the phosphoryl oxygens to RETURNS: NONE iiiN(t!createPartialChainObjectFromIndexR,R.R*RtaddPhosOxyFromIndex(R:RGt directionRXt prevResAtomsR}R((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pytbuildOnlyPhosOxy%s R'cBs5eZdZdZdZddZdZRS(sZA class for displaying a progress dialog while calculating/minimizing backbone coordinatescCs||_d|_d|_d|_d|_d|_||_d|_|jdk r|jj }|dk r|j |_||_|jj |qn t |_|j dS(sbInitialize a ProgressDialogObject object ARGUMENTS: window - the window object to display the progress dialog in if None, a new window will be created totalNum - the total number of steps for the progress bar akin to the deprecated set_discrete_blocks functionality RETURNS: an initialized ProgressDialogObject object EFFECTS: If provided, the contents of window are replaced by a progress bar The contents of window can later be restored using restoreWindow() iN(t_ProgressDialogObject__windowR*t$_ProgressDialogObject__oldWindowSizet(_ProgressDialogObject__oldWindowContentst,_ProgressDialogObject__progressFracIncrementt&_ProgressDialogObject__curProgressFract%_ProgressDialogObject__curProgressIntt_ProgressDialogObject__totalNumt"_ProgressDialogObject__progressbart get_childtget_sizetremoveRt+_ProgressDialogObject__createProgressDialog(tselfR;ttotalNumt windowChild((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyt__init__Hs            cCstjtt}|jj||jjddtjd}|jtj |j |ttt tj |_ |j jdt|jdtjdddd}|j|j |j |ttt |jjd |j|_d S( s|Add the ProgressBar to self.__window ARGUMENTS: None RETURNS: None is= Calculating backbone coordinates... Please wait... s Built 0 of s nucleotidestxscaleg?txaligng?g?N(RHtVBoxR5RRtaddtresizetLabelt set_justifytJUSTIFY_CENTERt pack_startRt ProgressBarRtset_textR[Rt Alignmenttshow_allR(Rt windowBoxtcalculatingLabelt progressAlign((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyt__createProgressDialogls ! icCs|j||j7_|j|7_|jdkr@d|_n|jj|j|jjdt|jdt|jddS(sIncrement the progress bar OPTIONAL ARGUMENTS: step - how many steps to increment the progress bar by, defaults to 1 RETURNS: None isBuilt s of s nucleotidesN(RRRRt set_fractionR-R[R(Rtstep((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyR1s  cCss|jj}|jj||jdk rD|jj|jn|jdk ri|jj|jnd}dS(sPRestore the original contents of the window and destroy the ProgressDialogObject object ARGUMENTS: None RETURNS: None EFFECTS: the original contents of the window are destroyed the ProgressDialogObject is set to None, since it is no longer useful N(RRRRR*R&RR'(RR!((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyRKs (t__name__t __module__t__doc__R"RR1RK(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyR'Es  $  (jR8tos.pathtostreRHtcopyRtcootRRRRRRRRR R R R R RRRRRRtrefine_residuesRRRRRRt ImportErrorRtbuildInitSugarRRRRRRRtguiUtilsRRRRtpathtdirnametabspatht__file__t rcranePathtjointdataPathR\RRRRRRRRRRRRRRRjRnRR5Rot frozensetRtsplitRRRYRRCRTR*R+RpRdReRiRstcompileRRRR)R6RRfR R R RgRR'(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/calcCoords.pyts   X     {   D #   8 +  Z