ó Ń%Tc@s(dZddlmZmZmZmZmZddlmZddl m Z m Z m Z m Z mZmZmZmZmZddlmZddlmZmZddlmZmZmZmZeZdZed ƒZdZ d Z!d Z"d Z#d Z$d Z%dZ&dfd„ƒYZ'd„Z(dS(sSA class to determine the coordinates of the next phosphate atom in electron densityi’’’’(tradianstpitcostsintsqrt(t LinearInterp( tdisttanglet crossProdt scalarProdtminustplust magnitudettorsiont rotateAtoms(tln(tmediant lowerQuartile(t map_peaks_pyt!map_peaks_near_point_from_list_pytdensity_at_pointtadd_molecule_pyi iiigŠ?itNextPhoscBsƒeZdZiZd„Zd„Zdd„Zdd„Zd„Zd„Z d„Z dd „Z d „Z d „Z ed „ZRS( sSA class to determine the coordinates of the next phosphate atom in electron densitycCsRt|ƒ|_t|ƒ|_t|ƒ|_|j|ƒ|_t|ƒ|_dS(sInitialize the NextPhos object with distance and angle data ARGUMENTS: phosDistFilename - the name of a file containing smoothed data about inter-phosphate distances phosAngleFilename - the name of a file containing smoothed data about inter-phosphate angles sugarPhosSugarAngleFilename - the name of a file containing smoothed data about sugar-phosphate-sugar angles basesFilename - the name of a PDB file containing structures of all four bases pseudoChiFilename - the name of a file containing smoothed data about the pseudo-chi torsion (i.e. about base rotation relative to a simple backbone trace) RETURNS: an initialized NextPhos object N(Rt_NextPhos__phosDistInterpt_NextPhos__phosAngleInterpt$_NextPhos__sugarPhosSugarAngleInterpt_NextPhos__readBasest_NextPhos__baseStrucst_NextPhos__pseudoChiInterp(tselftphosDistFilenametphosAngleFilenametsugarPhosSugarAngleFilenamet basesFilenametpseudoChiFilename((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyt__init__2s c CsWt|dƒ}tdtƒdtƒdtƒdtƒƒ}xµ|jƒD]§}|dd!dkrhqIn|d d !jƒ}|d d !jƒ}t|d d!ƒ}t|dd!ƒ}t|dd!ƒ} |jddƒ}||| g||| atom name => coordinates trtAtCtGtUiisATOM i iiiii&i.i6t*t'sC1'(topentdictt readlineststriptfloattreplacetkeysR ( RtfilenametinputtstructcurlinetatomNametresNametxtytztcurRestc1loctcurAtom((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyt __readBasesFs"-'ic Cs…|j||ƒ}g}x |D]}t||ƒdkr|dkr^|j|||ƒ} n|j|||ƒ} | dd|d} tt|jjt||ƒƒƒt|jjt|||ƒƒƒt|j jt||| ddd!ƒƒƒt t| ƒ} |j || | fƒqqW|j dd„ddƒg|D]} | d^qH} g|D]} | d^qe}| |fS(sśFind the next phosphate in a chain using phosphate distance and angle data ARGUMENTS: mapNum - the molecule number of the Coot map to use curPhos - the coordinates of the current phosphate prevPhos - the coordinates of the previous phosphate prevSugar - the coordinates of the previous C1' atom OPTIONAL ARGUMENTS: direction - which direction to trace the chain: 3 implies 5'->3' 5 implies 3'->5' defaults to 3 (5'->3') RETURNS: peakList - a list of potential phosphate peaks sugarList - a list of potential C1' locations for each phosphate peak iiitkeycSs|dS(Ni((R8((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pytœstreversei( tgetPeaksRt findSugartPHOS_DIST_WEIGHTRRtinterpRRRtDENSITY_WEIGHTtappendtsort(RtmapNumtcurPhostprevPhost prevSugart directiontpeakst peakScorestcurPeakt sugarLocst densityScoretscoreR8tpeakListt sugarList((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pytnextPhosjs  ‚  c Cs2|j||ƒ}g}xŗ|D]²}t||ƒdkr|dkr^|j|||ƒ}n|j|||ƒ}|dd|d}t|jjt||ƒƒƒtt|ƒ} |j|| |fƒqqW|jdd„ddƒg|D]} | d^qõ} g|D]} | d^q} | | fS(smfind the second phosphate in a chain using phosphate distance data ARGUMENTS: mapNum - the molecule number of the Coot map to use curPhos - the coordinates of the first phosphate OPTIONAL ARGUMENTS: direction - which direction to trace the chain: 3 implies 5'->3' 5 implies 3'->5' defaults to 3 (5'->3') RETURNS: peakList - a list of potential phosphate peaks sugarList - a list of potential C1' locations for each phosphate peak iiiR?cSs|dS(Ni((R8((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyR@ĻsRAi( RBRRCRRREtSECOND_PHOS_DENSITY_WEIGHTRGRH( RRIRJRMRNRORPRQRRRSR8RTRU((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyt secondPhos¬s  /cs/|j|ˆƒ}|jd‡fd†ƒ|S(s7find the first phosphate in a chain ARGUMENTS: mapNum - the molecule number of the Coot map to use curPos - where to start the search (i.e. the current screen center coordinates) RETURNS: peaks - a list of potential phosphate peaks R?cs tˆ|ƒS(N(R(R8(tcurPos(sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyR@ås(RBRH(RRIRYRN((RYsV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyt firstPhosŲs c Cs9t||ƒ}d|dd|d}d|d}tdddgt||ƒƒ}t|ƒd krŽtdddgt||ƒƒ}nt||t|ƒƒ}t||ƒ} t| |t| ƒƒ} t|| ƒ} t| |ƒ} |j||| ƒ} xd| D]\} | dd !} d}t| |ƒ}t|d td ƒ}x[td td ƒD]F}t|t||ƒƒ\}}}t ||||ƒ}||7}q\W| \}}}t ||||ƒ}||7}t|| ƒ}t|d td ƒ}x[td td ƒD]F}t| t||ƒƒ\}}}t ||||ƒ}||7}qW| j |ƒq Wg}| d d}| dd}| j | dƒxktdt | ƒd ƒD]P}|}|}| |d d}||kr¶||kr¶|j | |ƒq¶q¶W|j dd„dt ƒxtdt |ƒƒD]ų}||dd !}t|||ƒ}t||ƒ}tt||ƒ|ƒ}t|d t|ƒƒ}t||d|dƒ}t|dt|ƒƒ}t||| dƒ}t|d t|ƒƒ}t||dƒ}t||ƒ||dd +q9W|S(s¢find potential C1' locations between the given 5' and 3' phosphate coordinates ARGUMENTS: mapNum - the molecule number of the Coot map to use phos5 - the coordinates of the 5' phosphate phos3 - the coordinates of the 3' phosphate RETURNS: sugarMaxima - a list of potential C1' locations, each listed as [x, y, z, score] gŽ’°«ÉĒæigdu«ē¤÷ł?gįķAČæ?gĢĪ¢w*Ü?gPżƒH†ķ?i igü©ńŅMbP?igš?ii’’’’iR?cSs|dS(Ni((R8((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyR@TsRAgÆ°ą~@‘b@gģų/Äó?g1Šµ/ŚQĄ(RRR R R R t_NextPhos__rotateSugarCentertDENSITY_CHECK_POINTStrangeRRGtlenRHtTrueRtrotate( RRItphos5tphos3t phosPhosDisttperpDisttprojDisttnormalt perpVectort projVectortsugarLoctsugarRotationPointstcurSugarLocFullt curSugarLoctcurDensityTotaltphosSugarVectortiR8R9R:tcurPointDensitytsugarPhosVectort sugarMaximat curPeakHeighttnextPeakHeighttprevPeakHeighttcurSugart phosAnglet phos5vectortaxistc1vectphosBisectorAxis((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyRCźsn  !$  ! ! cCs…t||ƒ}t|dt|ƒƒ}|\}}}t||ƒ\}} } |dg} | g} t} x| dtdtkr€t| ƒ}t| ƒ}|||| || }|||||||| || ||d}||| ||||||| ||d}||| ||||| ||||d}| j|||| gƒ| t7} qnW| S(s±rotate the sugar center by 360 degrees in ROTATE_SUGAR_INTERVAL increments ARGUMENTS: phos5 - the coordinates of the 5' phosphate phos3 - the coordinates of the 3' phosphate sugarCenter - the coordinates of the sugar center to be rotated RETURNS: rotatedPoints - a list of the rotated points, each listed as [x, y, z, rotation angle] iiigą?(R R R tSUGAR_ROTATION_INTERVALRRRRG(RRaRbt sugarCenterRytutvtwR8R9R:tsugarCenterRott rotatedPointstcurAngletcosThetatsinThetatatnewXtnewYtnewZ((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyt__rotateSugarCenterms"     666c% Cs‰|dkr||}}nt||ƒ}t||ƒ}t||ƒ} t| dt| ƒƒ} t|||ƒ} t|| | dƒ} t| dt| ƒƒ} | g} xtdddƒtdddƒD]k}t| | |ƒ}| j|ƒxCtdddƒtdddƒD]}| jt|| |ƒƒqWqĻWxø| D]°}d}g}xhtd d ƒD]W}t|t|d|ƒƒ\}}}t ||||ƒ}||7}|j|ƒqgW|j|ƒ|jt |ƒƒ|jt |ƒƒqEWt | d d „ƒ}t|j d ddddg|ƒ}t|j d d|dd!ƒ}t|j d ||ƒ}d}d}xŪtdddƒD]Ē}t||d||ƒ} d}!xQddddddgD]7}"|!t || |"d| |"d | |"dƒ7}!qĖWt||| d| dƒ}#|!|jj|#ƒ9}!|!|kr|!}| }qqWd |g}$|d kr…|j|$|ƒ}$n|$S(sRotate the sugar center by 360 degrees in ROTATE_SUGAR_INTERVAL increments ARGUMENTS: mapNum - the molecule number of the Coot map to use sugar - the coordinates of the C1' atom phos5 - the coordinates of the 5' phosphate phos3 - the coordinates of the 3' phosphate baseType - the base type (A, C, G, or U) OPTIONAL ARGUMENTS: direction - which direction are we tracing the chain if it is 5 (i.e. 3'->5'), then phos5 and phos3 will be flipped all other values will be ignored defaults to 3 (i.e. 5'->3') RETURNS: baseObj - a list of [baseType, baseCoordinates] igš?g@i’’’’i¦’’’i i[iii R?cSs|dS(Ni((R8((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyR@ŅsR&tC4iiĮ½š’ihtN1tC2tN3tC5tC6iN(R RR R RR`R]RGR RRtmintmaxRRtNoneR RREt mutateBase(%RRItsugarRaRbtbaseTypeRMt sugarPhos5Vect sugarPhos3VecRftphosSugarPhosAngletbisectortstartingBasePost rotationstcurThetat curRotationtcurPhitcurBatonRmt densityListRoR8R9R:RptbaseDirt rotationAngleRyt orientedBaset bestFitBaset maxDensityRƒt rotatedBaset curDensityR=t pseudoChitbaseObj((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pytfindBase”s\  ) )! %  &!5    cCst|\}}d}|dks*|dkrDt|d|dƒ}n=t|d|dƒ}tdd|ƒ}t||dƒ}|j|}d}|dks¬|dkr¹|d}n*t|d|dƒ}tdd|ƒ}t|dddg|ƒ } t||ƒ} t|| | ƒ}d} |dks>|dkrrtt|d |d ƒt|d |d ƒƒ} n1tt|d |d ƒt|d |d ƒƒ} d} |dksĮ|dkrõtt|d |d ƒt|d |d ƒƒ} n1tt|d |d ƒt|d |d ƒƒ} t| dddg| ƒ } t| | ƒ}t||| |dƒ}||gS(sChange the base type. ARGUMENTS: curBase - the current base object in the form [baseType, baseCoordinates] newBaseType - the base type to mutate to RETURNS: baseObj - a list of [baseType, baseCoordinates] R&R(R‹sC1'Rgš?g@iRŽRŒRtN9tN7N(R“R R R RRRR(RtcurBaset newBaseTypet curBaseTypet curBaseCoordstcurAlignmentVectort curBaseCentert newBaseCoordstnewAlignmentVectorR£Ryt curNormalt newNormalt normalAnglet normalAxis((sV/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nextPhos.pyR”ōs8   4141c CsÄ|\}}|d}i}x1|jƒD]#\}}t|||ƒ||s((@" ’’k