%Tc@sYdZddlmZddlmZmZddlmZmZdddYZ dS( s0Predict rotamers from low resolution informationi(tThetaEtaPredictor(t SmoothProbtSmoothProbError(trotListtpuckerListFullNametPseudoPredictorc BsSeZdZddddddZdddddddddd ZdZRS(s0Predict rotamers from low resolution informationcCst}|d=||_d|_d|_d|_d|_d|_|dk rdt||_n|dk rt ||_n|dk rt ||_n|dk rt ||_n|dk rt ||_ndS(sCreate and initialize a PseudoPredictor object OPTIONAL ARGUMENTS: Note that at least one of these arugments must be provided thetaEta - A file contianing training data for theta eta Gaussian clusters pucker - A file contianing training data for P-perp distances sugarDist - A file contianing training data for sugar-sugar (C1'-C1') distances startPhosDist - A file contianing training data for starting phosphate-phosphate distances endPhosDist - A file contianing training data for ending phosphate-phosphate distances RETURNS: an initialized PseudoPredictor object tselfN( tlocalst_PseudoPredictor__inputFilestNonet _PseudoPredictor__thetaEtaPredict_PseudoPredictor__puckerPredict!_PseudoPredictor__sugarDistPredict%_PseudoPredictor__startPhosDistPredict#_PseudoPredictor__endPhosDistPredicRR(RtthetaEtatpuckert sugarDistt startPhosDistt endPhosDistt inputFiles((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.pyt__init__s$            c Cs|dk r|\}}ndgd\} } } } }}|jdk ry|dk ry|dk ry|jj||} n|jdk r|dk ry|jj|} Wqtk rd} qXn|jdk r|dk ry|jj|} Wqtk rd} qXn|jdk rc|dk rcy|jj|} Wqctk r_d} qcXn|jdk r|dk ry|jj|}Wqtk rd}qXn|jdk r| dk ry|jj| }Wqtk rd}qXni}xtD]}d}| dk r5|| |9}n| dk rR|| |9}n|dk ro|||9}n|dk r|||9}n| dk r|| t |d9}n| dk r|| t |d9}n||| probability iiig?N(R R tcalcProbR RR R RRt puckerListtsumtvaluestdictt iteritemstZeroDivisionErrortlen(RtrotRtthetatetat startPperptendPperpRRRt thetaEtaProbststartPuckerProbstendPuckerProbstsugarDistProbststartPhosDistProbstendPhosDistProbstprobstcurrottcurprobt totalProbt equalProb((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.pyR@sn '                 9 ) cCsE|jdkrdS|jj|}|d|dkr=dSdSdS(s"Calculate the most likely pucker of a sugar given only the base-phosphate perpendicular distance ARGUMENTS: pperp - the base-phosphate perpendicular (P-perp) distance RETURNS: 3 if a C3'-endo sugar pucker is more likely, 2 otherwise sC3'sC2'iiN(R R R(Rtpperpt puckerProbs((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.pyt calcPuckers N(t__name__t __module__t__doc__R RRR0(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.pyRs'$_N(( R3tthetaEtaPredictorRt smoothProbRRRRRR(((s]/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.pyts