ó Ñ%Tc @s:dZddlZddlmZddlmZddlmZmZm Z ddl m Z m Z ej jej jeƒƒZej jedƒZedej jed ƒd ej jed ƒd ej jed ƒdej jedƒdej jedƒƒZd„Zd„Zd„Zd„Zd„ZdS(sNDetermine the sequence of rotamers for a structure using a hidden Markov modeliÿÿÿÿN(tlog(tPseudoPredictor(t puckerListtrotListt rotsByPucker(tlntnegInftdatatthetaEtasthetaEtaClusts.csvtpuckerssmoothedPuckerDist.csvt sugarDistssugarDists.csvt startPhosDistsstartingPDists.csvt endPhosDistsendingPDists.csvcCs g}x|jƒD]s}tjd|jƒd|jƒd|jƒd|jƒd|jƒd|jƒd|j ƒƒ}|j |ƒqWt |ƒ}||fS(s´Determine the best sequence of rotamers for a structure. ARGUMENTS: builtChain - a Chain object containing phosphate and base coordinates RETURNS: bestPath - a list of the most likely rotamer for each suite predictedProbs - the probability for each suite for each rotamer formatted as a list of dictionaries predictedProbs[suiteNum][rotamer] = probability tthetatetat startPperptendPperpR R R ( tsuitest pseudoPredictcalcProbR Rt startingPperpt endingPperpR tstartingPhosDisttendingPhosDisttappendt rotamerHMM(t builtChaintpredictedProbstcurSuitetcurProbstbestPath((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.pytdetermineRotamerSeq$s       csŽt|ƒ}gt|ƒD] }i^q‰gt|ƒD] }i^q8}x*tD]"‰t|dˆƒˆdˆ