def __init__(self, thetaEta = None, pucker = None, sugarDist = None, startPhosDist = None, endPhosDist = None):
"""Create 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
"""
#create a dictionary of the input filenames
inputFiles = locals()
del inputFiles["self"]
self.__inputFiles = inputFiles
self.__thetaEtaPredic = None
self.__puckerPredic = None
self.__sugarDistPredic = None
self.__startPhosDistPredic = None
self.__endPhosDistPredic = None
if thetaEta is not None:
self.__thetaEtaPredic = ThetaEtaPredictor(thetaEta)
if pucker is not None:
self.__puckerPredic = SmoothProb(pucker)
if sugarDist is not None:
self.__sugarDistPredic = SmoothProb(sugarDist)
if startPhosDist is not None:
self.__startPhosDistPredic = SmoothProb(startPhosDist)
if endPhosDist is not None:
self.__endPhosDistPredic = SmoothProb(endPhosDist)
def __init__(self,
thetaEta=None,
pucker=None,
sugarDist=None,
startPhosDist=None,
endPhosDist=None):
"""Create 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
"""
#create a dictionary of the input filenames
inputFiles = locals()
del inputFiles["self"]
self.__inputFiles = inputFiles
self.__thetaEtaPredic = None
self.__puckerPredic = None
self.__sugarDistPredic = None
self.__startPhosDistPredic = None
self.__endPhosDistPredic = None
if thetaEta is not None:
self.__thetaEtaPredic = ThetaEtaPredictor(thetaEta)
if pucker is not None:
self.__puckerPredic = SmoothProb(pucker)
if sugarDist is not None:
self.__sugarDistPredic = SmoothProb(sugarDist)
if startPhosDist is not None:
self.__startPhosDistPredic = SmoothProb(startPhosDist)
if endPhosDist is not None:
self.__endPhosDistPredic = SmoothProb(endPhosDist)
class PseudoPredictor:
"""Predict rotamers from low resolution information"""
def __init__(self, thetaEta = None, pucker = None, sugarDist = None, startPhosDist = None, endPhosDist = None):
"""Create 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
"""
#create a dictionary of the input filenames
inputFiles = locals()
del inputFiles["self"]
self.__inputFiles = inputFiles
self.__thetaEtaPredic = None
self.__puckerPredic = None
self.__sugarDistPredic = None
self.__startPhosDistPredic = None
self.__endPhosDistPredic = None
if thetaEta is not None:
self.__thetaEtaPredic = ThetaEtaPredictor(thetaEta)
if pucker is not None:
self.__puckerPredic = SmoothProb(pucker)
if sugarDist is not None:
self.__sugarDistPredic = SmoothProb(sugarDist)
if startPhosDist is not None:
self.__startPhosDistPredic = SmoothProb(startPhosDist)
if endPhosDist is not None:
self.__endPhosDistPredic = SmoothProb(endPhosDist)
def calcProb(self, rot = None, thetaEta = None, theta = None, eta = None, startPperp = None, endPperp = None, sugarDist = None, startPhosDist = None, endPhosDist = None):
"""Calculate the probability of each rotamer for a suite from all given information
OPTIONAL ARGUMENTS:
rot - which rotamer to return the probability for
if not provided, a hash of all probabilities is returned
Note that at least one of the following arugments must be provided:
thetaEta - a list of the (theta, eta) coordinates of the suite
theta - the theta coordinates of the suite (ignored if thetaEta is given)
eta - the eta coordinates of the suite (ignored if thetaEta is given)
startPperp - the starting base-phosphate perpendicular (P-perp) distance
endPperp - the ending base-phosphate perpendicular (P-perp) distance
sugarDist - the C1'-C1' distance for the suite
startPhosDist - the phosphate-phosphate distance for the starting nucleotide of the suite
endPhosDist - the phosphate-phosphate distance for the ending nucleotide of the suite
RETURNS:
if rot is given, returns the probability that the described suite is of rotamer rot
if rot is not given, returns a hash in the form rotamer => probability
"""
#if thetaEta is given, use those values instead of theta and eta
if thetaEta is not None:
(theta, eta) = thetaEta
#initialize variables to None
(thetaEtaProbs, startPuckerProbs, endPuckerProbs, sugarDistProbs, startPhosDistProbs, endPhosDistProbs) = [None] * 6
#calculate individual probabilites using the given information
if self.__thetaEtaPredic is not None and theta is not None and eta is not None:
thetaEtaProbs = self.__thetaEtaPredic.calcProb(theta, eta)
if self.__puckerPredic is not None and startPperp is not None:
try:
startPuckerProbs = self.__puckerPredic.calcProb(startPperp)
except SmoothProbError:
startPuckerProbs = None
if self.__puckerPredic is not None and endPperp is not None:
try:
endPuckerProbs = self.__puckerPredic.calcProb(endPperp)
except SmoothProbError:
endPuckerProbs = None
if self.__sugarDistPredic is not None and sugarDist is not None:
try:
sugarDistProbs = self.__sugarDistPredic.calcProb(sugarDist)
except SmoothProbError:
sugarDistProbs = None
if self.__startPhosDistPredic is not None and startPhosDist is not None:
try:
startPhosDistProbs = self.__startPhosDistPredic.calcProb(startPhosDist)
except SmoothProbError:
startPhosDistProbs = None
if self.__endPhosDistPredic is not None and endPhosDist is not None:
try:
endPhosDistProbs = self.__endPhosDistPredic.calcProb(endPhosDist)
except SmoothProbError:
endPhosDistProbs = None
#calculate the overall probability for each rotamer
probs = {}
for currot in rotList:
curprob = 1
if thetaEtaProbs is not None: curprob *= thetaEtaProbs[currot]
if sugarDistProbs is not None: curprob *= sugarDistProbs[currot]
if startPhosDistProbs is not None: curprob *= startPhosDistProbs[currot]
if endPhosDistProbs is not None: curprob *= endPhosDistProbs[currot]
if startPuckerProbs is not None: curprob *= startPuckerProbs[puckerList[currot][0]]
if endPuckerProbs is not None: curprob *= endPuckerProbs[puckerList[currot][1]]
probs[currot] = curprob
#scale the raw probabilities so they add up to 1
totalProb = sum(probs.values())
try:
probs = dict([(currot, curprob/totalProb) for (currot, curprob) in probs.iteritems()])
except ZeroDivisionError:
#if totalProb is 0, then the structure is very, very bad
#our only reasonable options are to give up, or to give all rotamers equal likelihood
#we give all rotamers equal likelihood so that the user at least has a chance of improving the structure
equalProb = 1.0/len(rotList)
probs = dict([(currot, equalProb) for currot in rotList])
#return either the desired probability or the dictionary containing all probabilities
if rot is None:
return probs
else:
return probs[rot]
def calcPucker(self, pperp):
"""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
"""
if self.__puckerPredic is None:
return None
else:
puckerProbs = self.__puckerPredic.calcProb(pperp)
if puckerProbs["C3'"] > puckerProbs["C2'"]:
return 3
else:
return 2