def score(self,site,both_strands=False):
ef = self.directional_score(site)
if both_strands:
eb = self.directional_score(wc(site))
return log(exp(beta*ef) + exp(beta*eb))/(beta)
else:
return ef
def binding_energy(self,site,double_stranded=False):
"""Compute binding energy of site. See calcBindingEnergy,Organism.cpp"""
w = len(site)
E_f = self.activation(site) * w * (-2/beta) - 0.05
E_b = double_stranded and (self.activation(wc(site)) * w * (-2/beta) - 0.05)
E_t = ((1 / -beta) * log(exp(-beta * E_f) + exp(-beta * E_b))
if double_stranded
else E_f)
return E_t
def __init__(self,seq_line):
fields = seq_line.split(",")
numeric_fields = map(float,fields[1:])
self.site = fields[0]
(self.position,
self.strand,
self.ep,
self.act,
self.tProb,
self.gc,
self.tConc) = numeric_fields[:7]
self.position_energies = map(float,fields[6:])
self.complements = sum(map(lambda(x,y):x==y,zip(self.site,wc(self.site))))
def adjust(site):
if self.recognizer.score(site) < self.recognizer.score(wc(site)):
return site
else:
return wc(site)
def matched_base_pairs(self):
return sum(map(lambda(x,y):x==y,
zip(self.site,wc(self.site))))