Athemis/pyKinetics
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Reformat code using yapf

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This commit is contained in:
Alexander Minges 2015-08-31 19:06:35 +02:00
parent 93751a2b3d
commit 4b3fb762fb
2 changed files with 50 additions and 57 deletions
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53
libkinetics/__init__.py
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@ -21,8 +21,7 @@ class Replicate():
self.fitresult = self.fit()
def fit(self):
ind_min_max = np.where((self.x >= self.xlim[0]) &
(self.x <= self.xlim[1]))
ind_min_max = np.where((self.x >= self.xlim[0]) & (self.x <= self.xlim[1]))
x_for_fit = np.take(self.x, ind_min_max)
y_for_fit = np.take(self.y, ind_min_max)
@ -32,12 +31,10 @@ class Replicate():
category=RuntimeWarning,
message='invalid value encountered in sqrt')
(slope, intercept,
r_value,
p_value,
std_err) = stats.linregress(x_for_fit, y_for_fit)
(slope, intercept, r_value, p_value, std_err
) = stats.linregress(x_for_fit, y_for_fit)
r_squared = r_value**2
r_squared = r_value ** 2
conc = '{} {}'.format(self.owner.concentration,
self.owner.concentration_unit)
@ -57,12 +54,14 @@ class Replicate():
'value for further calculations!')
self.logger.info(' intercept: {}'.format(slope))
return {'slope': slope,
'intercept': intercept,
'r_value': r_value,
'r_squared': r_squared,
'p_value': p_value,
'std_err': std_err}
return {
'slope': slope,
'intercept': intercept,
'r_value': r_value,
'r_squared': r_squared,
'p_value': p_value,
'std_err': std_err
}
class Measurement():
@ -86,8 +85,7 @@ class Measurement():
length_x, num_replicates = self.y.shape
for n in range(num_replicates):
self.replicates.append(Replicate(n,
(self.x, self.y[:, n:n+1]),
self.replicates.append(Replicate(n, (self.x, self.y[:, n:n + 1]),
self))
for r in self.replicates:
@ -141,9 +139,7 @@ class Experiment():
self.fit_to_replicates = fit_to_replicates
# dictionary to store data for the kinetics calculation
self.raw_kinetic_data = {'x': [],
'y': [],
'yerr': []}
self.raw_kinetic_data = {'x': [], 'y': [], 'yerr': []}
self.xlim = xlim
# parse data files and generate measurements
@ -196,11 +192,11 @@ class Experiment():
m.plot(outpath)
def mm_kinetics_function(self, x, vmax, Km):
v = (vmax*x)/(Km+x)
v = (vmax * x) / (Km + x)
return v
def hill_kinetics_function(self, x, vmax, Kprime, h):
v = (vmax*(x**h))/(Kprime+(x**h))
v = (vmax * (x ** h)) / (Kprime + (x ** h))
return v
def do_mm_kinetics(self):
@ -218,10 +214,7 @@ class Experiment():
self.logger.info(' v_max: {} ± {}'.format(vmax, perr[0]))
self.logger.info(' Km: {} ± {}'.format(Km, perr[1]))
return {'vmax': float(vmax),
'Km': float(Km),
'perr': perr,
'x': x}
return {'vmax': float(vmax), 'Km': float(Km), 'perr': perr, 'x': x}
except:
msg = 'Calculation of Michaelis-Menten kinetics failed!'
if self.logger:
@ -248,11 +241,13 @@ class Experiment():
self.logger.info(' K_prime: {} ± {}'.format(Kprime, perr[1]))
self.logger.info(' h: {} ± {}'.format(h, perr[2]))
return {'vmax': float(vmax),
'Kprime': float(Kprime),
'perr': perr,
'h': h,
'x': x}
return {
'vmax': float(vmax),
'Kprime': float(Kprime),
'perr': perr,
'h': h,
'x': x
}
except:
msg = 'Calculation of Hill kinetics failed!'
if self.logger: