Athemis/pyKinetics
1
0
Fork 0
mirror of https://github.com/Athemis/pyKinetics.git synced 2025-05-24 03:45:55 +00:00
Code Issues Releases Wiki Activity

Adding logger

Browse source
This commit is contained in:
Alexander Minges 2015-08-19 00:22:15 +02:00
parent 7a943cb945
commit c90c18ee84
2 changed files with 73 additions and 12 deletions
Download patch file Download diff file Expand all files Collapse all files

33
libkinetics/__init__.py
View file

@ -1,4 +1,5 @@
#!/usr/bin/python
# -*- coding: utf-8 -*-
from scipy import stats, optimize
import numpy as np
@ -9,6 +10,7 @@ import csv
class Replicate():
def __init__(self, x, y, owner):
self.logger = owner.logger
self.x = x
self.y = y
self.owner = owner
@ -36,6 +38,7 @@ class Replicate():
class Measurement():
def __init__(self, x, y, conc, conc_unit, owner):
self.logger = owner.logger
self.concentration = float(conc)
self.concentration_unit = conc_unit
self.x = x
@ -89,7 +92,9 @@ class Measurement():
class Experiment():
def __init__(self, data_files, xlim, do_hill=False):
def __init__(self, data_files, xlim, do_hill=False, logger=None):
self.logger = logger
# collction of indepentend measurements
self.measurements = []
@ -163,7 +168,11 @@ class Experiment():
'perr': perr,
'x': x}
except:
print('Calculation of Hill kinetics failed!')
msg = 'Calculation of Michaelis-Menten kinetics failed!'
if self.logger:
self.logger.error('ERROR: {}'.format(msg))
else:
print(msg)
return None
def do_hill_kinetics(self):
@ -185,7 +194,11 @@ class Experiment():
'h': h,
'x': x}
except:
print('Calculation of Hill kinetics failed!')
msg = 'Calculation of Hill kinetics failed!'
if self.logger:
self.logger.error('ERROR: {}'.format(msg))
else:
print(msg)
return None
def plot_kinetics(self, outpath):
@ -200,12 +213,16 @@ class Experiment():
fmt='ok', ms=3, fillstyle='none', label="Data with error")
if self.mm:
ax.plot(self.mm['x'],
(self.mm['vmax']*self.mm['x'])/(self.mm['Km']+self.mm['x']), 'b-', label="Michaelis-Menten")
y = self.mm_kinetics_function(self.mm['x'],
self.mm['vmax'],
self.mm['Km'])
ax.plot(self.mm['x'], y, 'b-', label="Michaelis-Menten")
if self.hill:
ax.plot(self.hill['x'],
((self.hill['vmax']*(self.hill['x']**self.hill['h'])) /
(self.hill['Kprime'] + (self.hill['x']**self.hill['h']))), 'g-', label="Hill")
y = self.hill_kinetics_function(self.hill['x'],
self.hill['vmax'],
self.hill['Kprime'],
self.hill['h'])
ax.plot(self.hill['x'], y, 'g-', label="Hill")
ax.legend(loc='best', fancybox=True)
plt.savefig('{}/kinetics.png'.format(outpath), bbox_inches='tight')