def __init__(self, GDP=0, GTP=0, unbound=0):
box = DiffusionBox()
# We want absolute number of molecules.
self.GDP = box.membrane_to_absolute(GDP)
self.GTP = box.membrane_to_absolute(GTP)
self.unbound = box.cytosolic_to_absolute(unbound)
super().__init__(self.GDP + self.GTP + self.unbound)
def __init__(self, concentration=None, **kwargs):
if concentration is not None:
box = DiffusionBox()
if self.location == 'cytosolic':
self.num_molecules = box.cytosolic_to_absolute(concentration)
else:
self.num_molecules = box.membrane_to_absolute(concentration)
else:
super().__init__(**kwargs)
plt.legend()
plt.xlabel("Initial RasGRP1 Count")
plt.ylabel("Steady State Count")
title = "Das Minimal Model- Steady State RasGTP (SOS Initial={})".format(count)
dirname = os.path.join(output_dirname, "steady_states")
if not os.path.exists(dirname):
os.mkdir(dirname)
plt.title(title)
plt.savefig(os.path.join(dirname, title.replace(" ", "-") + ".png"))
# plt.show()
plt.close()
if __name__ == "__main__":
box = DiffusionBox()
# Rates are listed in uM, from table S1
# k_off and kcat rates are already in s^-1; k_on needs to be converted.
rates = [
box.convert_membrane_rate(0.12),
3.0,
box.convert_membrane_rate(0.11),
0.4,
box.convert_membrane_rate(0.05),
0.1,
0.038,
box.convert_membrane_rate(0.07),
1.0,
0.003,
box.convert_cytosolic_rate(1.74),
