def _dG0_prime_vector(self, pH, I, T):
"""
Calculates the difference in kJ/mol between dG'0 and
the dG0 of the MS with the least hydrogens (dG0[0])
Returns:
dG'0 - dG0[0]
"""
if self.inchi is None:
return 0
elif self.pKas == []:
dG0s = np.zeros((1, 1))
else:
dG0s = -np.cumsum([0] + self.pKas) * R * T * np.log(10)
dG0s = dG0s
DH = debye_huckel((I, T))
# dG0' = dG0 + nH * (R T ln(10) pH + DH) - charge^2 * DH
pseudoisomers = np.vstack(
[dG0s, np.array(self.nHs),
np.array(self.zs)]).T
dG0_prime_vector = pseudoisomers[:, 0] + \
pseudoisomers[:, 1] * (R * T * np.log(10) * pH + DH) - \
pseudoisomers[:, 2]**2 * DH
return dG0_prime_vector
def transform(self, pH, I, T):
if self.inchi is None:
return 0
elif self.pKas == []:
dG0s = np.zeros((1, 1))
else:
dG0s = -np.cumsum([0] + self.pKas) * R * T * np.log(10)
dG0s = dG0s - dG0s[self.majorMSpH7]
DH = debye_huckel((I, T))
# dG0' = dG0 + nH * (R T ln(10) pH + DH) - charge^2 * DH
pseudoisomers = np.vstack([dG0s, np.array(self.nHs), np.array(self.zs)]).T
dG0_prime_vector = pseudoisomers[:, 0] + \
pseudoisomers[:, 1] * (R * T * np.log(10) * pH + DH) - \
pseudoisomers[:, 2]**2 * DH
return -R * T * logsumexp(dG0_prime_vector / (-R * T))
def transform(self, pH, I, T):
if self.inchi is None:
return 0
elif self.pKas == []:
dG0s = np.zeros((1, 1))
else:
dG0s = -np.cumsum([0] + self.pKas) * R * T * np.log(10)
dG0s = dG0s - dG0s[self.majorMSpH7]
DH = debye_huckel((I, T))
# dG0' = dG0 + nH * (R T ln(10) pH + DH) - charge^2 * DH
pseudoisomers = np.vstack(
[dG0s, np.array(self.nHs),
np.array(self.zs)]).T
dG0_prime_vector = pseudoisomers[:, 0] + \
pseudoisomers[:, 1] * (R * T * np.log(10) * pH + DH) - \
pseudoisomers[:, 2]**2 * DH
return -R * T * logsumexp(dG0_prime_vector / (-R * T))
def _transform(self, pH, I, T):
"""
Returns the difference between the dG0 of microspecies with the least hydrogens
and the transformed dG0' (in kJ/mol)
"""
if self.inchi is None:
return 0
elif self.pKas == []:
dG0s = np.zeros((1, 1))
else:
dG0s = -np.cumsum([0] + self.pKas) * R * T * np.log(10)
dG0s = dG0s
DH = debye_huckel((I, T))
# dG0' = dG0 + nH * (R T ln(10) pH + DH) - charge^2 * DH
pseudoisomers = np.vstack([dG0s, np.array(self.nHs), np.array(self.zs)]).T
dG0_prime_vector = pseudoisomers[:, 0] + \
pseudoisomers[:, 1] * (R * T * np.log(10) * pH + DH) - \
pseudoisomers[:, 2]**2 * DH
return -R * T * logsumexp(dG0_prime_vector / (-R * T))
def _dG0_prime_vector(self, pH, I, T):
"""
Calculates the difference in kJ/mol between dG'0 and
the dG0 of the MS with the least hydrogens (dG0[0])
Returns:
dG'0 - dG0[0]
"""
if self.inchi is None:
return 0
elif self.pKas == []:
dG0s = np.zeros((1, 1))
else:
dG0s = -np.cumsum([0] + self.pKas) * R * T * np.log(10)
dG0s = dG0s
DH = debye_huckel((I, T))
# dG0' = dG0 + nH * (R T ln(10) pH + DH) - charge^2 * DH
pseudoisomers = np.vstack([dG0s, np.array(self.nHs), np.array(self.zs)]).T
dG0_prime_vector = pseudoisomers[:, 0] + \
pseudoisomers[:, 1] * (R * T * np.log(10) * pH + DH) - \
pseudoisomers[:, 2]**2 * DH
return dG0_prime_vector
