def get_free_energy_in_solution_method3(
vac_conf: Chem.Mol,
m_vac: list,
m_solv: list,
solv_conf,
correct_for_symmetry: bool = False,
):
if correct_for_symmetry:
entropy_corr = calc_molecular_graph_entropy(
solv_conf)[0].value_in_unit(unit.kilocalorie_per_mole)
else:
entropy_corr = 0.0
free_energy_in_solution = []
# iterating over gas confs, adding energy in gas/solvation and free energy in gas for each conf
for m_v, m_s in zip(m_vac, m_solv):
G_gas = float(m_v.GetProp("G with S_rot corrected")) + entropy_corr
E_gas = float(m_v.GetProp("E_B3LYP_631G_gas"))
E_solv = float(m_s.GetProp("E_B3LYP_631G_solv"))
free_energy_in_solution.append(
(G_gas + (E_solv - E_gas)) * unit.kilocalorie_per_mole)
mols, e_list = prune_conformers(vac_conf,
free_energy_in_solution,
rmsd_threshold=0.1)
return e_list
def get_min_free_energy_in_solution_method1(m_solv: list,
correct_for_symmetry: bool = False
):
# getting min values for vac/solv energy and free energy in vac
if correct_for_symmetry:
entropy_corr = calc_molecular_graph_entropy(
m_solv[0])[0].value_in_unit(unit.kilocalorie_per_mole)
else:
entropy_corr = 0.0
G_solv_min = min([
float(m.GetProp("G with S_rot corrected")) + entropy_corr
for m in m_solv
])
# getting min solvation free energty
return G_solv_min * unit.kilocalorie_per_mole
def get_min_free_energy_in_solution_method3(
m_vac: list,
m_solv: list,
solv_conf,
correct_for_symmetry: bool = False):
if correct_for_symmetry:
entropy_corr = calc_molecular_graph_entropy(
solv_conf)[0].value_in_unit(unit.kilocalorie_per_mole)
else:
entropy_corr = 0.0
# getting min values for vac/solv energy and free energy in vac
dE_vac_min = min([float(m.GetProp("E_B3LYP_631G_gas")) for m in m_vac])
dE_solv_min = min([float(m.GetProp("E_B3LYP_631G_solv")) for m in m_solv])
G_vac_min = min([
float(m.GetProp("G with S_rot corrected")) + entropy_corr
for m in m_vac
])
# getting min solvation free energty
return (G_vac_min + (dE_solv_min - dE_vac_min)) * unit.kilocalorie_per_mole
def get_free_energy_in_solution_method1(solv_conf: Chem.Mol,
m_solv: list,
correct_for_symmetry: bool = False):
free_energy_in_solution = []
if correct_for_symmetry:
entropy_corr = calc_molecular_graph_entropy(
solv_conf)[0].value_in_unit(unit.kilocalorie_per_mole)
else:
entropy_corr = 0.0
# iterating over gas confs, adding energy in gas/solvation and free energy in gas for each conf
for m in m_solv:
G_solv = float(m.GetProp("G with S_rot corrected")) + entropy_corr
free_energy_in_solution.append(G_solv * unit.kilocalorie_per_mole)
mols, e_list = prune_conformers(solv_conf,
free_energy_in_solution,
rmsd_threshold=0.1)
return e_list