def get_pka(mol: Molecule, coskf_mol: Optional[str],
coskf_mol_conj: Optional[str], water: str, hydronium: str,
job: Type[Job], s: Settings) -> List[float]:
if coskf_mol is None:
return 5 * [np.nan]
elif coskf_mol_conj is None:
return 5 * [np.nan]
s = Settings(s)
s.input.compound[1]._h = water
s.ignore_molecule = True
s_dict = {}
for name, coskf in _iter_coskf(coskf_mol_conj, coskf_mol, water,
hydronium):
_s = s.copy()
_s.name = name
_s.input.compound[0]._h = coskf
s_dict[name] = _s
# Run the job
mol_name = mol.properties.name
job_list = [CRSJob(settings=s, name=name) for name, s in s_dict.items()]
results_list = [_crs_run(job, mol_name) for job in job_list]
# Extract solvation energies and activity coefficients
E_solv = {}
for name, results in zip(("acid", "base", "solvent", "solvent_conj"),
results_list):
results.wait()
try:
E_solv[name] = _E = results.get_energy()
assert _E is not None
logger.info(f'{results.job.__class__.__name__}: {mol_name} pKa '
f'calculation ({results.job.name}) is successful')
except Exception:
logger.error(f'{results.job.__class__.__name__}: {mol_name} pKa '
f'calculation ({results.job.name}) has failed')
E_solv[name] = np.nan
try:
mol.properties.job_path += [
join(job.path, job.name + '.in') for job in job_list
]
except IndexError: # The 'job_path' key is not available
mol.properties.job_path = [
join(job.path, job.name + '.in') for job in job_list
]
ret = [E_solv[k] for k in ("acid", "base", "solvent", "solvent_conj")]
ret.append(_get_pka(**E_solv))
return ret
def get_solv(mol: Molecule, solvent_list: Iterable[str], coskf: Optional[str],
job: Type[Job], s: Settings) -> List[float]:
"""Calculate the solvation energy of *mol* in various *solvents*.
Parameters
----------
mol : |plams.Molecule|_
A PLAMS Molecule.
solvent_list : |List|_ [|str|_]
A list of solvent molecules (*i.e.* .coskf files).
coskf : str, optional
The path+filename of the .coskf file of **mol**.
job : |Callable|_
A type Callable of a class derived from :class:`Job`, e.g. :class:`AMSJob`
or :class:`Cp2kJob`.
s : |plams.Settings|_
The settings for **job**.
Returns
-------
|list|_ [|float|_] & |list|_ [|float|_]
A list of solvation energies and gammas.
"""
# Return 3x np.nan if no coskf is None (i.e. the COSMO-surface construction failed)
if coskf is None:
i = 1 + 2 * len(solvent_list)
return i * [np.nan]
# Prepare a list of job settings
s = Settings(s)
s.input.compound[0]._h = coskf
s.ignore_molecule = True
s_list = []
for solv in solvent_list:
_s = s.copy()
_s.name = solv.rsplit('.', 1)[0].rsplit(os.sep, 1)[-1]
_s.input.compound[1]._h = solv
s_list.append(_s)
# Run the job
mol_name = mol.properties.name
job_list = [CRSJob(settings=s, name=s.name) for s in s_list]
results_list = [
_crs_run(job, mol_name, calc_type="pKa") for job in job_list
]
# Extract solvation energies and activity coefficients
E_solv = []
Gamma = []
for results in results_list:
results.wait()
try:
E_solv.append(results.get_energy())
Gamma.append(results.get_activity_coefficient())
logger.info(
f'{results.job.__class__.__name__}: {mol_name} activity coefficient '
f'calculation ({results.job.name}) is successful')
except Exception:
logger.error(
f'{results.job.__class__.__name__}: {mol_name} activity coefficient '
f'calculation ({results.job.name}) has failed')
E_solv.append(np.nan)
Gamma.append(np.nan)
try:
mol.properties.job_path += [
join(job.path, job.name + '.in') for job in job_list
]
except IndexError: # The 'job_path' key is not available
mol.properties.job_path = [
join(job.path, job.name + '.in') for job in job_list
]
logp = _get_logp(s_list[0], name=mol_name, logger=logger)
return E_solv + Gamma + [logp]
