def set_cp2k_param(settings: Settings, param_dict: dict) -> None:
"""Placeholder."""
for block_name, block in param_dict.items():
# Create a to-be formatted string with user-specified units
unit = f'[{block.unit}]' + ' {}' if 'unit' in block else '{}'
# Get the to-be update list of settings
s = settings.get_nested(block['keys'])
if not isinstance(s, list):
_s = settings.get_nested(block['keys'][:-1])
s = _s[block['keys'][-1]] = []
for k, v in block.items():
if k in ('keys', 'unit'): # Skip
continue
value = unit.format(v)
atom = 'atoms' if len(k.split()) > 1 else 'atom'
atom_list = [i[atom] for i in s]
try: # Intersecting set
idx = atom_list.index(k)
s[idx].update({block_name: value})
except ValueError: # Disjoint set
new_block = Settings({atom: k, block_name: value})
s.append(new_block)
def recreate_settings(self) -> Settings:
"""Construct a |Settings| instance from ``"$JN.run"``."""
runfile = self['$JN.run']
# Ignore the first 2 lines
with open(runfile, 'r') as f:
for i in f:
if 'MATCH.pl' in i:
args = next(f).split()
break
else:
raise FileError(
f"Failed to parse the content of ...{os.sep}{runfile!r}")
# Delete the executable and pop the .pdb filename
del args[0]
pdb_file = args.pop(-1)
s = Settings()
for k, v in zip(args[0::2], args[1::2]):
k = k[1:].lower()
s.input[k] = v
s.input.filename = pdb_file
return s
def get_surface_charge_adf(mol: Molecule, job: Type[Job],
s: Settings) -> Settings:
"""Perform a gas-phase ADF single point and return settings for a COSMO-ADF single point.
The previous gas-phase calculation as moleculair fragment.
Parameters
----------
mol : |plams.Molecule|_
A PLAMS Molecule.
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
-------
|plams.Settings|_
A new Settings intance, constructed from **s**, suitable for DFT COSMO-RS calculations.
"""
s.input.allpoints = ''
results = mol.job_single_point(job, s, ret_results=True)
coskf = get_coskf(results)
for at in mol:
at.properties.adf.fragment = 'gas'
s.update(get_template('qd.yaml')['COSMO-ADF'])
s.input.fragments.gas = coskf
return s
def update_adf_defaults(ams_settings: Settings) -> None:
"""Add the COSMO-RS compound defaults to *ams_settings*, returning a copy of the new settings.
The engine block (*ams_settings.input.adf*) is soft updated
with the following Settings:
.. code::
Engine ADF
Basis
Type TZP
Core Small
End
XC
GGA BP86
End
Relativity
Level Scalar
End
BeckeGrid
Quality Good
End
EndEngine
"""
# Find the solvation key
# solvation = ams_settings.input.adf.find_case('solvation')
# solvation_block = ams_settings.input.adf[solvation]
adf = ams_settings.input.find_case('adf')
adf_block = ams_settings.input[adf]
# Find all keys for within the adf block
keys = ('basis', 'xc', 'relativity', 'BeckeGrid')
basis, xc, relativity, BeckeGrid = [
adf_block.find_case(item) for item in keys
]
# Construct the default solvation block
adf_defaults_block = Settings({
basis: {
'Type': 'TZP',
'Core': 'Small'
},
xc: {
'GGA': 'BP86'
},
relativity: {
'Level': 'Scalar'
},
BeckeGrid: {
'Quality': 'Good'
}
})
# Copy ams_settings and perform a soft update
ret = ams_settings.copy()
ret.input.adf.soft_update(adf_defaults_block)
return ret
def get_template(template_name: str, from_cat_data: bool = True) -> Settings:
"""Grab a yaml template and return it as Settings object."""
if from_cat_data:
path = join('data/templates', template_name)
xs = pkg.resource_string('CAT', path)
return Settings(yaml.load(xs.decode(), Loader=yaml.FullLoader))
with open(template_name, 'r') as file:
return Settings(yaml.load(file, Loader=yaml.FullLoader))
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 copy(self, deep: bool = False) -> 'FrozenSettings':
"""Create a copy of this instance.
The returned instance is a recursive copy, the **deep** parameter only affecting the
function used for copying non-:class:`dict` values:
:func:`copy.copy` if ``deep=False`` and :func:`copy.deepcopy` if ``deep=True``.
"""
copy_func = copy.deepcopy if deep else copy.copy
ret = type(self)()
for key, value in self.items():
value_cp = copy_func(value)
Settings.__setitem__(ret, key, value_cp)
return ret
def qd_opt(mol: Molecule,
jobs: Tuple[Optional[Type[Job]], ...],
settings: Tuple[Optional[Settings], ...],
use_ff: bool = False) -> None:
"""Perform an optimization of the quantum dot.
Performs an inplace update of **mol**.
Parameters
----------
mol : |plams.Molecule|_
The to-be optimized molecule.
job_recipe : |plams.Settings|_
A Settings instance containing all jon settings.
Expects 4 keys: ``"job1"``, ``"job2"``, ``"s1"``, ``"s2"``.
forcefield : bool
If ``True``, perform the job with CP2K with a user-specified forcefield.
"""
# Prepare the job settings
if use_ff:
qd_opt_ff(mol, jobs, settings)
return None
# Expand arguments
job1, job2 = jobs
s1, s2 = settings
# Extra options for AMSJob
if job1 is AMSJob:
s1 = Settings(s1)
s1.input.ams.constraints.atom = mol.properties.indices
if job2 is AMSJob:
s2 = Settings(s2)
s2.input.ams.constraints.atom = mol.properties.indices
# Run the first job and fix broken angles
mol.job_geometry_opt(job1, s1, name='QD_opt_part1')
fix_carboxyl(mol)
fix_h(mol)
mol.round_coords()
# Run the second job
if job2 is not None:
mol.job_geometry_opt(job2, s2, name='QD_opt_part2')
mol.round_coords()
return None
def read_mol_folder(mol_dict: Settings) -> Optional[List[Molecule]]:
"""Read all files (.xyz, .pdb, .mol, .txt or further subfolders) within a folder."""
try:
mol_type = 'input_cores' if mol_dict.is_core else 'input_ligands'
_file_list = os.listdir(mol_dict.mol)
optional_dict = Settings(
{k: v
for k, v in mol_dict.items() if k not in ('mol', 'path')})
file_list = [{i: optional_dict} for i in _file_list]
validate_mol(file_list, mol_type, mol_dict.path)
return read_mol(file_list)
except Exception as ex:
print_exception('read_mol_folder', mol_dict.name, ex)
def repr_Settings(self, obj: Settings, level: int) -> str: # noqa: N802
"""Create a :class:`str` representation of a |plams.Settings| instance."""
n = len(obj)
if not obj:
return f'{obj.__class__.__name__}()'
elif level <= 0:
return '\n...'
pieces: List[str] = []
indent = 4 * ' '
newlevel = level - 1
for k, v in islice(obj.items(), self.maxSettings):
key = str(k)
value = self.repr1(v, newlevel)
pieces.append(f'\n{key}:')
if type(obj) is type(value):
pieces.append(f'{textwrap.indent(value, indent)}:')
else:
pieces.append(f'{textwrap.indent(value, indent)}')
if n > self.maxSettings:
pieces.append('\n...')
ret = ''.join(pieces)
if level == self.maxlevel:
return f'{obj.__class__.__name__}(\n{textwrap.indent(ret[1:], indent)}\n)'
return ret
def set_header(s: Settings, *values: str) -> None:
"""Assign *value* to the ``["_h"]`` key in *s.input.compound*."""
s.input.compound = []
for item in values:
s.input.compound.append(Settings({'_h': item}))
s.input.compound[
0].frac1 = 1.0 # The first item in *values should be the solvent
def _overlay_s_plams(self, lj: Iterable[Mapping],
sigma_dict: MutableMapping,
epsilon_dict: MutableMapping) -> None:
"""Extract PLAMS-style settings from **lj** and put them in **sigma_dict** and **epsilon_dict**.""" # noqa: E501
for block in lj:
with Settings.suppress_missing():
atoms = tuple(block['atoms'].split())
try:
unit_sigma, sigma = block['sigma'].split()
except ValueError:
unit_sigma, sigma = '[angstrom]', block['sigma']
except (TypeError, KeyError):
unit_sigma = sigma = None
try:
unit_eps, epsilon = block['epsilon'].split()
except ValueError:
unit_eps, epsilon = '[kcalmol]', block['sigma']
except (TypeError, KeyError):
unit_eps = epsilon = None
if sigma is not None:
unit_sigma = unit_sigma[1:-1]
unit_sigma = self.UNIT_MAPPING.get(unit_sigma, unit_sigma)
sigma_dict[unit_sigma][atoms] = float(sigma)
if epsilon is not None:
unit_eps = unit_eps[1:-1]
unit_eps = self.UNIT_MAPPING.get(unit_eps, unit_eps)
epsilon_dict[unit_eps][atoms] = float(epsilon)
def frequencies():
s = Settings()
s.input.ams.properties.NormalModes = 'Yes'
s.input.ams.Properties.PESPointCharacter = 'No'
s.input.ams.NormalModes.ReScanFreqRange = '-1000 0'
s.input.ams.PESPointCharacter.NegativeEigenvalueTolerance = -0.001
return s
def DFTB():
s = Settings()
s.input.ams.task = 'GeometryOptimization'
s.input.DFTB
s.input.DFTB.Model = "GFN1-xTB"
s.input.ams.System.Charge = 0
return s
def get_surface_charge(mol: Molecule, job: Type[Job],
s: Settings) -> Optional[str]:
"""Construct the COSMO surface of the **mol**.
Parameters
----------
mol : |plams.Molecule|_
A PLAMS Molecule.
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
-------
|plams.Settings|_
Optional: The path+filename of a file containing COSMO surface charges.
"""
s = Settings(s)
# Special procedure for ADF jobs
# Use the gas-phase electronic structure as a fragment for the COSMO single point
if job is ADFJob:
s = get_surface_charge_adf(mol, job, s)
s.runscript.post = '$ADFBIN/cosmo2kf "mopac.cos" "mopac.coskf"'
results = mol.job_single_point(job, s, ret_results=True)
return get_coskf(results)
def _md2opt(s: Settings) -> Settings:
"""Convert CP2K MD settings to CP2K geometry optimization settings."""
s2 = s.copy()
del s2.input.motion.md
s2.input['global'].run_type = 'geometry_optimization'
# Delete all user-specified parameters; rely on MATCH
del s2.input.force_eval.mm.forcefield.charge
del s2.input.force_eval.mm.forcefield.nonbonded
return s2
def read_mol_smiles(mol_dict: Settings) -> Optional[Molecule]:
"""Read a SMILES string."""
try:
mol = _from_smiles(mol_dict.mol)
mol.properties.smiles = Chem.CanonSmiles(mol_dict.mol)
if mol_dict.get('indices'):
for i in mol_dict.indices:
mol[i].properties.anchor = True
canonicalize_mol(mol)
if mol_dict.get('indices'):
mol_dict.indices = tuple(i for i, at in enumerate(mol, 1)
if at.properties.pop('anchor', False))
if mol_dict.guess_bonds and not mol_dict.is_qd:
mol.guess_bonds()
return mol
except Exception as ex:
print_exception('read_mol_smiles', mol_dict.name, ex)
def get_recipe(self) -> Dict[Tuple[str], JobRecipe]:
"""Create a recipe for :meth:`WorkFlow.to_db`."""
settings_names = [i[1:] for i in self.export_columns if i[0] == 'settings']
uff_fallback = {
'key': f'RDKit_{rdkit.__version__}', 'value': f'{UFF.__module__}.{UFF.__name__}'
}
ret: Dict[Tuple[str], JobRecipe] = Settings()
for name, job, settings in zip(settings_names, self.jobs, self.settings):
# job is None, *i.e.* it's an RDKit UFF optimziation
if job is None:
ret[name].update(uff_fallback) # type: ignore
continue
settings = Settings(settings)
if self.read_template: # Update the settings using a QMFlows template
template = qmflows.geometry['specific'][self.type_to_string(job)].copy()
settings.soft_update(template)
ret[name]['key'] = job
ret[name]['value'] = settings
return ret
def read_mol_txt(mol_dict: Settings) -> Optional[List[Molecule]]:
"""Read a plain text file containing one or more SMILES strings."""
try:
row = 0 if 'row' not in mol_dict else mol_dict.row
column = 0 if 'column' not in mol_dict else mol_dict.column
mol_type = 'input_cores' if mol_dict.is_core else 'input_ligands'
with open(mol_dict.mol, 'r') as f:
iterator = itertools.islice(f, row, None)
_file_list = [
i.rstrip('\n').split()[column] for i in iterator if i
]
optional_dict = Settings(
{k: v
for k, v in mol_dict.items() if k not in ('mol', 'path')})
file_list = [{i: optional_dict} for i in _file_list]
validate_mol(file_list, mol_type, mol_dict.path)
return read_mol(file_list)
except Exception as ex:
print_exception('read_mol_txt', mol_dict.name, ex)
def pre_process_settings(mol: Molecule, s: Settings, job_type: Type[Job],
template_name: str) -> Settings:
"""Update all :class:`Settings`, **s**, with those from a QMFlows template (see **job**)."""
ret = Settings()
type_key = type_to_string(job_type)
ret.input = getattr(qmflows, template_name)['specific'][type_key].copy()
ret.update(s)
if job_type is AMSJob:
mol.properties.pop('charge', None)
# ret.input.ams.system.BondOrders._1 = adf_connectivity(mol)
if 'uff' not in s.input:
ret.input.ams.system.charge = int(
sum(at.properties.get('charge', 0) for at in mol))
elif job_type is ADFJob:
mol.properties.pop('charge', None)
if not ret.input.charge:
ret.input.charge = int(
sum(at.properties.get('charge', 0) for at in mol))
return ret
def overlay_cp2k_settings(self,
cp2k_settings: MutableMapping,
psf: Optional[PSFContainer] = None) -> None:
r"""Overlay **df** with all :math:`q`, :math:`\sigma` and :math:`\varepsilon` values from **cp2k_settings**.""" # noqa
charge = cp2k_settings['input']['force_eval']['mm']['forcefield'][
'charge']
charge_dict = {
block['atom']: float(block['charge'])
for block in charge
}
if psf is not None:
psf_charge_dict = dict(zip(psf.atom_type, psf.charge))
for k, v in psf_charge_dict.items():
if k not in charge_dict:
charge_dict[k] = v
epsilon_s = Settings() # type: ignore[var-annotated]
sigma_s = Settings() # type: ignore[var-annotated]
# Check if the settings are qmflows-style generic settings
lj = cp2k_settings.get('lennard-jones') or cp2k_settings.get(
'lennard_jones')
if lj is not None:
self._overlay_s_qmflows(cp2k_settings, sigma_s, epsilon_s)
else:
lj = cp2k_settings['input']['force_eval']['mm']['forcefield'][
'nonbonded']['lennard-jones'] # noqa
self._overlay_s_plams(lj, sigma_s, epsilon_s)
self.set_charge(charge_dict)
for unit, dct in epsilon_s.items():
self.set_epsilon_pairs(dct, unit=unit)
for unit, dct in sigma_s.items():
self.set_sigma_pairs(dct, unit=unit)
def overlay_cp2k_settings(self, cp2k_settings: Settings) -> None:
"""Extract forcefield information from PLAMS-style CP2K settings.
Performs an inplace update of this instance.
Examples
--------
Example input value for **cp2k_settings**.
In the provided example the **cp2k_settings** are directly extracted from a CP2K .inp file.
.. code:: python
>>> import cp2kparser # https://github.com/nlesc-nano/CP2K-Parser
>>> filename = str(...)
>>> cp2k_settings: dict = cp2kparser.read_input(filename)
>>> print(cp2k_settings)
{'force_eval': {'mm': {'forcefield': {'nonbonded': {'lennard-jones': [...]}}}}}
Parameters
----------
cp2k_settings : :class:`~collections.abc.Mapping`
A Mapping with PLAMS-style CP2K settings.
"""
if 'input' not in cp2k_settings:
cp2k_settings = Settings({'input': cp2k_settings})
# If cp2k_settings is a Settings instance enable the `suppress_missing` context manager
# In this manner normal KeyErrors will be raised, just like with dict
if isinstance(cp2k_settings, Settings):
context_manager = cp2k_settings.suppress_missing
else:
context_manager = nullcontext
with context_manager():
for prm_map in self.CP2K_TO_PRM.values():
name = prm_map['name']
columns = list(prm_map['columns'])
key_path = prm_map['key_path']
key = prm_map['key']
unit = prm_map['unit']
default_unit = prm_map['default_unit']
post_process = prm_map['post_process']
self._overlay_cp2k_settings(cp2k_settings,
name, columns, key_path, key, unit,
default_unit, post_process)
def extract_args(args: Optional[List[str]] = None) -> Settings:
"""Extract and return all arguments."""
input_file = args.YAML[0]
if exists(input_file):
pass
elif exists(join(getcwd(), input_file)):
input_file = join(getcwd(), input_file)
else:
input_file2 = join(getcwd(), input_file)
raise FileNotFoundError(
f'No file found at {input_file} or {input_file2}')
with open(input_file, 'r') as file:
return Settings(yaml.load(file, Loader=yaml.FullLoader))
def update_ff_jobs(s: Settings) -> None:
"""Update forcefield settings."""
if NANO_CAT is not None:
raise NANO_CAT
ff = Settings()
set_cp2k_param(ff, s.optional.forcefield)
optimize = s.optional.qd.optimize
if optimize and optimize.use_ff:
if optimize.job1 and str(optimize.job1) == str(Cp2kJob):
optimize.s1 = Settings() if optimize.s1 is None else optimize.s1
optimize.s1 += get_template('qd.yaml')['CP2K_CHARM_opt']
optimize.s1 += ff
if optimize.job2 and str(optimize.job1) == str(Cp2kJob):
optimize.s2 = Settings() if optimize.s2 is None else optimize.s2
optimize.s2 += get_template('qd.yaml')['CP2K_CHARM_opt']
optimize.s2 += ff
dissociate = s.optional.qd.dissociate
if dissociate and dissociate.use_ff:
if dissociate.job1 and str(dissociate.job1) == str(Cp2kJob):
dissociate.s1 = Settings(
) if dissociate.s1 is None else dissociate.s1
dissociate.s1 += get_template('qd.yaml')['CP2K_CHARM_opt']
dissociate.s1 += ff
activation_strain = s.optional.qd.activation_strain
if activation_strain and activation_strain.use_ff:
if activation_strain.job1 and str(
activation_strain.job1) == str(Cp2kJob):
key = 'CP2K_CHARM_singlepoint' if not activation_strain.md else 'CP2K_CHARM_md'
activation_strain.s1 = Settings(
) if activation_strain.s1 is None else activation_strain.s1 # noqa
activation_strain.s1 += get_template('qd.yaml')[key]
activation_strain.s1 += ff
def run_cdft_job(mol: Molecule, job: Type[ADFJob], s: Settings) -> pd.Series:
"""Run a conceptual DFT job and extract & return all global descriptors."""
results = mol.job_single_point(job,
s.copy(),
name='CDFT',
ret_results=True,
read_template=False)
if results.job.status in {'crashed', 'failed'}:
return _BACKUP
ret = get_global_descriptors(results)
ret.index = pd.MultiIndex.from_product([['cdft'], ret.index],
names=['index', 'sub index'])
return ret
def DFT():
s = Settings()
s.input.ams.task = 'GeometryOptimization'
s.input.adf.basis.type = 'TZ2P'
s.input.adf.basis.core = 'None'
s.input.adf.xc.hybrid = 'B3LYP'
s.input.adf.xc.Dispersion = 'GRIMME3 BJDAMP'
s.input.adf.Relativity.Level = 'None'
s.input.adf.NumericalQuality = 'Good'
s.input.adf.Symmetry = 'NOSYM'
s.input.ams.UseSymmetry = 'No'
s.input.adf.Unrestricted = 'No'
s.input.adf.SpinPolarization = 0
s.input.ams.System.Charge = 0
return s
def _get_logp(s: Settings, name: str, logger: logging.Logger) -> float:
logp_s = s.copy()
logp_s.update(get_template('qd.yaml')['COSMO-RS logp'])
for v in logp_s.input.compound:
v._h = v._h.format(os.environ["ADFRESOURCES"])
logp_job = CRSJob(settings=logp_s, name='LogP')
results = _crs_run(logp_job, name)
try:
logp = results.readkf('LOGP', 'logp')[0]
logger.info(f'{results.job.__class__.__name__}: {name} LogP '
f'calculation ({results.job.name}) is successful')
except Exception:
logger.error(f'{results.job.__class__.__name__}: {name} LogP '
f'calculation ({results.job.name}) has failed')
logp = np.nan
return logp
def start_crs_jobs(mol_list: Iterable[Molecule], jobs: Iterable[Type[Job]],
settings: Iterable[Settings],
**kwargs: Any) -> List[pd.Series]:
# Parse the job type
job, *_ = jobs
if job is not ADFJob:
raise NotImplementedError(f"job: {job.__class__.__name__} = {job!r}")
# Parse and update the input settings
_s, *_ = settings
s = Settings(_s)
s.input += cdft.specific.adf
ret = []
for mol in mol_list:
ret.append(run_cdft_job(mol, job, s))
return ret
def _get_logp(solutes: _NDArray[np.object_]) -> _NDArray[np.float64]:
"""Perform a LogP calculation."""
ret = np.full_like(solutes, np.nan, dtype=np.float64)
mask = solutes != None
count = np.count_nonzero(mask)
if count == 0:
return ret
s = copy.deepcopy(LOGP_SETTINGS)
for v in s.input.compound[:2]:
v._h = v._h.format(os.environ["AMSRESOURCES"])
s.input.compound += [Settings({"_h": f'"{sol}"', "_1": "compkffile"}) for sol in solutes[mask]]
ret[mask] = _run_crs(
s, count,
logp=lambda r: r.readkf('LOGP', 'logp')[2:],
)
return ret
def finalize_lj(mol: Molecule, s: List[Settings]) -> None:
"""Assign UFF Lennard-Jones parameters to all missing non-bonded core/ligand interactions.
.. _LENNARD_JONES: https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD/NONBONDED/LENNARD-JONES.html
Parameters
----------
mol : |plams.Molecule|_
A PLAMS molecule containing a core and ligand(s).
s : |list|_ [|plams.Settings|_]
A list of settings constructed from the
CP2K FORCE_EVAL/MM/FORCEFIELD/NONBONDED/`LENNARD-JONES`_ block.
The settings are expected to contain the ``"atoms"`` keys.
""" # noqa
# Create a set of all core atom types
core_at, lig_at = _gather_core_lig_symbols(mol)
# Create a set of all user-specified core/ligand LJ pairs
if not s:
s = []
elif isinstance(s, dict):
s = [s]
atom_pairs = {frozenset(s.atoms.split()) for s in s}
# Check if LJ parameters are present for all atom pairs.
# If not, supplement them with UFF parameters.
for at1, symbol1 in core_at.items():
for at2, symbol2 in lig_at.items():
at1_at2 = {at1, at2}
if at1_at2 in atom_pairs:
continue
s.append(
Settings({
'atoms':
f'{at1} {at2}',
'epsilon':
f'[kcalmol] {round(combine_epsilon(symbol1, symbol2), 4)}',
'sigma':
f'[angstrom] {round(combine_sigma(symbol1, symbol2), 4)}'
}))