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 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 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 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)
