def _parse_name_type(mol_dict: Settings) -> None:
"""Set the ``"name"`` and ``"type"`` keys in **mol_dict**.
The new values of ``"name"`` and ``"type"`` depend on the value of ``mol_dict["mol"]``.
Parameters
----------
mol_dict : |plams.Settings|_
A Settings instance containing the ``"mol"`` key.
``mol_dict["mol"]`` is exp
Raises
------
TypeError
Raised ``mol_dict["mol"]`` is an instance of neither :class:`str`, :class:`Molecule` nor
:class:`mol`.
"""
mol = mol_dict.mol
if isinstance(mol, str):
if isfile(mol): # mol is a file
mol_dict.type = mol.rsplit('.', 1)[-1]
mol_dict.name = basename(mol.rsplit('.', 1)[0])
elif isdir(mol): # mol is a directory
mol_dict.type = 'folder'
mol_dict.name = basename(mol)
else: # mol is (probably; hopefully?) a SMILES string
i = 1 + len(mol_dict.path) if 'path' in mol_dict else 0
mol_dict.type = 'smiles'
mol_dict.mol = mol[i:]
mol_dict.name = santize_smiles(mol_dict.mol)
elif isinstance(mol, Molecule): # mol is an instance of plams.Molecule
mol_dict.type = 'plams_mol'
if not mol.properties.name:
mol_dict.name = Chem.MolToSmiles(Chem.RemoveHs(molkit.to_rdmol(mol)), canonical=True)
else:
mol_dict.name = mol.properties.name
elif isinstance(mol, Chem.rdchem.Mol): # mol is an instance of rdkit.Chem.Mol
mol_dict.type = 'rdmol'
mol_dict.name = Chem.MolToSmiles(Chem.RemoveHs(mol), canonical=True)
else:
raise TypeError(f"mol_dict['mol'] expects an instance of 'str', 'Molecule' or 'Mol'; "
f"observed type: '{mol.__class__.__name__}'")
def validate_mol(args: Sequence[Union[Any, Settings]],
mol_type: str,
path: Optional[str] = None,
validate_path: bool = True) -> None:
r"""Validate the ``"input_ligands"``, ``"input_cores"`` and ``"input_qd"`` blocks in the input.
Performs an inpalce update of **args**.
Examples
--------
An example using a list of .xyz files as input
.. code:: python
# A list of .xyz files
>>> args1 = ['mol1.xyz', 'mol2.xyz']
>>> mol_type = 'input_ligands'
>>> validate_mol(args1, mol_type)
>>> print(args1[0], '\n', args1[1]) # doctest: +SKIP
is_core: False
mol: /path/to/my/current/working/dir/mol1.xyz
name: mol1
path: /path/to/my/current/working/dir
type: smiles
is_core: False
mol: /path/to/my/current/working/dir/mol2.xyz
name: mol2
path: /path/to/my/current/working/dir
type: smiles
Another example using a list of .pdb-containing dictionaries as input
.. code :: python
# A list of Settings instances with .xyz files
>>> print(args2) # doctest: +SKIP
[mol3.pdb:
guess_bonds: True
mol4.pdb:
guess_bonds: True
]
>>> mol_type = 'input_ligands'
>>> path = '/path/to/custom/working/dir'
>>> validate_mol(args2, mol_type, path) # doctest: +SKIP
>>> print(args2[0], '\n', args2[1]) # doctest: +SKIP
guess_bonds: True
is_core: True
mol: /path/to/custom/working/dir/mol3.pdb
name: mol3
path: /path/to/custom/working/dir
type: smiles
guess_bonds: True
is_core: True
mol: /path/to/custom/working/dir/mol4.pdb
name: mol4
path: /path/to/custom/working/dir
type: smiles
Parameters
----------
args : |list|_ [|plams.Settings|_]
A list of input molecules.
Accepts strings, PLAMS molecules and RDKit molecules.
Additional arguments can be provided by putting above-mentioned molecules in a dictionary.
mol_type : str
The type of molecule.
Accepted values are ``"input_ligands"`` and ``"input_cores"``.
path : str
Optional: The path to the molecule-containing directory.
Raises
------
FileNotFoundError
Raised if **path** cannot be found.
NotADirectoryError
Raised if **path** is not a directory.
ValueError
Raised if the **mol_type** parameter is neither ``"input_cores"`` nor ``"input_ligands"``.
SchemaError
Raised if invalid input settings are found in while validating **args**.
"""
# Validate arguments
is_core = _check_core(mol_type)
is_qd = _check_qd(mol_type)
if validate_path:
_path = validate_path_func(path)
else:
_path = path
for i, dict_ in enumerate(args):
if not isinstance(dict_, dict): # No optional arguments provided
mol = dict_
mol_dict = Settings({'path': _path, 'is_core': is_core, 'is_qd': is_qd})
else: # Optional arguments have been provided: parse and validate them
if dict_.get('parsed'):
continue
mol, mol_dict = next(iter(dict_.items()))
mol_dict.setdefault('is_core', is_core)
mol_dict.setdefault('is_qd', is_qd)
mol_dict = mol_schema.validate(mol_dict)
mol_dict.setdefault('path', _path)
if isinstance(mol, str) and not isfile(mol):
mol = join(mol_dict.path, mol)
mol_dict.mol = mol
mol_dict.parsed = True
_parse_name_type(mol_dict)
args[i] = mol_dict
