data.oc.core.adsorbate#
Classes#
Initializes an adsorbate object in one of 4 ways: |
Functions#
|
Module Contents#
- class data.oc.core.adsorbate.Adsorbate(adsorbate_atoms: ase.Atoms = None, adsorbate_id_from_db: int | None = None, adsorbate_smiles_from_db: str | None = None, adsorbate_db_path: str = ADSORBATE_PKL_PATH, adsorbate_db: dict[int, tuple[Any, Ellipsis]] | None = None, adsorbate_binding_indices: list | None = None)#
Initializes an adsorbate object in one of 4 ways: - Directly pass in an ase.Atoms object.
For this, you should also provide the index of the binding atom.
Pass in index of adsorbate to select from adsorbate database.
Pass in the SMILES string of the adsorbate to select from the database.
Randomly sample an adsorbate from the adsorbate database.
- Parameters:
adsorbate_atoms (ase.Atoms) – Adsorbate structure.
adsorbate_id_from_db (int) – Index of adsorbate to select.
adsorbate_smiles_from_db (str) – A SMILES string of the desired adsorbate.
adsorbate_db_path (str) – Path to adsorbate database.
adsorbate_binding_indices (list) – The index/indices of the adsorbate atoms which are expected to bind.
- adsorbate_id_from_db#
- adsorbate_db_path#
- __len__()#
- __str__()#
Return str(self).
- __repr__()#
Return repr(self).
- _get_adsorbate_from_random(adsorbate_db)#
- _load_adsorbate(adsorbate: tuple[Any, Ellipsis]) None #
Saves the fields from an adsorbate stored in a database. Fields added after the first revision are conditionally added for backwards compatibility with older database files.
- data.oc.core.adsorbate.randomly_rotate_adsorbate(adsorbate_atoms: ase.Atoms, mode: str = 'random', binding_idx: int | None = None)#