Explicit Solvent#
Warning
Explicit solvation is experimental and not implemented apart from autode.Molecule.explicitly_solvate
- class autode.solvent.explicit_solvent.ExplicitSolvent(solvent: Species, num: int, solute: Species | None = None, **kwargs)#
Explicit solvation
- __eq__(other: Any) bool #
Equality between two explicit solvent environments
- __init__(solvent: Species, num: int, solute: Species | None = None, **kwargs)#
Explicit solvent. Initial construction attempts to generate a reasonable distribution around the (unmodified) solute. Only supports unicomponent uncharged solvents.
- Parameters:
num (int) – Number of solvent molecules to add
- Keyword Arguments:
solute (autode.species.species.Species | None) – Solute which this solvent surrounds. If None then no translation to the explicit solvent molecules will be applied
aliases (list(str)) – List of aliases of this solvent
- property is_implicit: bool#
Is this solvent implicit?
- Returns:
False
- Return type:
(bool)
- property n_solvent_molecules: int#
Number of solvent molecules comprising this explicit solvent cluster
- Returns:
n
- Return type:
(int)
- randomise_around(solute: Species) None #
Randomise the positions of the solvent molecules around the solute, for example using a methane solute and water solvent:
H2O H20 H2o H2O H2O H2O CH4 H2O H2O H2O
where the solvent molecules are roughly packed in shells around the solute.
- Parameters:
solute (autode.species.species.Species)
- solvent_atom_idxs(i: int) ndarray #
Atom indexes of an particular solvent molecule
- Returns:
Atom indexes
- Return type:
(np.ndarray)