Molecule

class mlptrain.molecule.Molecule(arg: str = 'molecule', smiles: str | None = None, atoms: List[Atom] | None = None, solvent_name: str | None = None, charge: int | None = None, mult: int | None = None, **kwargs)

Bases: Molecule

property centroid: ndarray

Centroid of this molecule

is_in_box(box: Box) → bool

Is this molecule totally inside a box with an origin at (0,0,0) and top right corner (a, b, c) = box.size

Return type:

(bool)

min_distance_to(coords: ndarray) → float

Calculate the minimum distance from this molecule to a set of coordinates

Returns:

Minimum distance (Å)

Return type:

(float)

random_normal_jiggle(sigma: float = 0.01) → None

Add a random displacement to each atoms position.