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Molecule

Molecule#

class autode.species.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)#
__init__(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)#

A molecular species constructable from SMILES or a set of atoms, has default charge and spin multiplicity.

Parameters:

  • atoms – List of atoms in the species

  • solvent_name – Solvent that the molecule is immersed in

  • charge – Charge on the molecule. If unspecified defaults to, if present, that defined in a xyz file or 0

  • mult – Spin multiplicity on the molecule. If unspecified defaults to, if present, that defined in a xyz file or 1

Keyword Arguments:

name – Name of the molecule. Overrides arg if arg is not a .xyz filename

populate_conformers(n_confs: int | None = None) → None#

Populate self.conformers with a conformers generated using a default method

to_product() → Product#

Generate a copy of this reactant as a product

to_reactant() → Reactant#

Generate a copy of this product as a reactant

class autode.species.molecule.Product(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)#

Product molecule

class autode.species.molecule.Reactant(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)#

Reactant molecule

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