Molecules from SMILES

autode.smiles.smiles.calc_multiplicity(molecule, n_radical_electrons)

Calculate the spin multiplicity 2S + 1 where S is the number of unpaired electrons. Will only override non-default (unity multiplicity)

Keyword Arguments:

n_radical_electrons (int | None)

Returns:

multiplicity of the molecule

Return type:

(int)

autode.smiles.smiles.check_bonds(molecule, bonds)

Ensure the SMILES string and the 3D structure have the same bonds, but don’t override

Parameters:

bonds (list)

autode.smiles.smiles.init_organic_smiles(molecule, smiles)

Initialise a molecule from a SMILES string, set the charge, multiplicity ( if it’s not already specified) and the 3D geometry using RDKit

Parameters:

smiles (str) – SMILES string

autode.smiles.smiles.init_smiles(molecule, smiles)

Initialise a molecule from a SMILES string

Parameters:

smiles (str) – SMILES string