quemb.molbe.chemfrag.PurelyStructureFragmented.from_mole

classmethod PurelyStructureFragmented.from_mole(mol, n_BE, *, treat_H_different=True, bonds_atoms=None, vdW_radius=None, autocratic_matching=True)

Construct a PurelyStructureFragmented from a pyscf.gto.mole.Mole.

Parameters:

  • mol (Mole) – The Molecule to extract the connectivity data from.

  • n_BE (int) – The coordination sphere to consider.

  • treat_H_different (bool) – If True, we treat hydrogen atoms differently from heavy atoms.

  • autocratic_matching (bool) – Assume autocratic matching for possibly shared centers. Will call get_autocratically_matched() upon construction. Look there for more details.

Return type:

Self