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, swallow_replace=False)

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

Parameters:

  • mol (TypeVar(_T_chemsystem, Mole, Cell)) – 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.

  • swallow_replace (bool) – If a fragment would be swallowed, it is instead replaced by the largest fragment that contains the smaller fragment. The definition of the origin is taken from the smaller fragment. This means, there will be no centers other than origins.

Return type:

Self