quemb.molbe.chemfrag.PurelyStructureFragmented.from_mole

classmethod PurelyStructureFragmented.from_mole(mol, n_BE, *, h_treatment='treat_H_diff', 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.

  • h_treatment (Literal['treat_H_diff', 'treat_H_like_heavy_atom', 'at_most_one_H']) –

    How do we treat the hydrogen atoms? Options include:

    • "treat_H_diff": Default, treating each H different from heavy atoms. Using the given vdW_radius to determine which H belong to which motif

    • "treat_H_like_heavy_atom": Treating each H the same as the heavy atoms when determining fragments

    • "at_most_one_H": Enforcing that each H can belong to at most one H, if a H is assigned to multiple motifs

  • 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