quemb.molbe.chemfrag.Fragmented.from_mole

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

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

Parameters:

• mol (Mole) – The pyscf.gto.mole.Mole to extract the connectivity data from.

• n_BE (int) – The BE fragmentation level.

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

• bonds_atoms (Mapping[int, set[int]] | None) – Can be used to specify the connectivity graph of the molecule. Has exactly the same format as the output of chemcoord.Cartesian.get_bonds(), which is called internally if this argument is not specified. Allows it to manually change the connectivity by modifying the output of chemcoord.Cartesian.get_bonds(). The keyword is mutually exclusive with vdW_radius.

• vdW_radius (Real | Callable[[Real], Real] | Mapping[str, Real] | None) –

  If bonds_atoms is None, then the connectivity graph is determined by the van der Waals radius of the atoms. It is possible to pass:

  • a single number which is used as radius for all atoms,

  • a callable which is applied to all radii and can be used to e.g. scale via lambda r: r * 1.1,

  • a dictionary which maps the element symbol to the van der Waals radius, to change the radius of individual elements, e.g. {"C": 1.5}.

  The keyword is mutually exclusive with bonds_atoms.

Return type:

Self