quemb.molbe.chemfrag.BondConnectivity.from_mole

classmethod BondConnectivity.from_mole(mol, *, bonds_atoms=None, vdW_radius=None, h_treatment='treat_H_diff')

Create a BondConnectivity from a pyscf.gto.mole.Mole.

Parameters:

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

• 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 (int | float | floating | Callable[[int | float | floating], int | float | floating] | Mapping[str, int | float | floating] | 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.

• 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

Return type:

Self