quemb.molbe.chemfrag.Fragmented.from_mole

classmethod Fragmented.from_mole(mol, n_BE, *, frozen_core=False, treat_H_different=True, bonds_atoms=None, vdW_radius=None, iao_valence_basis=None, autocratic_matching=True, swallow_replace=False)
Construct a Fragmented from pyscf.gto.mole.Mole

or pyscf.pbc.gto.cell.Cell.

Parameters:

  • mol (TypeVar(_T_chemsystem, Mole, Cell)) – The pyscf.gto.mole.Mole or pyscf.pbc.gto.cell.Cell 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 (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.

  • autocratic_matching (bool) – Assume autocratic matching for possibly shared centers. Will call PurelyStructureFragmented.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