quemb.molbe.chemfrag.BondConnectivity.from_cartesian

classmethod BondConnectivity.from_cartesian(m, *, bonds_atoms=None, vdW_radius=None, h_treatment='treat_H_diff')

Create a BondConnectivity from a chemcoord.Cartesian.

Parameters:

  • m (Cartesian) – The Cartesian object to extract the connectivity data from.

  • bonds_atoms (Mapping[int, Set[int]] | Mapping[NewType(AtomIdx, int), OrderedSet[NewType(AtomIdx, 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. This can also take in a modified processed_bonds_atoms object (dict) when specifying certain h_treatment options

  • 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