quemb.molbe.chemfrag.BondConnectivity¶

class quemb.molbe.chemfrag.BondConnectivity(bonds_atoms, motifs, bonds_motifs, H_atoms, H_per_motif, atoms_per_motif, h_treatment='treat_H_diff')¶

Data structure to store the connectivity data of a molecule.

This collects all information that is independent of the chosen fragmentation scheme, i.e. BE1, BE2, etc., and is independent of the basis set, i.e. STO-3G, 6-31G, etc.

Attributes

bonds_atoms: Final[Mapping[NewType(AtomIdx, int), OrderedSet[NewType(AtomIdx, int)]]]¶: The connectivity graph of the molecule.

motifs: Final[OrderedSet[NewType(MotifIdx, NewType(AtomIdx, int))]]¶: The heavy atoms/motifs in the molecule. If hydrogens are not treated differently then every hydrogen is also a motif on its own.

bonds_motifs: Final[Mapping[NewType(MotifIdx, NewType(AtomIdx, int)), OrderedSet[NewType(MotifIdx, NewType(AtomIdx, int))]]]¶

H_atoms: Final[OrderedSet[NewType(AtomIdx, int)]]¶: The hydrogen atoms in the molecule. If hydrogens are not treated differently, then this is an empty set.

H_per_motif: Final[Mapping[NewType(MotifIdx, NewType(AtomIdx, int)), OrderedSet[NewType(AtomIdx, int)]]]¶: The hydrogen atoms per motif. If hydrogens are not treated differently, then the values of the dictionary are empty sets.

atoms_per_motif: Final[Mapping[NewType(MotifIdx, NewType(AtomIdx, int)), OrderedSet[NewType(AtomIdx, int)]]]¶: All atoms per motif. Lists the motif/heavy atom first.

h_treatment: Final[Literal['treat_H_diff', 'treat_H_like_heavy_atom', 'at_most_one_H']]¶: How do we treat hydrogen atoms?

Methods

`__init__`(bonds_atoms, motifs, bonds_motifs, ...)	Method generated by attrs for class BondConnectivity.
`from_cartesian`(m, *[, bonds_atoms, ...])	Create a `BondConnectivity` from a `chemcoord.Cartesian`.
`from_cell`(cell, *[, bonds_atoms, ...])	Create a `BondConnectivity` from a `pyscf.pbc.gto.cell.Cell`.
`from_mole`(mol, *[, bonds_atoms, vdW_radius, ...])	Create a `BondConnectivity` from a `pyscf.gto.mole.Mole`.
`get_BE_fragment`(i_center, n_BE)	Return the BE fragment around atom `i_center`.
`get_all_BE_fragments`(n_BE)	Return all BE-fragments