add /connectivity group

[PythonFZ]

A group of either time dependent or time independent data:

/connectivity/

• bonds
• bond_order ?
• particle_group

see https://h5md.nongnu.org/h5md.html#connectivity-group

class Atoms(ase.Atoms):
    bonds

    def get_graph() -> networkx

also see https://github.com/imagdau/aseMolec

[PythonFZ]

Add a custom NLTool to the io - some preprocessor maybe?

import ase.neighborlist as nl
import networkx as nx
import numpy as np

cutoffs = nl.natural_cutoffs(atoms) # scale for bond order
neighbor_list = nl.NeighborList(cutoffs, self_interaction=False, bothways=False)
neighbor_list.update(atoms)
matrix = neighbor_list.get_connectivity_matrix()
g = nx.from_scipy_sparse_array(matrix)
np.array(g.edges)

RDKit might also have some very handy tools on hand to compute bond order or some ML toolset.