IndexError when trying to construct Graph for single-atom molecule

[rwxayheee]

Hi,

Thank you for developing and maintaining espaloma. It has been a very valuable source of the parameters to our project, Meeko, interface for AutoDock and molecule parameterization. Our user (forlilab/Meeko#310) encountered an issue when trying to construct Graph for single-atom molecules. Initially, the issue was raised for Zn2+. Please see a non-metal example:

Input

from openff.toolkit.topology import Molecule
import espaloma as esp
from espaloma import Graph
mol = Molecule.from_smiles("[O-2]", allow_undefined_stereo=True)
Graph(mol)

Output

/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/dgl/heterograph.py:92: DGLWarning: Recommend creating graphs by `dgl.graph(data)` instead of `dgl.DGLGraph(data)`.
  dgl_warning(
Traceback (most recent call last):
  File "/Users/amyhe/Downloads/single_atom_graph.py", line 5, in <module>
    Graph(mol)
  File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/espaloma-0.3.2+3.g907d183-py3.10.egg/espaloma/graphs/graph.py", line 63, in __init__
    heterograph = self.get_heterograph_from_graph_and_mol(
  File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/espaloma-0.3.2+3.g907d183-py3.10.egg/espaloma/graphs/graph.py", line 137, in get_heterograph_from_graph_and_mol
    heterograph = esp.graphs.utils.read_heterogeneous_graph.from_homogeneous_and_mol(
  File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/espaloma-0.3.2+3.g907d183-py3.10.egg/espaloma/graphs/utils/read_heterogeneous_graph.py", line 150, in from_homogeneous_and_mol
    for x in idxs["n%s" % big_idx][
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

espaloma version:

'0.3.2+3.g907d183'

We understand that not all elements are supported, but would very much appreciate it if you could point us to a possible workaround or clarify the definition of graph - does it still make sense to single-atom molecules to have graph, or should we avoid constructing it at all?

Thank you for your time and kind advice in advance.

[rwxayheee]

Just saw #191 and think it's the same issue. Closing to avoid duplicates