17 tiny molecules cause issues

[ntampellini]

• Added checks for linear molecules, single atoms, and non-heavy molecules (i.e. only made up of "H" atoms, for now).
• Avoids RuntimeWarnings and appears to have the desired behavior.
• Does not seem too detrimental to the performance of large ensembles.

@corinwagen Do you want to give this a try and see if performance is not impacted on your end as well?

[corinwagen]

seems good to me!