Thank you! The functionality has now been developed into a MoleculeComplex paclet with additional features. You can install it by following the steps below:

First, install the paclet by the code below: PacletInstall["RobertNachbar/MoleculeComplex"]

Next, load the paclet by the code below: Needs["RobertNachbarMoleculeComplex"] Note that there should be backtick before and after MoleculeComplex for Needs.

Congratulations on accomplishing this impressive work! The MoleculeComplex appears to be such a useful function — do you plan to release this and associated functions as ResourceFunctions? They would truly increase the capabilities of the Wolfram language.