Hello,
I’ve been having trouble converting between formats. I have generated some MOL
files using RDKit for various substituted subphthalocyanines (attached below)
which, when opened with any molecule viewer, show the correct bond order (1 or
2 depending on the atom) between the nitrogen and ca
Neither PDB nor XYZ files store the bond order. XYZ files do not even store
which atoms are connected to which atoms. If you want to learn more about
this, you should open chemical structure files in a text editor and
familiarise yourself with the information contained within. I gave a talk
which t
> Is there an option that I haven’t included that can solve this problem, or is
> this a bug that hasn’t been addressed? Any help would be appreciated.
The two formats you mention don't store bond orders. (In particular XYZ only
stores atoms - not even bond connections.)
OB includes an algorith
