#989 Lost of connectivity data during minimization, conversion of MOL2 files

[Jernej Zidar]

Hi,
I would like to report what is likey a bug in Babel.

I use a SMILES code to generate the initial structure (a MOL2 file) of a molecule, it will have the correct connectivity as specified by the SMILES code.

In the next step, I further minimize this MOL2 file using obminimize (or just generate a new MOL2 file), only to find the connectivity is now completely wrong. The problem/bug is most acute in aromatic molecules, where the loss of aromaticity information means there are many hydrogen atoms missing.

Attached are some examples for your use.

I'm using Babel 2.3.2 on MacOS Sierra, though I was able to replicate the error in Debian Linux using the same version of Babel.

Thanks again for the great work with Babel!

Cheers,
Jernej