Re: [Open Babel] Including molecular charge when converting xyz to SMILES

> Is there a way to tell babel what the charge of the molecule in the xyz file > is? From the command-line? No. Even if there was, it’s not going to suddenly assign formal charges to your de-protonated functional groups. (Yes, as humans we can find the most likely places to put the negative c

[Open Babel] Including molecular charge when converting xyz to SMILES

Here is an xyz file for a dianion (acetic acid and phenol deprotonated). When I use obabel to convert it to SMILES I get a neural SMILES string: CC1=C(C(=O)[O])N2C(=O)[C@@H](NC(=O)[C@H](N)[C]3C=CC(=O)C=C3)[C@H]2SC1 Is there a way to tell babel what the charge of the molecule in the xyz file is