> -problems with bond order (e.g. it makes non-aromatic ring out of aromatic
> one)
> -problems with charges (e.g. it converts charged group like NH3+ to radical
> NH3);
Can you post the PDB file? Since PDB does not usually contain bond orders, Open
Babel needs to perceive aromaticity, etc. and
Hi guys!
My task is to convert a multi-model PDB file to SMILES. I've tried different
programs and OpenBabel does the job the best - but still not perfect. My
major concerns:
-problems with bond order (e.g. it makes non-aromatic ring out of aromatic
one)
-problems with charges (e.g. it converts ch
