Hi Stefano,
the problem with the PDBQT format is that connectivity is implicit and bond
order is lost.
If your atom coordinates are close to ideal (i.e., bond lengths are optimal,
non-distorted) you have a good chance of OB to be able to re-build the correct
bond order.
Although, there's been
Hi Stefano,
I might suggest trying VS module in oddt (https://github.com/oddt/oddt)
which is based on Pybel (DISCLAIMER: I'm the author of oddt). To overcome
the connectivity problem it just copy the coordinates of docked
conformationson the input molecules. This way you should retain the
