Difference in Avogadro and obabel conversions

General Discussion
#1

Dear Developers,

I have the following PDB file (Tryptophan) without the connectivity information:
try_no_connect.pdb

  1. I use Avogadro and re-save it to the the file: try_frm_Avg.pdb
  2. I also use obabel to get: try_frm_OB.pdb

There is a difference in the connectivity information written out b/w 1 & 2
(specifically double bonds).

I tried using Openbabel’s OBMOl::PerceiveBondOrders(), OBAtomTyper::AssignHyb,
OBAtomTyper::AssignImplicitValence().

I was wondering if you could share what classes/methods Avogadro uses?
[I have a modeling program that likes what Avogadro writes out but not the other format]

Thanks in advance for your suggestions – I appreciate it.

Best,–
Prashanth Athri