Dear Open Babel Developers,
I am Ibrahim Roshan, a developer at EMBL-EBI maintaining the
protein-ligand interaction pipeline. Open Babel is one of the main
component of our interaction pipeline and we have been using the 2.4.1
version so far. We recently made an update to Open Babel 3. However, for
so many protein entires the below warning was observed.
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders
Moreover, the interactions calculated using Open Babel 3 and 2.4.1 are
not the same for the same protein.The same issue was reported by the
developer, Lukas who was working on the pipeline earlier. I found
communication between him and O` Neil here
<https://sourceforge.net/p/openbabel/mailman/openbabel-discuss/thread/a9e7f432-e248-4ae4-a289-aa8ba93a8...@ebi.ac.uk/>
I would like to know if you have any plans to update the PDB structure
perception in version 3 as same as in version 2.4.1. It would be really
helpful if you could do that as we are planning to open-source our
interaction pipeline and most of the users are now using Open Babel 3.
If there is something that I can do to make PDB structure perception
method same as in 2.4.1 version, please kindly let me know. Looking
forward to your reply
Thanks,
IBRAHIM ROSHAN
Bioinformatician,
EMBL-EBI
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