Hi David,
in principle I agree with your analysis, but to me the place where the function
breaks is when you perform the same operation in two steps instead of one and
you obtain a different result.
The pH transformation rule works just fine if you perform the hybridization
perception before
Hi Madeleine,
It might be helpful to start a GitHub Issue where you upload example files.
I believe the main issue here is Gaussian files do not contain bond
information and so OpenBabel has to infer them with ConnectTheDots
(identifying bonding atoms) and PerceiveBondOrders. These functions
I think the problem here is in the ph model since the problem doesn't
happen if you omit the ph specification. Passing a pH causes
AddHydrogens to be called with correctForPH set to true, which is not
the default. That is, it's not that there is a default pH that is used,
but the default is
