There is AssignTotalChargeToAtoms which is called when parsing the gamess format, but not, apparently, gaussian.

Again, if you could upload examples of failures to a GitHub Issue (or even better, start a pull request with failing tests added to the testing framework) that would be helpful.

David Koes

Associate Professor
Computational & Systems Biology
University of Pittsburgh

On 6/7/21 8:22 AM, Marie-Madeleine Walz wrote:
Hi David,

thank you for your reply. I tested your code that assigns a sp2 hybridisation to a N as e.g. in azete (in mol.cpp), and it solves the incorrect bond orders.

However, I think that this is a general problem: I have numerous compounds that get incorrect bond orders and that end up with a different charge than specified in the Gaussian output file (like e.g. sulfite and sulfur trioxide). I think it might be a good idea to have somewhere a general "charge checkā€. (Maybe there is and I miss to use it? I checked whether OB is getting the specified charge and it seems to get it.)

For example, it would be great if there is a function that checks (i) the charge of the compound (or whether it is a radical) and (ii) the sum of bond orders to a certain atom (I guess that is done with GetExplicitValence()). If a compound is neutral (and not a radical) and ends up with e.g. a C that only has three single bonds, this should be somehow corrected.

Is there any way to do this with the existing OB functions, i.e. without changing the code?

With kind regards,
Madeleine


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