Hi David,
thank you for your advice regarding using AssignTotalChargeToAtoms. Adding it
resulted in less errors in the bond order assignment.
Unfortunately, it did not remove e.g. the error with sulfite (SO3^2-) that is
still getting three double bonds.
Another issue is that some of the small rings (e.g. thiirene, C2H2S) are not
recognised as rings.
This is really confusing as the coordinates fullfil the requirement set in
mol.cpp, ConnectTheDots(), lines 3027-3028:
// bonded if closer than elemental Rcov + tolerance
cutoff = SQUARE(rad[j] + rad[k] + 0.45);
If you have any advice I would really appreciate it.
With kind regards,
Madeleine
> On 7 Jun 2021, at 15:34, David Koes <dk...@pitt.edu> wrote:
>
> 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 check”. (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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