On 2021-06-08 15:42, David Koes wrote:
Hi Madeleine,
It sounds like you have a really excellent set of test structures. It
would be fantastic if you could contribute these to the testing
framework.
We would be happy to do that, but maybe you can give a suggestion on
where in the testing framework? Or should we just add a new python
script there with in and output data?
FYI, we have made quite a few fixes already that likely are of interest
to others:
% git diff master:data/bondtyp.txt data/bondtyp.txt | wc
128 784 4532
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/8/21 8:15 AM, Marie-Madeleine Walz wrote:
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
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