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.
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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