On 2021-07-27 12:33, David van der Spoel wrote:
On 2021-07-27 10:39, Noel O'Boyle wrote:
OBBond.IsAromatic(). See the docs.
Thanks for the suggestion. That works fine for aromatic rings, but not
for COO- or NO2 groups. Is there another flag to test, I cannot find
anything in the documentation.
An OBbond.IsResonant() would be great...
Just some feed back that I was able to implement a hack in my own code
turning both aromatic bonds and specific others like COO- into bond
orders of 1.5.
Cheers, David.
I would not use Smarts patterns to type atoms or bonds, but rather do
it in code. The former is just too error prone, slow and less readable.
On Tue, 27 Jul 2021, 07:18 David van der Spoel,
<david.vandersp...@icm.uu.se <mailto:david.vandersp...@icm.uu.se>>
wrote:
On 2021-07-27 07:51, Noel O'Boyle wrote:
> Is there a particular problem you are trying to solve where
underlying
> kekule representation is causing a problem?
>
Yes, I am extracting bond orders from OB and they go into my force
field
code. Different bond orders means different bond properties which in
addition yield different charges in my force field code.
If I understand it correctly the kekulization code checks for
resonance
but in order to get the chemistry of single and double bonds
right we
had to add over 100 lines to bondtyp.txt, so I am not sure that
the code
alone is enough.
If it would be easy to extract the aromaticity of a bond that
would be
sufficient for my purpose indeed.
>
> On Mon, 26 Jul 2021, 21:28 David Koes, <dk...@pitt.edu
<mailto:dk...@pitt.edu>
> <mailto:dk...@pitt.edu <mailto:dk...@pitt.edu>>> wrote:
>
> In my opinion, if the only fractional value will be 1.5 then
> non-integer
> bond orders aren't worth the pain of breaking compatibility
since
> this
> state can be (and is, for rings) represented by setting the
aromatic
> property of the bond. Perhaps we should provide additional,
more
> nuanced properties to indicate resonance vs aromaticity?
>
> If there is a reason for fractions other than 1.5, then I
think this
> should be a separate property entirely (e.g., like formal
charges vs
> partial charges).
>
> I would point out that although O=CO is represented with a
double and
> single bond, the oxygens still get an identical partial
charge as the
> carboxylic acid group is recognized as such:
> print(pybel.readstring('smi','O=CO').write('mol2'))
>
> David Koes
>
> Associate Professor
> Computational & Systems Biology
> University of Pittsburgh
>
> On 7/26/21 5:36 AM, David van der Spoel wrote:
> > Hi,
> >
> > maybe this has been discussed earlier, but I would like to
hear your
> > opinion on implementing non-integer bond orders. For e.g.
> benzene the
> > average CC bond order would be 1.5, and likewise for COO-
groups
> or NOO
> > groups. Quantum-chemically such resonant groups turn out
to be
> > symmetrical and e.g. with identical charges on the O in
those cases.
> >
> > When using integer bond orders we are enforcing an asymmetry
> that is not
> > there. So would it be worthwhile implementing non-integer
bond
> orders or
> > is there a workaround that I am overlooking?
> >
> > Cheers,
> >
> > --
> > David van der Spoel, Ph.D.,
> > Professor of Computational Molecular Biophysics
> > Uppsala University.
>
>
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--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org <http://virtualchemistry.org>
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Uppsala University.
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Uppsala University.
http://virtualchemistry.org
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vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
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