Hi all,
I've sent in a pull request (
https://github.com/openbabel/openbabel/pull/1847) regarding to DeleteAtom()
and aromaticity, and Geoff asked me to bring it up here.
Currently, when you delete an atom (to be exact, it's actually
Begin/EndModify that I'm changing), the flag that indicates that
aromaticity is detected is cleared. This means that the reported
aromaticity on an atom or bond will always be in synch with the molecule's
current structure.
I propose to change this so that the aromaticity flag on the molecule is
unaffected by deleting atoms (or indeed by any API call that involves
Begin/EndModify).
The reason I propose this is:
(a) to make it obvious how the user can retain the original aromaticity if
they wish, even after modifying the molecule (this is the main reason).
With the current behavior, a user would never realise that aromaticity
information is still present, or that they just need to set that it has
been perceived (which is counter-intuitive).
(b) to avoid unneccessary work (e.g.calling DeleteHydrogens should not
invalidate aromaticity (if it currently does))
I could also argue that it simplifies toolkit behavior a bit (only the user
can invalidate aromaticity), but that's not really a reason for doing this,
just a possible silver lining.
I think this is a reasonably safe change because:
(a) aromaticity is stored on atoms and bonds, rather than involving a data
structure that retains pointers to atoms or bonds.
(b) if the user does not wish this behavior, it should be fairly (?)
obvious that it's happening, and there's a clear fix
Regards,
- Noel
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
