Hi Juuso,
Reading aromatic bonds from a mol file is problematic (the mol file spec is
clear that aromatic bond orders are only for use in queries), but ignoring
that for a moment...
There's an RDKit blog post on this very topic:
http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html
I hope this helps,
-greg
On Wed, Jan 11, 2017 at 3:36 PM, Juuso Lehtivarjo <
juuso.lehtiva...@gmail.com> wrote:
> Dear RDKit users,
>
> Interpreting the default sanitization order (in
> http://www.rdkit.org/docs/RDKit_Book.html), I assume that
> SetAromaticity must be preceded with Kekulization (otherwise, why to
> Kekulize at all if atoms and bonds are to be marked as aromatic
> anyway). However, I wonder if any of the other sanitization steps, or
> e.g. any stereochemistry-related operations are dependent on
> Kekulization as well? The bottom line question is, if I read in a
> molfile that has reliable aromatic bonds (e.g. it has gone through
> successful default sanitization procedure previously), can I just mark
> the corresponding atoms as aromatic and then skip both Kekulization
> and SetAromaticity steps, without having anything important missing?
>
> Thanks in advance!
> Juuso
>
> ps.
> The underlying reason for the whole mess is that some aromatic-N
> containing molecules require the "sanifix4" correction (from this post
> http://www.mail-archive.com/rdkit-discuss@lists.
> sourceforge.net/msg01901.html),
> which I can't use from C++ side obviously. Wonder if there is any
> better solutions to this?
>
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