Re: [Rdkit-discuss] fragments aromaticity

[Greg L. <gre...@gm...>]

On Wed, Oct 21, 2009 at 12:08 PM, Evgueni Kolossov <eko...@gm...> wrote:
> Sorry Greg,
>
> Actually I found the problem - in this case to pass structure into the
> viewer I been using MolToMolBlock(*mol, true, -1, false) instead of SDWriter
> function write(*mol) and this is what making the difference - write(*mol)
> doing it OK but MolToMolBlock producing an effect I described to you.
> I have moved into write(*mol) now and everything is OK.
> I can only suggest you take a look at MolToMolBlock function.

MolToMolBlock is fine, in fact it's what the SDWriter is using (look
at line 75 of SDWriter.cpp). The problem that you are having is maybe
the last argument you provide to MolToMolBlock, which tells it that
the molecule should *not* be kekulized on output. The default value
for this (which is what the SDWriter uses) is true.

None of this explains why you are getting double bonds in the output.

Are you *sure* that there are double bonds? The bond type flag in the
output mol blocks is really equal to "2"? Could it be that your viewer
is seeing aromatic bonds in the output (bond type "4") and drawing
them as double bonds?

-greg