Hi,
While testing the changes to correctly canonicalize multi-fragment SMILES,
I noticed the same problem and it seems to only occur for multi-fragment
molecules. I reported this on the openbabel-devel mailing list with title "More
multi-fragment canonical SMILES tests". I'm not sure where things go wrong
though.
Tim
On Sun, Mar 2, 2014 at 4:52 AM, Lee-Ping Wang <leep...@stanford.edu> wrote:
> Hi there,
>
> I'm converting some molecules to 2D format, and some of them are extremely
> small and/or uncommon in normal chemistry (e.g. nitrogen atoms). I'm
> running into an issue where sometimes it automatically adds hydrogen atoms.
> For example, I have a reaction where NH is split into N and H atoms, and I
> really just want it to display H-N on the left and N H on the right.
> Files are attached below. Thanks. :)
>
> - Lee-Ping
>
> Watch the right panel when I want to convert a separate nitrogen atom and
> hydrogen atom into PNG format:
>
> obabel reactants.cml products.cml -O ~/Dropbox/tmp.png --gen2d -xw 1200
> -xh 600
>
>
>
> As you can see (above), it adds three "blue" hydrogen atoms to N which is
> not desired, plus it puts N and H on top of each other.
>
> If I use "--gen3d", it adds a hydrogen atom to H as well and makes them
> all gray. Adding "-h" does the same thing (below). It seems the stacking
> problem is gone, but having a balanced chemical equation is more important.
>
>
>
> If I use "-d", now it deletes the hydrogen atom but adds three to the
> nitrogen atom.
>
>
>
>
>
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