Oops, forgot to mention: This is with the solution to github issue #233<https://github.com/rdkit/rdkit/issues/233>patched into my RDKit build.
Yours,
Toby Wright
--
InhibOx Ltd
On 28 March 2014 15:43, Toby Wright <toby.wri...@inhibox.com> wrote:
> Hi,
>
> I believe I've found a bug in the new code that deals with reactions that
> have chirality specified for untagged product atoms. Consider the following:
>
> > rxn = AllChem.ReactionFromSmarts("[C:1].[C:2]>>C1C[C@@H](C[C:1])CC[C@
> @H](C[C:2])1")
> > m1 = Chem.MolFromSmiles('FC')
> > m2 = Chem.MolFromSmiles('BrC')
> > p = rxn.RunReactants((m1,m2))[0][0]
> > Chem.SanitizeMol(p)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
> > Chem.MolToSmiles(p, isomericSmiles=True)
> 'FCC[C@@H]1CC[C@@H](CCBr)CC1'
>
> The output looks about right, the [C@@H]s are both still [C@@H] but
> whereas before they were both being approached from around the ring now the
> canonicalisation has us approaching one from outside the ring. Both
> extensions from the ring should be towards and if I convert the product
> part of the above reaction to a png I get:
> [image: Inline images 1]
> but in the output one is towards and the other is away:
> [image: Inline images 2]
>
> Note that I can work around this, if I specify my reaction as
> [C:1].[C:2]>>[C:1]C[C@H]1CC[C@@H](C[C:2])CC1 thus apeing the atom
> ordering of the product RDKit will give me I get the chirality I want, at
> least in my test cases so far.
>
> Yours,
>
> Toby Wright
>
> --
> InhibOx Ltd
>
<<inline: ReactionProduct.png>>
<<inline: MadeProduct.png>>
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