On Thu, Apr 4, 2013 at 8:23 AM, Robert Feinstein <r...@kelaroo.com> wrote:
> ...
>> In [7]: rxn = AllChem.ReactionFromSmarts('[C:1]-O>>[C:1]-S')
>> In [8]: ps = rxn.RunReactants((Chem.MolFromSmiles('F[C@H](O)Cl'),))
>> In [9]: Chem.MolToSmiles(ps[0][0],True)
>> Out[9]: 'F[C@H](S)Cl'
>>
>> It seems nice to be able to preserve chirality in these cases.
>>
>> The question that comes up is: "*Should* we be preserving chirality in
>> these cases?". The change makes it impossible to indicate a reaction
>> that scrambles stereochemistry. That doesn't seem right.
>
> This should be the default behavior since it covers the vast majority
> of rxns, chiral and achiral.So the default should be to preserve chirality whenever possible unless information is provided to indicate otherwise? This is what the example above is doing. >> >> So... the question to you guys: How should stereochemistry >> inversion/retention/loss be indicated in Reaction SMARTS? > > This is my just my opinion... don't mistake me for an expert. > Stereocenter selectivity (or inversion) requires that the reaction > components be chiral. > In your example, C-O >> C-S is not chiral even if the C can map onto a > chiral reactant. > > In contrast, F[C@H](O)Cl>>F[C@H](S)Cl is chiral, as is > F[C@H](O)Cl>>F[C@@H](O)Cl. > [C@]O>>C[@}S is not chiral due to insufficient neighbors being provided. > Having to specify the neighboring atoms is a pain and reduces the > transform's value for generic reuse.. > But (in my experience anyway) stereoselective transforms should be > depicted with explicit stereocenters, i.e. with neighboring atoms (or > atom lists) present. Stereoselectivity is another mess that I will at least try to address in a bit in my reply to James. In short though: I agree that if you want to indicate stereochemistry, you should have to provide the full environment of the atom in your reaction specification. -greg ------------------------------------------------------------------------------ Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
