Dear Richard,
On Fri, Aug 5, 2011 at 8:34 AM, Richard Cooper
<richard.coo...@chem.ox.ac.uk> wrote:
> Dear Greg,
>
>> One final note: I would not trust the current code to get this stuff
>> right. Here's an example:
>>
>>>>> rxn2 = AllChem.ReactionFromSmarts(
>>>>> '[C@H:1]([Cl:2])([Br:3])[I]>>[C@@H:1]([Cl:2])([Br:3])F')
>>>>> ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@H](Cl)(Br)I'),))
>>>>> Chem.MolToSmiles(ps[0][0],True)
>> 'F[C@H](Cl)Br'
>>
>> Now provide the same input molecule with a different atom ordering:
>>>>> ps =rxn2.RunReactants((Chem.MolFromSmiles('[C@@H](Br)(Cl)I'),))
>>>>> Chem.MolToSmiles(ps[0][0],True)
>> 'F[C@@H](Cl)Br'
>>
>> The first example is what you would expect, the second is not (it's a bug).
>
> Is this a bug in the reaction code (e.g. assumes the input atoms will
> be in canonicalized smiles order) or is
> it in the smiles code?
I'm 90% certain that it's in the reaction code.
>
>> I'd like to do this systematically, and include some documentation of
>> expected behavior.
>> Something like (note: things don't currently work this way):
>>
>> Reaction: [C@H:1]([Cl:2])([Br:3])[I]>>[C@H:1]([Cl:2])([Br:3])F
>> Behavior:
>> Stereochemistry exists: preserve
>> Missing stereochemistry: add
>> Reaction: [C@H:1]([Cl:2])([Br:3])[I]>>[C@@H:1]([Cl:2])([Br:3])F
>> Behavior:
>> Stereochemistry exists: invert
>> Missing stereochemistry: add
>> Reaction: [C@H:1]([Cl:2])([Br:3])[I]>>[C:1]([Cl:2])([Br:3])F
>> Behavior:
>> Stereochemistry exists: remove
>> Missing stereochemistry: nothing
>> Reaction: [CH:1]([Cl:2])([Br:3])[I]>>[C@H:1]([Cl:2])([Br:3])F
>> Behavior:
>> Stereochemistry exists: ???
>> Missing stereochemistry: add
>>
>> Things get more difficult in cases like this:
>> [C@H:1]([Cl:2])[I]>>[C@@H:1]([Cl:2])F
>> What would you expect to happen there?
>
> I've been worrying about that too - worst case only one bond from a
> tetrahedral carbon is in the product template how might one specify
> what to do with the chirality in a SMARTS expression?
Exactly the problem.
-greg
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