On May 11, 2012, at 10:12 AM, Greg Landrum wrote:
> The handling of R groups in mol blocks and their translation into
> something sensible on SMILES output is something that needs to be
> fixed. It's a good bug to report.
Added.
>
>> - Two records contain atom maps:
>>
>> [*:0]C1C(=O)N2C1(OC)SCC([*:0])=C2C(=O)O CHEBI:55429
>> [*:0]C(=O)NC1C(=O)N2C1CCC([*:0])=C2C(O)=O CHEBI:55504
>>
>> How do I tell the SMILES reader to accept atom maps, or the SMILES writer to
>> filter those out?
>
> The SMILES reader does accept atom maps. Unfortunately it only accepts
> positive integer atom maps. It should be accepting non-negative atom
> maps. I'll fix this.
Indeed. I knew that it handled atom maps. When I work late, my sphere of
attention gets rather small. :)
> I see a number of possible solutions:
> 1) modify the SMILES parser to recognize "?" as a bond with
> unspecified order. I don't like introducing completely new syntax like
> this.
> 2) modify the SMILES writer to write "~" in these cases and the SMILES
> parser to recognize that. I like this better because "~" at least has
> meaning in SMARTS.
> 3) modify the SMILES writer to fail when it sees query features like this.
Agreed with #1.
Testing OpenBabel and OEChem, and looking at the CDK output from
the ChEBI site, all of them generate a single-bond for that case.
Neither OpenBabel nor OEChem will parse "C~C".
I do not have the experience with SD files to know which is the
right solution semantically. Observationally, using a single bond
there is the most portable, and therefore what I would likely do
in the same situation.
Andrew
[email protected]
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