Re: [Cdk-devel] Possible bug in AnyAtom matcher

[Nina J. <jel...@gm...>]

On 25 February 2012 17:36, Rajarshi Guha <raj...@gm...> wrote:

>
>
> On Sat, Feb 25, 2012 at 4:46 AM, Nina Jeliazkova <
> jel...@gm...> wrote:
>
>
>> "Updated code to handle the * SMARTS pattern so that it ignores H's
>> unless they have an isotopic mass specification. This means * no
>> longer matches [H][H] but will match [1H][1H]. Added unit tests to
>> take care of this and also updated Javadocs for the query tool to note
>> this behavior. Note that even matching isotopic hydorgens is slightly
>> ambiguous since it implicitly assumes that one is dealing with an
>> explicit H (i.e., an IAtom object with symbol H). ideally, * should
>> not match any hydrogen at all, and this may become the behavior in
>> future version"
>>
>> This makes sense, if the expected behaviour of SMARTS star pattern is
>> to ignore hydrogens - is this the case?
>>
>
> If I remember correctly, this was based on a discussion with Andrew Dalke
> and the behavior of matching explicit H's in SMARTS. So, yes, I updated it
> so that * does ignore H's
>

Just for the record, other wild card matchers (e.g those matching "A" )
perhaps should be modified in the same way, as currently "A" would match
explicit hydrogens.

Best regards,
Nina


>
>
>> There is still an inconsistency in how massNumbers are set,
>> SmilesParser will leave null values, while reading the same structure
>> from  SD file will result in mass numbers correctly set.  It would be
>> good to have a consistent behaviour; I am not sure when the mass
>> numbers should be set - probably on atom type configuration?
>>
>
> This inconsistency should be resolved - I would assume that the
> SmilesParser should use the most common mass number (unless a particular
> isotopic form is specified) using the same code as the MDL reader code
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
>
>
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