On Nov 12, 2009, at 4:40 AM, Mark Rijnbeek wrote:
>>>>>
>>>>> Not sure I can... those lines were actually added by Rajarshi:
>>>>>
>>>>> Updated code to handle the * SMARTS pattern so that it ignores
>>>>> H's
>>>>> unless they have an isotopic mass specification. This means * no
>>>>> longe...
>>>> Aah, indeed. I think this was based on some discussion on the
>>>> OpenBabel or BO lists regarding interpretation of SMARTS matching
>>>> for H's. I know that h<n> was deprecated in favor of H<n> and
>>>> this maybe related to that.
>>>> One general solution might be to have 2 modes, like daylight:
>>>> normal matching (ignore H's) and explicit H matching
>>>
>>> The problem seems to me that the hydrogen in for example [H]
>>> [C@@]1(CCC(C)=CC1=O)C(C)=C isn't "ignored". Method
>>> HydrogenAtom.match() returns false, and that makes the match
>>> false. Perhaps I don't get it, but I'd say to ignore would mean to
>>> return true.
>> Aah, indeed.
>
> What do you think the best patch would be? I'm a bit lost, because I
> don't know what was discussed on the OpenBabel lists.
>
> Would this change tackle it ?
>
> if ( atom.getMassNumber() == null ||
> (atom.getMassNumber() != null && atom.getMassNumber() > 1)) {
> return true;
> }
>
> The match is then true for all these test cases
>
> test("[C@@]1(CCC(C)=CC1=O)C(C)=C[H]");
> test("[H][C@@]1(CCC(C)=CC1=O)C(C)=C");
> test("[H][H]");
> test("[2H]");
> test("[H]");
I think this is correct. Does this patch change the number of failures
in SMARTSSearchTest? (There are currently 9 failures I think). If not,
then this is likely OK.
I wonder, wouldn't a simple patch just be: if atom symbol == 'H"
return true? I don't remember the reason for the multiple conditions
being checked for in HydrogenAtom.match() (which was written by Dazhi)
----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
Nothing spoils fun like finding out it builds character"
-Calvin
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