On Nov 11, 2009, at 10:30 AM, Egon Willighagen wrote:
> On Wed, Nov 11, 2009 at 4:07 PM, Mark Rijnbeek <ma...@ebi.ac.uk>
> wrote:
>> There is something related in AnyAtom.java..
>>
>> public boolean matches(IAtom atom) {
>> if (atom.getSymbol().equals("H")) {
>> Integer massNumber = atom.getMassNumber();
>> return massNumber != null;
>> }
>> return true;
>> }
>>
>> So it looks to me that not matching [H] to itself is intentional,
>> considering what I see in AnyAtom. Perhaps Egon can comment?
>
> 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
----------------------------------------------------
Rajarshi Guha | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
----------------------------------------------------
In matrimony, to hesitate is sometimes to be saved.
-- Butler
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