>
>>>>
>>>> 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]");
thanks
Mark
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