Re: [Cdk-user] SMARTS question

[Mark R. <ma...@eb...>]

>>
>> 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.

Mark