Re: [Ambit-users] combining smarts into one smarts expression

Hello Yannick,

Nick might answer later this week, but generally, SMARTS are unable to
express variable length chains, unless one do all the enumeration (which
might be prohibitively large).

Best regards,
Nina

On 30 July 2015 at 00:39, Yannick .Djoumbou <y.d...@gm...> wrote:

> Hello,
>
> I would like to express the smarts for a class of compounds with an
> aliphatic carbon chain of 13 to 21 carbon atoms, where  the longest chain
> of carbon has between 13 and 21 carbons and is attached to a Nitrogen atom.
> Examples include:
>
>     - CCCCCCCCCCCCCNH2 ; CCCCCC(C)C\C=C\C(C)CCCNH2 ;
>  CCCCCCCCCCC\C=C\CCCCNH2
>
>  However, I do not want to include compounds containing a carbon chain of
> more than 21 carbon atoms. Which means that the following compounds should
> not be included:
>
>    -  CCCCCCCCCCCCCCCC\C=C\CCCCNH2; CC/C=C\CCCCCCCCCCCC\C=C\CCCCNH2
>
>
> I first generated the patterns for each of the two types:
>
> 13 carbons attached to N: (A)  =>
>  [#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-[#7]([H])[H]
>
> 22 carbons attached to N: (B)  =>
>  [#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-,=[#6]-[#7]([H])[H]
>
> I then tried to combined those into  1 smarts [$(A)!$(B)] to mean that the
> compound of interest should match A but not match B. This does not work!
>
> What would be the best way of describing this in one SMARTS string?
>
> Thank you
>
> Regards,
>
> MrYan
>