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

[Yannick .D. <y.d...@gm...>]

Thank you Nina,

I still hope I will get an answer form Nick.

Regards,

Yannick

On Mon, Aug 3, 2015 at 7:20 AM, Nina Jeliazkova <jel...@gm...>
wrote:

> 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
>>
>
>