If we take following SMARTS.
c1ccncc1-aaaa-[r5]
First of all [r5] defines the property of a single atom. It doesn't define
5 member ring. If you define property for one atom, why not for other 4?
Another point,
It will attach 5 membered ring to the meta position of N in pyridine ring.
OR You should move N a position before. Like c1cnccc1-aaaa-[r5].
Following is my step-wise creation of SMARTS you need.
Daylight SMARTS examples show:
Ortho*-!:aa-!:*Ortho-substituted ring
Meta*-!:aaa-!:*Meta-substituted ring
Para*-!:aaaa-!:*Para-substituted ring
It means, we must modify this according to our need for para position.
We must change first 'a' to 'n' (aromatic N of Pyridine). Before and after
are single bonds which specify to extend our ring in way we like. For
example if you have pyridine:
* must be replaced by c1 and c before n. and other 'a' must be replaced by
c. Where it again joins and finish the ring, we must specify number of ring
closure, for example 1 here.
c1c-!:nccc1-!:*
After last single bond you can put a 5-member ring.
c1c-!:nccc1-!:a2aaaa2
And, I don't think -!: is required here. So,
c1cnccc1a2aaaa2
And this is SMARTS written in simplest manner, not smile. You can use
directly this.
On Wed, Mar 30, 2016 at 12:40 PM John M <john.wilkinson...@gmail.com> wrote:
> As David has pointed out from you description you don't need the 'aaaa'.
> Might be a typo but wanted to say
>
> [c1ccncc1]-!:aaaa-!:[r5]
>
>
> Is not valid SMILES, you've put the whole ring inside a single atom, it
> should be.
>
> c1ccncc1-!:aaaa-!:[r5]
>
>
> Also, '-!:' is the same as '-' since in SMARTS a single bond never matches
> an aromatic atom.
>
> c1ccncc1-aaaa-[r5]
>
>
> But from you description, David's SMARTS should be correct.
>
> - John
>
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 29 March 2016 at 14:39, Hitesh Patel <hiteshpatel...@gmail.com> wrote:
>
>> I have put any aromatic atom there. It depends on you. What you want.
>>
>> SymbolSymbol nameAtomic property requirementsDefault
>> * wildcard any atom (no default)
>> a aromatic aromatic (no default)
>> A aliphatic aliphatic (no default)
>>
>> On Tue, Mar 29, 2016 at 3:37 PM David Hall <li...@cowsandmilk.net> wrote:
>>
>>> I’m confused by why there is -!:aaaa
>>>
>>> Your description suggests this to me:
>>>
>>> [cH]1[cH]n[cH][cH]c1[r5]
>>>
>>> It at least looks nice on
>>> http://smartsview.zbh.uni-hamburg.de/smartsview/calculate?method=get
>>>
>>>
>>> On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH <
>>> david.gravest...@syngenta.com> wrote:
>>>
>>> Good day,
>>>
>>> I wonder if somebody could please help me with the construction of a
>>> SMARTS query.
>>>
>>> I am trying to search for compounds that have a five-membered ring
>>> attached to the para- position of an unsubstituted pyridine ring.
>>>
>>> I have tried the following SMARTS expression:
>>>
>>> [c1ccncc1]-!:aaaa-!:[r5]
>>> However when I ran this SMARTS pattern it doesn’t appear to be bringing
>>> back the expected structures.
>>> I was also not sure how to specify explicit hydrogen atoms on the
>>> pyridine ring in the SMARTS expression.
>>> I wonder if you could please help me with this query? What is the best
>>> way to construct the necessary SMARTS?
>>>
>>> Best regards,
>>> David
>>>
>>> ______________________________________________________________________________
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>>>
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>> --
>>
>> Regards,
>>
>> Dr. Hitesh Patel
>> Post-Doctoral Fellow,
>> Technische Universität Dortmund,
>> Chemische Biologie,
>> Otto-Hahn-Straße 6,
>> 44227, Dortmund,
>> Germany
>>
>> Room: C1-05-181
>> Work: 0231 755-4740
>> Mob.: +49 (0)176 5544 6467
>> Website: http://www.hiteshpatel379.com/
>> Email: hitesh.pa...@tu-dortmund.de
>>
>>
>> ------------------------------------------------------------------------------
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>> Intel Data Analytics Acceleration Library.
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>>
> --
Regards,
Dr. Hitesh Patel
Post-Doctoral Fellow,
Technische Universität Dortmund,
Chemische Biologie,
Otto-Hahn-Straße 6,
44227, Dortmund,
Germany
Room: C1-05-181
Work: 0231 755-4740
Mob.: +49 (0)176 5544 6467
Website: http://www.hiteshpatel379.com/
Email: hitesh.pa...@tu-dortmund.de
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