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
>>
>> ______________________________________________________________________________
>> David Gravestock, Ph.D.
>>
>> Chemical Indexing Unit, Syngenta, Jealott's Hill International Research
>> Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom
>> Room 113, Building 170 | ( +44 (0)1344 414314 | *
>> david.gravest...@syngenta.com | URL http://www.syngenta.com
>> BT MeetMe Participant Code: 15349511# | BT Global Access:
>> http://www.btconferencing.com/syngenta/globalaccess/
>>
>> ______________________________________________________________________________
>>
>>
>> <image001.gif> <image002.png>
>>
>>
>> ------------------------------
>>
>> *Syngenta Limited, Registered in England No 2710846;Registered Office :
>> Syngenta Limited, European Regional Centre, Priestley Road, Surrey Research
>> Park, Guildford, Surrey, GU2 7YH, United Kingdom*
>> ------------------------------
>> *This message may contain confidential information. If you are not the
>> designated recipient, please notify the sender immediately, and delete the
>> original and any copies. Any use of the message by you is prohibited.*
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140_______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
> --
>
> 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
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
