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SMARTS query

Gravestock David GBJH

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  | *  [hidden email]  | URL  http://www.syngenta.com

BT MeetMe Participant Code: 15349511# | BT Global Access: http://www.btconferencing.com/syngenta/globalaccess/

______________________________________________________________________________

 

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Re: SMARTS query

David Hall
I’m confused by why there is -!:aaaa

Your description suggests this to me:

[cH]1[cH]n[cH][cH]c1[r5]



On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH <[hidden email]> 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  | *  [hidden email]  | 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


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Re: SMARTS query

Hitesh Patel
I have put any aromatic atom there. It depends on you. What you want. 

SymbolSymbol nameAtomic property requirementsDefault
*wildcardany atom(no default)
aaromaticaromatic(no default)
Aaliphaticaliphatic(no default)

On Tue, Mar 29, 2016 at 3:37 PM David Hall <[hidden email]> wrote:
I’m confused by why there is -!:aaaa

Your description suggests this to me:

[cH]1[cH]n[cH][cH]c1[r5]



On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH <[hidden email]> 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  | *  [hidden email]  | 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


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Dr. Hitesh Patel
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Technische Universität Dortmund,
Chemische Biologie,
Otto-Hahn-Straße 6,
44227, Dortmund,
Germany


Room: C1-05-181
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Re: SMARTS query

Hitesh Patel
In reply to this post by Gravestock David GBJH
Hi David,

Do you expect something like this?:
c1(a2aaaa2)ccncc1
You may check the result of SMARTS pattern in SMARTSviewer (http://smartsview.zbh.uni-hamburg.de/).
I hope it helps.


On Tue, Mar 29, 2016 at 3:08 PM Gravestock David GBJH <[hidden email]> 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  | *  [hidden email]  | URL  http://www.syngenta.com

BT MeetMe Participant Code: 15349511# | BT Global Access: http://www.btconferencing.com/syngenta/globalaccess/

______________________________________________________________________________

 

       

 


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


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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: [hidden email]

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Re: SMARTS query

John May
In reply to this post by Hitesh Patel
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
[hidden email]

On 29 March 2016 at 14:39, Hitesh Patel <[hidden email]> wrote:
I have put any aromatic atom there. It depends on you. What you want. 

SymbolSymbol nameAtomic property requirementsDefault
*wildcardany atom(no default)
aaromaticaromatic(no default)
Aaliphaticaliphatic(no default)

On Tue, Mar 29, 2016 at 3:37 PM David Hall <[hidden email]> wrote:
I’m confused by why there is -!:aaaa

Your description suggests this to me:

[cH]1[cH]n[cH][cH]c1[r5]



On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH <[hidden email]> 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  | (  <a href="tel:%2B44%20%280%291344%20414314" value="+441344414314" target="_blank">+44 (0)1344 414314  | *  [hidden email]  | 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


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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.: <a href="tel:%2B49%20%280%29176%205544%206467" value="+4917655446467" target="_blank">+49 (0)176 5544 6467

Website: http://www.hiteshpatel379.com/
Email: [hidden email]

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Re: SMARTS query

Hitesh Patel

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 <[hidden email]> 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
[hidden email]

On 29 March 2016 at 14:39, Hitesh Patel <[hidden email]> wrote:
I have put any aromatic atom there. It depends on you. What you want. 

SymbolSymbol nameAtomic property requirementsDefault
*wildcardany atom(no default)
aaromaticaromatic(no default)
Aaliphaticaliphatic(no default)

On Tue, Mar 29, 2016 at 3:37 PM David Hall <[hidden email]> wrote:
I’m confused by why there is -!:aaaa

Your description suggests this to me:

[cH]1[cH]n[cH][cH]c1[r5]



On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH <[hidden email]> 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  | (  <a href="tel:%2B44%20%280%291344%20414314" value="+441344414314" target="_blank">+44 (0)1344 414314  | *  [hidden email]  | 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


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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.: <a href="tel:%2B49%20%280%29176%205544%206467" value="+4917655446467" target="_blank">+49 (0)176 5544 6467

Website: http://www.hiteshpatel379.com/
Email: [hidden email]

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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: [hidden email]

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