subject:"\[Open Babel\] SMARTS query"

Re: [Open Babel] SMARTS query

2016-03-30 Thread Hitesh Patel

Hi David,

Do you expect something like this?:
c1(a22)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 <
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]-!:-!:[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/
>
>
> __
>
>
>
> [image: cid:image001.gif@01CC6979.5085FF60][image:
> cid:image002.png@01CC6979.5085FF60]
>
>
> --
>
> *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.*
>
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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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Re: [Open Babel] SMARTS query

2016-03-30 Thread Hitesh Patel

If we take following SMARTS.

c1ccncc1--[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--[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*-!:-!:*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-!:a22

And, I don't think -!: is required here. So,

c1cnccc1a22

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  wrote:

> As David has pointed out from you description you don't need the ''.
> Might be a typo but wanted to say
>
> [c1ccncc1]-!:-!:[r5]
>
>
> Is not valid SMILES, you've put the whole ring inside a single atom, it
> should be.
>
> c1ccncc1-!:-!:[r5]
>
>
> Also, '-!:' is the same as '-' since in SMARTS a single bond never matches
> an aromatic atom.
>
> c1ccncc1--[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  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  wrote:
>>
>>> I’m confused by why there is -!:
>>>
>>> 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]-!:-!:[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/
>>>
>>> __
>>>
>>>
>>> 
>>>
>>>
>>> --
>>>
>>> *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=/4140___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>>

Re: [Open Babel] SMARTS query

2016-03-30 Thread John M

As David has pointed out from you description you don't need the ''.
Might be a typo but wanted to say

[c1ccncc1]-!:-!:[r5]


Is not valid SMILES, you've put the whole ring inside a single atom, it
should be.

c1ccncc1-!:-!:[r5]


Also, '-!:' is the same as '-' since in SMARTS a single bond never matches
an aromatic atom.

c1ccncc1--[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  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  wrote:
>
>> I’m confused by why there is -!:
>>
>> 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]-!:-!:[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/
>>
>> __
>>
>>
>> 
>>
>>
>> --
>>
>> *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=/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=/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=/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

Re: [Open Babel] SMARTS query

2016-03-29 Thread Hitesh Patel

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  wrote:

> I’m confused by why there is -!:
>
> 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]-!:-!:[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/
>
> __
>
>
> 
>
>
> --
>
> *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=/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.
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> ___
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> 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.
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Re: [Open Babel] SMARTS query

2016-03-29 Thread David Hall

I’m confused by why there is -!:

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 
>  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]-!:-!:[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/ 
> 
> __
>  
> 
>  
> 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=/4140___
>  
> 
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net 
> 
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 
> 
--
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Re: [Open Babel] SMARTS query

Re: [Open Babel] SMARTS query

Re: [Open Babel] SMARTS query

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Re: [Open Babel] SMARTS query

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