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SMARTS question

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

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Chemical Indexing Unit, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom
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Re: SMARTS question

Chris Swain
Hi,

I notice that you have defined the five-membered ring SMARTS with aromatic atoms, I’ve sometimes found unexpected behaviour with the definition of aromatic systems with small heterocyclic rings, especially if tautomeric forms are possible.

Cheers,

Chris


Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
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Message: 2
Date: Tue, 29 Mar 2016 10:41:57 +0000
From: Gravestock David GBJH <[hidden email]>
Subject: [Open Babel] SMARTS question
To: "[hidden email]"
<[hidden email]>
Message-ID:
<[hidden email]>

Content-Type: text/plain; charset="us-ascii"

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]<[hidden email]>  | URL  http://www.syngenta.com<http://www.syngenta.com/>
BT MeetMe Participant Code: 15349511# | BT Global Access: http://www.btconferencing.com/syngenta/globalaccess/
______________________________________________________________________________

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Re: SMARTS question

Andrew Dalke
In reply to this post by Gravestock David GBJH
On Mar 29, 2016, at 12:41 PM, Gravestock David GBJH wrote:
> 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]

There is an excellent SMARTS visualization tool at http://smartsview.zbh.uni-hamburg.de/ which can help understand SMARTS queries. Unfortunately it would not help here because it doesn't like the "c1", saying:

  SMARTS syntax is not correct:
  Error: syntax error, unexpected INTEGER, expecting BRACKET_CLOSE at position 4 of input. [c1<-

The SMARTS is correct, but unusual. The SMARTS term '[c1ccncc1]' looks for an atom which is:
   an aromatic carbon, and
   has atomic mass of 1, an
   an aromatic carbon, and
   an aromatic carbon, and
   an aromatic nitrogen, and
   an aromatic carbon, and
   an aromatic carbon, and
   has atomic mass of 1, an

In other words, is both a carbon and a nitrogen, and has a mass of 1, and is aromatic.

If I take out the two "1"s from the term, then SMARTSView reports:

  SMARTS semantic is not correct:
  ERROR: Elements combined by AND! Removed

because it's not possible for an element to be both a carbon and a nitrogen.

I believe what you want is:

   c1cnccc1-[R]~1~[R]~[R]~[R]~[R]~1

Oddly, a PubChem substructure search for that SMARTS returns "InternalError@Get error message from search server" for that error. If I search for

  c1cnccc1-[R]1[R][R][R][R]1

then it finds such hits as:

  4-cyclopentylpyridine
  5,8-Methanoisoquinoline, 5,6,7,8-tetrahydro-, 2-oxide
  4-(5-bicyclo[2.2.1]hept-2-enyl)-3-butylpyridine

and many more. If you want the only substitution to be on the para position, then something like

  [cX3H1]1[cX3H1][nX2][cX3H1][cX3H1][cX3]1-[R]~1~[R]~[R]~[R]~[R]~1
(or the PubChem usable
  [cX3H1]1[cX3H1][nX2][cX3H1][cX3H1][cX3]1-[R]1[R][R][R][R]1
)

should work. The "X3H1", etc. require that the atoms not be connected to anything, or anything other than a single atom.

The visualization in SMARTView should help make it more understandable.


> I was also not sure how to specify explicit hydrogen atoms on the pyridine ring in the SMARTS expression.

Does the above help?

Cheers,


                                Andrew
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Re: SMARTS question

Gravestock David GBJH
In reply to this post by Gravestock David GBJH

Good day,

 

I wonder if somebody could help me with the construction of a SMARTS pattern?

 

How does one specify a non-hydrogen atom?  For example, when I use [CH3]C([!H])=O to specify the generalised molecule below where A = any non-hydrogen atom I don’t get back the correct results.

 

 

The [!H] seems to specify that the atom does not have one further H atom.

 

Regards,

David


Syngenta Limited, Registered in England No 2710846; Registered Office : Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom


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Re: SMARTS question

Noel O'Boyle
Administrator
Does [!#1] work?

On 12 September 2016 at 09:23, Gravestock David GBJH <[hidden email]> wrote:

Good day,

 

I wonder if somebody could help me with the construction of a SMARTS pattern?

 

How does one specify a non-hydrogen atom?  For example, when I use [CH3]C([!H])=O to specify the generalised molecule below where A = any non-hydrogen atom I don’t get back the correct results.

 

 

The [!H] seems to specify that the atom does not have one further H atom.

 

Regards,

David


Syngenta Limited, Registered in England No 2710846; Registered Office : Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom


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Re: SMARTS question

Noel O'Boyle
Administrator
Sorry - just reread your question. The correct solution is to specify the heavy atom valence of the carbonyl carbon rather than adding in an additional smarts atom. This avoids any potential problems with implicit versus explicit hydrogens, for example, as well as being more efficient to match. I forget the syntax but you I'm sure you can find it.

- Noel

On 12 September 2016 at 10:01, Noel O'Boyle <[hidden email]> wrote:
Does [!#1] work?

On 12 September 2016 at 09:23, Gravestock David GBJH <[hidden email]> wrote:

Good day,

 

I wonder if somebody could help me with the construction of a SMARTS pattern?

 

How does one specify a non-hydrogen atom?  For example, when I use [CH3]C([!H])=O to specify the generalised molecule below where A = any non-hydrogen atom I don’t get back the correct results.

 

 

The [!H] seems to specify that the atom does not have one further H atom.

 

Regards,

David


Syngenta Limited, Registered in England No 2710846; Registered Office : Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom


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Re: SMARTS question

Chris Swain
In reply to this post by Gravestock David GBJH
Hi,

I think Noel’s suggestion is correct.

I use SMARTSviewer to work out SMARTS queries.


Cheers
Chris


Message: 2
Date: Mon, 12 Sep 2016 10:01:10 +0100
From: "Noel O'Boyle" <[hidden email]>
Subject: Re: [Open Babel] SMARTS question
To: Gravestock David GBJH <[hidden email]>
Cc: "[hidden email]"
<[hidden email]>
Message-ID:
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Content-Type: text/plain; charset="utf-8"

Does [!#1] work?

On 12 September 2016 at 09:23, Gravestock David GBJH <
[hidden email]> wrote:

Good day,



I wonder if somebody could help me with the construction of a SMARTS
pattern?



How does one specify a non-hydrogen atom?  For example, when I use
[CH3]C([!H])=O to specify the generalised molecule below where A = any
non-hydrogen atom I don?t get back the correct results.





The [!H] seems to specify that the atom does not have one further H atom.



Regards,

David


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Re: SMARTS question

Gravestock David GBJH
In reply to this post by Gravestock David GBJH

I wonder if anybody could please help me construct a specific SMARTS pattern.

 

I want to describe the following general compound where Ch = chain of indeterminate length (i.e. non-ring linker) and Rn = ring linker (any size ring, aliphatic or aromatic).

 

 

I have developed the following SMARTS pattern but I don’t know how to adapt it to fully describe the general compound above.

 

[*R0](~[CX3]([NX3])=[OX1])C[*R1]~[CX3]-,=[OX1]

 

Any help you could give me would be much appreciated.

 

Many thanks

David


Syngenta Limited, Registered in England No 2710846; Registered Office : Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom


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Re: SMARTS question

Noel O'Boyle
Administrator
As described it cannot be done using SMARTS. Every query atom in a SMARTS pattern must correspond to a single real atom in a molecule. This is true even for [*] which matches exactly one atom (not like the regular expression *).

You'll have to do it in code, or else use a different query language that might support it (and something other than OB in that case).

- Noel

On 16 January 2017 at 09:10, Gravestock David GBJH <[hidden email]> wrote:

I wonder if anybody could please help me construct a specific SMARTS pattern.

 

I want to describe the following general compound where Ch = chain of indeterminate length (i.e. non-ring linker) and Rn = ring linker (any size ring, aliphatic or aromatic).

 

 

I have developed the following SMARTS pattern but I don’t know how to adapt it to fully describe the general compound above.

 

[*R0](~[CX3]([NX3])=[OX1])C[*R1]~[CX3]-,=[OX1]

 

Any help you could give me would be much appreciated.

 

Many thanks

David


Syngenta Limited, Registered in England No 2710846; Registered Office : Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom


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