Hi Lochana,
The problem is with your SMARTS query. The dollar sign means recursive
matching and the X means the number of atoms.
So you are asking for any atom that is connected to an aliphatic nitrogen
with 4 other atoms attached to the nitrogen or an atom that is connected
to an aliphatic nitrogen with 4 other atoms attached to the nitrogen. I
cannot think of any compounds that have an aromatic nitrogen connected to
4 atoms. What you probably want to check for is valence (which is a v
instead of an X). Also, there is no reason to use a recursive query here,
nor is there a reason to have two separate queries for the aromatic and
aliphatic (the atomic number can be used instead which matches both).
This is the query I would use: [#7v4]
The CDK implementation of SMARTS is pretty good. I don't believe
chirality or regiochemistry has been included yet, but otherwise
http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html has
a very good tutorial.
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Date:
10/15/2011 07:05 AM
Subject:
Cdk-user Digest, Vol 65, Issue 8
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Today's Topics:
1. SMARTS Matching (lochana menikarachchi)
2. Re: SMARTS Matching (Rajarshi Guha)
----------------------------------------------------------------------
Message: 1
Date: Fri, 14 Oct 2011 08:10:50 -0700 (PDT)
From: lochana menikarachchi <[email protected]>
Subject: [Cdk-user] SMARTS Matching
To: "[email protected]" <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Hi All,
?
I was trying to use SMARTSQueryTool to match all aliphatic and aromatic N
with 4 connections.
?[$([NX4+]),$([nX4+])]
?The molecules were read from PubChem SDF files. The query gives me only
aliphatic, it also gives me things with 3 bonds say N connected to a =O
and 2 others ?
Thanks.
______________________________________
Lochana C. Menikarachchi
Post Doctoral Research Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
69, North Eagleville Rd, Unit 3092
University of Connecticut
Storrs, CT 06269-3092
Lab: 860-486-1591
Home: 860-450-1335
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Message: 2
Date: Fri, 14 Oct 2011 11:20:13 -0400
From: Rajarshi Guha <[email protected]>
Subject: Re: [Cdk-user] SMARTS Matching
To: lochana menikarachchi <[email protected]>
Cc: "[email protected]" <[email protected]>
Message-ID:
<CAC8sKVf9rqgGOTJ8O=kp242mrqnmgzbs8d0ctswmmdch5xn...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
please send examples of molecules that don't match the patterns
On Fri, Oct 14, 2011 at 11:10 AM, lochana menikarachchi
<[email protected]> wrote:
> Hi All,
>
> I was trying to use SMARTSQueryTool to match all aliphatic and aromatic
N
> with 4 connections.
>
> ?[$([NX4+]),$([nX4+])]
>
> ?The molecules were read from PubChem SDF files. The query gives me only
> aliphatic, it also gives me things with 3 bonds say N connected to a =O
and
> 2 others ?
>
> Thanks.
>
>
> ______________________________________
> Lochana C. Menikarachchi
> Post Doctoral Research Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> 69, North Eagleville Rd, Unit 3092
> University of Connecticut
> Storrs, CT 06269-3092
> Lab: 860-486-1591
> Home: 860-450-1335
>
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> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> Cdk-user mailing list
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> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
--
Rajarshi Guha
NIH Chemical Genomics Center
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