: John May [john...@ebi.ac.uk]
Sent: Friday, February 07, 2014 6:48 PM
To: Nick Vandewiele
Cc: cdk-user@lists.sourceforge.net
Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
conversion and SSSRing finder
Okay now I’ve actually tracked it down - the issue is to do
the 1.5.4 or master branch?
Regards,
Nick
From: John May [mailto:john...@ebi.ac.uk]
Sent: Friday, February 07, 2014 5:28 PM
To: Nick Vandewiele
Cc: cdk-user@lists.sourceforge.net
Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
conversion and SSSRing finder
Confirm - I’ll look into it tonight.
For now if you don’t need the SMARTS stereochemistry you can actually use the
Pattern directly with the query container. This gives the correct answer:
Pattern pattern = Pattern.findSubstructure(SMARTSParser.parse(smarts, blr));
for (IAtomContainer
@lists.sourceforge.net
Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
conversion and SSSRing finder
Okay it's the bond matching... C-1-C-C-C-C1 works but C1-C-C-C-C1 doesn't.
Should be an easy fix.
J
On 7 Feb 2014, at 16:03, Nick Vandewiele
nick.vandewi
(Rajarshi Guha)
--
Message: 1
Date: Fri, 14 Oct 2011 08:10:50 -0700 (PDT)
From: lochana menikarachchi locha...@yahoo.com
Subject: [Cdk-user] SMARTS Matching
To: cdk-user@lists.sourceforge.net cdk-user@lists.sourceforge.net
Message-ID
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 ?
Using CDK 1.2.2 SMARTSQueryTool and SmilesParser.
the SMARTS query:[F,Cl,Br,I]C-C=C doesn't hit the left two
smiles, but does hit the right two smiles. I have also found that the
query hits the sd file related to the right two smiles using
SDV2000Reader, aromaticity detection, and
7 matches
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