Re: [Cdk-devel] SMARTSQueryTool question

[Mark R. <ma...@eb...>]

Indeed c1ccncn1 works, thanks.

I still find this a bit confusing though. If I do use C1=CN=CN=C1, and I 
make an IAtomContainer atc = sp.parseSmiles(smiles), and I make a basic 
printout of atc, I see:

Sym Hashcode
------------
C  5230193
C  33208902
N  29839159
C  2208288
N  3502256
C  7958910
arom DOUBLE  33208902 5230193
arom SINGLE  29839159 33208902
arom DOUBLE  2208288 29839159
arom SINGLE  3502256 2208288
arom DOUBLE  7958910 3502256
arom SINGLE  7958910 5230193

So the SMILES parser detects aromaticity.

If I create: QueryAtomContainer query = SMARTSParser.parse(smiles),
and then this query prints I get:

Sym Hashcode
------------
C  2478770
C  19653053
N  32603767
C  27653945
N  17431955
C  15138573
non arom DOUBLE  2478770 19653053
arom     null    19653053 32603767
non arom DOUBLE  32603767 27653945
arom     null    27653945 17431955
non arom null    2478770 15138573
non arom DOUBLE  17431955 15138573

So is there no match because the SMARTS parser will create an atom 
container with only some bonds being aromatic? How would I fix that?

Mark



> not having actually looked at the code yet, my guess that the problem  
> has to do with aromaticity. Does the first one work if you use c1ccncn1?
> 
> On Oct 27, 2009, at 7:06 AM, Mark Rijnbeek wrote:
> 
>> I've got a question regarding the SMARTS query tool. See class below.
>> I have no experience with this class, and was starting to look into it
>> to be wrapped into my Oracle cartridge.
>>
>> Question is, for some SMILES (the first three listed) it seems that  
>> the
>> SMARTS query tool does not give a match when querying the atom  
>> container
>> to itself. For the last three examples it does. Is this explainable  
>> or a
>> bug ?
>>
>> thanks,
>> Mark
>>
>>
>> ------------
>>
>>
>> package org.openscience.cdk;
>>
>> import org.openscience.cdk.interfaces.IAtomContainer;
>> import org.openscience.cdk.smiles.SmilesParser;
>> import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
>>
>> public class SMARTSTest {
>>
>> public static void main(String[] args) throws Exception {
>>
>>     SmilesParser sp =
>>     new SmilesParser(DefaultChemObjectBuilder.getInstance());
>>
>>     String smiles =
>>        // No match?
>>          "C1=CN=CN=C1";
>>        //"CN1CCN 
>> (CC1)C1=C(F)C=C2C(=O)C(=CN(C3=CC=C(F)C=C3)C2=C1)C(O)=O";
>>        //"O5CCN(CC=3C=1C=CC=CC=1C(=C2C=CC=CC2=3)CN4CCOCC4)CC5";
>>
>>        // Okay:
>>        //"CC(=O)OC(=O)C";
>>        //"C1CCC12CCCC2";
>>        //"c1ccccc1";
>>
>>     IAtomContainer at = sp.parseSmiles(smiles);
>>     SMARTSQueryTool querytool = new SMARTSQueryTool(smiles);
>>
>>     if (querytool.matches(at))
>>         System.out.println("match");
>>     else
>>         System.out.println("no match");
>>
>> }
>> }
>>
>>
>>
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> 
> ----------------------------------------------------
> Rajarshi Guha        | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> A meeting is an event at which the minutes are
> kept and the hours are lost.
> 
> 
> 
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