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Possible incorrect SMARTS matching
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Derek

Joined: 10 Mar 2009
Posts: 23

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Link to postPosted: Thu Jul 30, 2009 10:09 amPost subject: Possible incorrect SMARTS matching Reply with quote

JChem Version: 5.1.3_2

Environment: WinXP

Problem:  I have a SMILES which I would expect to not match a particluar SMARTS but instead I am getting a hit.  I would expect the non-aromatic C in the SMARTS to prevent the match.  Is there something I have missed?

Eg:

 


            Molecule target = MolImporter.importMol("c1c(O)ccc1=O","smiles");
           
            Molecule smartsFilter;
            smartsFilter = MolImporter.importMol("[OH]-a~a~C=[OX1]", "smarts");
            MolSearch ms = new MolSearch();
            ms.setTarget(target);
            ms.setQuery(smartsFilter);

            hits = ms.findAll();

 

Robert
ChemAxon personnel
Joined: 23 Nov 2007
Posts: 221

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Link to postPosted: Thu Jul 30, 2009 3:43 pmPost subject: Reply with quote

Hi,

There is a bug regarding the SMARTS import of such inputs. The atom with the double bond connecting to an oxigen is not ensured to be aliphatic.

If the structure is opened by marvin sketch then it's apparent that this atom doesn't have aliphatic query property. Until the bug is fixed as a work-around you can import the query from mrv format and there you can specify the problematic carbon atom to be aliphatic.

My colleague responsible for smarts import will handle this bug.

Thanks for reporting it,

Regards,

Robert

Derek

Joined: 10 Mar 2009
Posts: 23

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Link to postPosted: Fri Jul 31, 2009 7:14 pmPost subject: Reply with quote

Thanks for looking into this.

 

Best wishes

 

Derek

Volfi
ChemAxon personnel
Joined: 07 Jun 2004
Posts: 996

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Link to postPosted: Tue Aug 11, 2009 12:51 pmPost subject: Reply with quote

Hi,

I have corrected the bug.

Thank you for the report.

Marvin 5.2.5 will contain the fix.

Andras

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