#1064 Aromaticity not detected ?

jchempaint-primary
closed
nobody
5
2012-10-08
2010-05-14
No

Testing with Orchem, we noticed that a certain valid substructure was not found for a target compound.
The problem looks to be in the aromaticity. The query compound is N1C=NC2=CC=CC=C12, the 5-ring with nitrogen in it marked as aromatic using the aromaticity detector. I include a sample program below that shows this (it\'s runnable, standalone)

The second SMILES is OC(=O)N1C=NC2=CC=CC=C12, a simplified version of the target.
It\'s basically the query with an extra OC=O attached. The 5-ring with the nitrogens now no longer is seen as aromatic. I cross checked with Marvin, which seems to think it should be still aromatic.


import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

public class TestAromaticity {

public static void main(String[] args) throws Exception{

    test(\"N1C=NC2=CC=CC=C12\");
    test(\"OC(=O)N1C=NC2=CC=CC=C12\");
}

private static void test (String smiles) throws Exception{
    SmilesParser sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
    IMolecule mol = sp.parseSmiles(smiles);

    System.out.println(\"SMILES=\"+smiles);

    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    CDKHueckelAromaticityDetector.detectAromaticity(mol);

    for (IBond bond : mol.bonds()) {
        if ( bond.getFlag(CDKConstants.ISAROMATIC)  
            && (bond.getAtom(0).getSymbol().equals(\"N\") || bond.getAtom(1).getSymbol().equals(\"N\"))
        ) 
        {
            System.out.println(bond.getAtom(0).getSymbol()+\"\"+bond.getAtom(1).getSymbol());
        }
    }
    System.out.println(\"-------\");
}

}

Discussion

  • Mark Rijnbeek

    Mark Rijnbeek - 2010-05-14
     
  • Rajarshi Guha

    Rajarshi Guha - 2010-10-19

    Problem seems to have been cleared up in 1.4.x

    Added unit test to check for this

     

Log in to post a comment.

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

JavaScript is required for this form.





No, thanks