On Sun, Jul 11, 2010 at 7:04 AM, Rajarshi Guha <rajarshi.guha at gmail.com>wrote:

>
> On Jul 10, 2010, at 11:33 PM, chung wrote:
>
>  Is smiles case sensitive?
>>
>
>
> Absolutely!
>
> See http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
>
>
Yes, they are  (though the interpretation of the lower case may slightly
differ between implementations as have been discussed many times :)


The reason of c1cccccc1 (7membered ring in your first example) being
displayed as C1CCCCCC1 is the aromaticity is somehow lost when parsing the
aromatic SMILES.

Tests below will be better suited for the CDK list.  Perhaps I am missing
something and there is a quick workaround?

    //fails
    @Test
    public void testAromaticityRing7() throws Exception {
        SmilesParser parser = new
SmilesParser(NoNotificationChemObjectBuilder.getInstance());
        IMolecule mol = parser.parseSmiles("c1cccccc1");
        for (IAtom atom : mol.atoms())
            Assert.assertTrue(atom.getFlag(CDKConstants.ISAROMATIC));
    }
    //fails
    @Test
    public void testAromaticityRing7a() throws Exception {
        SmilesParser parser = new
SmilesParser(NoNotificationChemObjectBuilder.getInstance());
        IMolecule mol = parser.parseSmiles("c1cccccc1");
        //AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
        for (IAtom atom : mol.atoms())
            Assert.assertTrue(atom.getFlag(CDKConstants.HYBRIDIZATION_SP2));
    }
    //succeeds
    @Test
    public void testAromaticityRing6() throws Exception {
        SmilesParser parser = new
SmilesParser(NoNotificationChemObjectBuilder.getInstance());
        IMolecule mol = parser.parseSmiles("c1ccccc1");
        for (IAtom atom : mol.atoms())
            Assert.assertTrue(atom.getFlag(CDKConstants.ISAROMATIC));
    }

Best regards,
Nina


>
> ----------------------------------------------------
> Rajarshi Guha        | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> I put up my thumb... and it blotted out the planet Earth.
>        -- Neil Armstrong
>
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