I now adjusted the test and I get the same amount if hits when using
ExtendenFingerprinter and UIT or UIT only.
CDK ChemFinder
CCC(C)C(C)C(C)C 427 427
O(C)C(C)C(C)C(C)C 77 77
CCCCCC(C)CC 1521 1825
N(C)(C)CC(C)C 10487 11412
O(CC)C(N(C)C)C 64 109
CC(C)C(C)C(C(C)C)C(C)C 0 0
While the differences between cdk and chemfinder are not nice I do see that
it can be due to settings. (chemfinder was set to ignore stereo chemistry
in this case).
For the PubchemFingerprinter I first want to recreate the Fingerprints.
Will get back to you once I have the results.
Regards,
Joos
2011/12/19 Joos Kiener <[email protected]>
> Hi All,
>
> ok, I found the issue. In the used code I parse SMILES into IAtomContainer
> and then create an IQueryAtomContainer from it (which my search method
> accepts as parameter)
> Taking the IAtomContainer from smiles directly for usage in UIT and then
> results are as expected.
>
> Hence I assume the method*QueryAtomContainerCreator.createBasicQueryContainer(
> **atomContainer)* has a bug or I misunderstand the documentation:
>
> *Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's
> and OrderQueryBond's. If a IBond of the input container is flagged
> aromatic, then it disregards bond order information and only match against
> an aromatic target atom instead.*
>
> As far as I understand this, the method takes Aromaticity into account by
> requiring both atoms of the bond to be aromatic for a match? But obviously
> none of the atoms are aromatic in my query.
>
> I just created following "test":
>
> *import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.DefaultChemObjectBuilder;
> import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
> import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
> import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
> import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
> import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
>
> public class UitTest {
>
> public static void main(String[] args) throws Exception {
>
> String querySmiles = "CCC(C)C(C)C(C)C";
>
> String structureOneFromSdFile =
> "O=C2NC=1C=CC=CC=1C26(N(C)CC(C=3C=CC=CC=3(F))C46(C(=O)C=5C=CC=CC=5(OC4)))";
> // first molecule in the sd-file i previously sent
>
> SmilesParser smilesParser = new
> SmilesParser(DefaultChemObjectBuilder.getInstance());
> IMolecule queryMol = smilesParser.parseSmiles(querySmiles);
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(queryMol);
> CDKHueckelAromaticityDetector.detectAromaticity(queryMol);
>
> IQueryAtomContainer query =
> QueryAtomContainerCreator.createBasicQueryContainer(queryMol);
> //
> AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(query);
> **// uncommenting has no impact on result.*
> * // CDKHueckelAromaticityDetector.detectAromaticity(query); //
> uncommenting has no impact on result.
>
> IMolecule target =
> smilesParser.parseSmiles(structureOneFromSdFile);
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(target);
> CDKHueckelAromaticityDetector.detectAromaticity(target);
>
> **System.out.println(UniversalIsomorphismTester.isSubgraph(target,
> queryMol)); *// false
> * System.out.println(UniversalIsomorphismTester.isSubgraph(target,
> query)); // true
>
> }
>
> }*
>
> So UIT is working correctly.
>
> Best Regards,
>
> Joos
>
> Am 19.12.2011 17:30, schrieb Egon Willighagen:
>
> Joos,
>
> On Mon, Dec 19, 2011 at 5:16 PM, Nina Jeliazkova<[email protected]>
> <[email protected]> wrote:
>
> For example "CCC(C)C(C)C(C)C" does not (and should not) match aromatic
> carbons, as in http://tinyurl.com/7h7havf (no highlighted structures in the
> CDK depiction at the top right )
>
> The above SMILES/SMARTS should indeed not match aromatic systems. That
> leaves the question why the UIT does match them... Joos, what code are
> you using for that experiment?
>
> Egon
>
>
>
>
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