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]> 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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