[Cdk-user] Susbtructure detection problem

[allouche m. <mir...@ho...>]

 Hi,
I am using the class UniversalIsomorphismTester to detect subtructures.=20
I have a problem with the method isSubgraph() which does not return what I =
expect for some fragments .
Here is an example :
fragment 1 represented by the SMILES : "CCCC"=20
fragment 2 represented by the SMILES : "c1ccc2c(c1)ccc3ccccc2"

SmilesParser sp =3D new SmilesParser(DefaultChemObjectBuilder.getInstance()=
);
IAtomContainer atomContainer;
atomContainer =3D sp.parseSmiles("c1ccc2c(c1)ccc3ccccc2");
 IAtomContainer SMILESquery =3D sp.parseSmiles("CCCC"); =20
QueryAtomContainer query =3D QueryAtomContainerCreator.createBasicQueryCont=
ainer(SMILESquery);
=20
the call to:
UniversalIsomorphismTester.isSubgraph(atomContainer, query)) returns true
The problem is that CCCC cannot be a substructure of c1ccc2c(c1)ccc3ccccc2 =
which carbons are all included in aromatic rings.
I would have expected the method to return true if the fragment 1 was repre=
sented with lower cases : cccc which would mean that it contains double bon=
ds.

Is it normal? If I use the MoleculeViewer2D to draw the fragment CCCC, it s=
eems correctly represented without double bond, so it it not a problem of t=
he SmilesParser.
Do you have an idea of how to solve my problem?

Miriame ALLOUCHE
=20
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