[Cdk-devel] AnyOrderQueryBond does not work

[Nina J. <ni...@ac...>]

Hi all,

I've just submited this bug on sourceforge, but i am reposting here since it
may be a general issue after  interfaces introduction (this was not a problem
in the 28/06/2005 release )

Essentially, when UniversalIsomorphismTester invokes AnyOrderQueryBond matches
method, the SMARTSBond matches method is called instead!

This is because 
<code>
AnyOrderQueryBond in package  org.openscience.cdk.isomorphism.matchers.smarts;

</code>
should have 	public boolean matches(Bond bond) 
declared as
<code>
public boolean matches(org.openscience.cdk.interfaces.Bond bond) 
</code>
Now it assumes bond is of type org.openscience.cdk.Bond (because of the import
statement) and therefore matches method DOES NOT replace the inherited matches
method of SMARTSBond (which returns false ).

Here the fix is simple, but there can be other hidden situation like this.

The effect is clear from the test below :

<code>
    public void testmatchInherited() {
    	try {
        SymbolQueryAtom c1 = new SymbolQueryAtom(new Atom("C"));
        SymbolAndChargeQueryAtom c2 = new SymbolAndChargeQueryAtom(new
Atom("C"));
    	org.openscience.cdk.interfaces.AtomContainer c =
MoleculeFactory.makeAlkane(2); 
        
    	QueryAtomContainer query1 = new QueryAtomContainer();
        query1.addAtom(c1);
        query1.addAtom(c2);
        query1.addBond(new OrderQueryBond(c1,c2,
CDKConstants.BONDORDER_SINGLE));
    	assertTrue(UniversalIsomorphismTester.isSubgraph(c,query1));
    	
    	QueryAtomContainer query = new QueryAtomContainer();
        query.addAtom(c1);
        query.addAtom(c2);
        query.addBond(new AnyOrderQueryBond(c1,c2,
CDKConstants.BONDORDER_SINGLE));
    	assertTrue(UniversalIsomorphismTester.isSubgraph(c,query));
    	
    	} catch (CDKException x) {
    		fail();
    	}
    	
    }
</code>


Regards,
Nina Jeliazkova


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