[Cdk-user] Possible solution to graph matching problem?

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I think I may have found the cause of the graph matching problem I
mentioned recently. 
The getOverlaps() method of UniversalIsomorphismTester works as follows:
a)It does a search for all possible mappings
b)It projects the solutions on the first molecule
c)It reduces the solutions by checking for possible subgraphs or
isomorphic graphs.

The problem is I think in part (c). The series of calls to methods is
as follows:

getOverlaps() -> getMaximum() -> isIsomorph() -> getIsomorphMap()
->search()

I think the problem is the way the search method is called:
List rMapsList = search(g1, g2, getBitSet(g1),
        getBitSet(g1), false, false);
(line 140 in UniversalIsomorphismTester.java)

Shouldn't that be:
List rMapsList = search(g1, g2, getBitSet(g1),
        getBitSet(g2), false, false);

so that all bonds in BOTH graphs must be matched? Isn't this the
definition of isomorphic graphs?

Hope this is of some help towards solving the problem for the next
release.

I.

On Tue, 25 Jan 2005 cdk...@li... wrote:

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>    1. Graph matching problem (Irilenia Nobeli)
> 
> --__--__--
> 
> Message: 1
> Date: Tue, 25 Jan 2005 18:05:40 +0000 (GMT)
> From: Irilenia Nobeli <no...@eb...>
> To: cdk...@li...
> Subject: [Cdk-user] Graph matching problem
> 
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> --380388872-788217705-1106676340=:25814
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> 
> Hi,
> 
> I have noticed that there are cases where the graph matching algorithm
> seems to return different results for a pair of molecules depending on the
> order these molecules are passed onto the method getOverlaps of the class
> UniversalIsomorphismTester. I don't mean that the mappings are different
> (which they should be as they are projections always on the first
> molecule) but that the maximum common structure returned has a different
> size. I may be wrong, but this looks like a bug.
> 
> For example, take the two molecules attached as MDL files. If you run
> UniversalIsomorphismTester.getOverlaps(mol1, mol2) on these two, in
> one case
> you get a clique of 2 atoms, in the other a clique of 11 atoms. These two
> molecules both have hydrogens in the original file. If the hydrogens are
> removed, you get mappings with the same number of atoms, regardless of
> which molecule is first and which is second, i.e. the problem is not there
> anymore (actually there could be other examples where even after removal
> of hydrogens the problem remains - I just haven't come across them yet).
> 
> Well, if anyone has any ideas why this happens, I could do with some help.
> 
> Thanks,
> 
> Irilenia
> 
> ++++++++++++++++++++++++++++++++++++++++
> Irilenia (Irene) Nobeli
> EMBL - European Bioinformatics Institute
> Wellcome Genome Campus
> Hinxton
> Cambridge CB10 1SD
> tel: +44 (0) 1223 492550
> fax: +44 (0) 1223 494468
> e-mail: no...@eb...
> 
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++++++++++++++++++++++++++++++++++++++++
Irilenia (Irene) Nobeli
EMBL - European Bioinformatics Institute
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
tel: +44 (0) 1223 492550
fax: +44 (0) 1223 494468
e-mail: no...@eb...