Re: [Joelib-devel] Atom mapping in substructure searching

[Christoph S. <c.s...@un...>]

Sorry for not answering this question comprehensively,
I just want to point out that we have convenience methods for getting=20
the atom-to-atom mapping in CDK MCSS, not just bond maps.

> (1) which of the tools can be easily configured to output one or more=20
> substructure mappings (including null) from A=3D>C, A=3D>D, A=3D>E. B=3D=
>C,=20
> B=3D>D, B=3D>E. And the reverse C=3D>A, C=3D>B, etc. . This only works =
when one=20
> species is a precise substructure of another.
> (2) Maximal common subgraph mapping A<=3D>C, A<=3D>D, etc.

I don't see why the
org.openscience.cdk.isomorphism.UniversalIsomorphismTester should not be=20
able to give you exactly what you ask for in (1) and (2), as atom-atom=20
mappings.

> (3) ditto, but for (A+B) <=3D> (C+D+E) without overlaps.

Don't quite get this one.
Suppose you put AtomContainer A and B into a new AtomContainer "educts",=20
which yields a disconnected graph and the same with putting C and D and=20
E into a new AtomContainer "products". You would then do a MCSS of both?!=
?

Cheers,

Chris

--=20
Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

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