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

[Peter Murray-R. <pm...@ca...>]

At 15:09 30/03/2005, Christoph Steinbeck wrote:
>Sorry for not answering this question comprehensively,
>I just want to point out that we have convenience methods for getting the=
=20
>atom-to-atom mapping in CDK MCSS, not just bond maps.

Thanks - that's great. Wasn't aware that those were now in.

Are there any examples of code so we can get off the ground quickly?

>>(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=
, B=3D>D,=20
>>B=3D>E. And the reverse C=3D>A, C=3D>B, etc. . This only works when one=
 species=20
>>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.

Excellent

>>(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 E=
=20
>into a new AtomContainer "products". You would then do a MCSS of both?!?

Maybe this is rubbish, but consider the reaction:
CCC(=3DO)OCC+ O -> CCC(=3DO)O + CCO
If you do a MCS of O vs CCC(=3DO)OC you will get 2 hits. Only one is=
 "useful"=20
and you don't know which. However if you require that all MCS are=20
simultaneously matched then the O will match what is left after the larger=
=20
fragments have been matched.

In many (not all) reactions we have all the atoms in the reaction so it=20
makes sens to map them all at once - it's a strong constraint.

P.


>Cheers,
>
>Chris
>
>--
>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
>
>What is man but that lofty spirit - that sense of enterprise.
>... Kirk, "I, Mudd," stardate 4513.3..

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076