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

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

At 14:10 30/03/2005, Joerg K. Wegner wrote:
>Hi all,
>
>JOELib has an unpublished extended module for MCS, and the publication is 
>still in the review process for the QSAR&Comb.Sci.

Understood. Of course if we were in any other discipline than chemistry you 
could have posted the preprint...

>We can also deal with physicochemical atom properties, which can make 
>sense for reactions.

Do you mean more than formal charges and isotopes? Ore atom subtyping? Most 
other properties will be doubles so cannot match exactly and there is some 
judgment.

>The method returns all, full combinatorial and/or unique, MCS, so there 
>are a lot of index lists for two molecules.

Looks very useful.


>graph isomorphism(1) is a special case of maximum subgraph isomorphism(2) 
>so this is no problem.

I listed them separately because other implementations might not have MCS

>  I am not sure if I understand (3)

this requires the disjoint graphs in the reactants to be mapped to the 
disjoint graphs in the products. For example a water molecule will probably 
map to all products. However if many of the O atoms have already been 
mapped, then it has less possibilities. IOW it is a mapping of graphLists 
(forests), not just graphs.


>Are there plans for a publication?

Yes, but we cannot promise timescales or the type of publication(s).

>This module is a real developer version and looks also like a developer 
>version and I am ambigious to share it, until it was not published.
>You know GPL, means sharing all or nothing.

Indeed. And probably technically you have to send us the full source and so on.

That is an advantage of WS - you can share the functionality without 
releasing the code.

P.



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