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

[Joerg K. W. <we...@in...>]

Hi all,

JOELib has an unpublished extended module for MCS, and the publication 
is still in the review process for the QSAR&Comb.Sci. We can also deal 
with physicochemical atom properties, which can make sense for 
reactions. The method returns all, full combinatorial and/or unique, 
MCS, so there are a lot of index lists for two molecules.

graph isomorphism(1) is a special case of maximum subgraph 
isomorphism(2) so this is no problem. I am not sure if I understand (3)

Are there plans for a publication? 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.

Kind regards, Joerg

> Crossposted to 3 lists. Please reply carefully.
> 
> We have a requirement to extract atom-atom mapping from a substructure 
> search (or a maximal common subgraph).  It's because our MACiE database 
> contains reactions without atom-atom maps. We have the complete products 
> and reactions for each step in CMLReact and want to either create a map 
> or relabel the atoms consistently. Since these are multistep reactions 
> the products of step N and usually the reactants of stepN+1 though some 
> components may be missing.
> 
> I've used obgrep (SMARTS) but only to give a boolean answer - which 
> molecules in a list have a given substructure. I used CDK a long time 
> ago for maximal common subgraph, but that was based on bonds, not atoms 
> and I haven't used it since. I haven't used JOELib.
> 
> If I have something like A + B => C + D + E
> (1) which of the tools can be easily configured to output one or more 
> substructure mappings (including null) from A=>C, A=>D, A=>E. B=>C, 
> B=>D, B=>E. And the reverse C=>A, C=>B, etc. . This only works when one 
> species is a precise substructure of another.
> (2) Maximal common subgraph mapping A<=>C, A<=>D, etc.
> (2) ditto, but for (A+B) <=> (C+D+E) without overlaps.
> 
> Performance is not an issue - this only (we hope) has to be done once as 
> then we shall use JChempaint as the entry tool. Even a webservice would 
> do. Nor (in principle) is semistructured output though we'd prefer XML 
> or a clear API. But we'd prefer not to have to write new code if possible.
> 
> Hope this makes sense. The only alternative is to reinput hundreds of 
> reactions by hand :-(
> 
> 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
> 
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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