[Cdk-devel] Atom mapping in substructure searching

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

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