[Cdk-devel] Re: substructure searching in CDK

[Christoph S. <ste...@ic...>]

Dear Shyamal,

thanks for your kind email. And thanks for pointing me to these 
articles. I currently have a student working on the implementation of an 
algorithm which both does isomorphims and subgraph isomorphism checking. 
I hope that this part will be available soon. With respect to your 
wishes regarding the structure diagram layout, I can only say that the 
design of the StructureDiagramGenerator class is such that it should be 
able to handle a wide range of subgraph cleaning. Probably not all, but 
a lot of them. Some code would have to be written to handle specially 
marked sections of the molecule, do the layout and move and rotate the 
rest of the molecular fragments into the right position.

And yes, the combinatorial section would be great, too. I once wrote a 
nice little program in Visual Basic, which does this kind of job [1], 
but having a such an engine (with a little more sophistication than in 
MASP) in the CDK would certainly open a whole new field of application 
for it. However, currently none of our coworkers seems to be working on 
this. What we would need to do is implement something like a macro atom 
concept. This would be very deserving also for the field of structure 
generators.

Cheers,

Chris

1. Steinbeck C, Berlin K, Richert C: Masp - a Program Predicting Mass 
Spectra of Combinatorial Libraries. Journal of Chemical Information & 
Computer Sciences 1997, 37:449-457.



L. Shyamal wrote:
> Greetings Dr. Steinbeck,
> 
> I have been looking at your excellent work on the CDK, JChemPaint etc.
> I notice that whereas isomorphism is implemented substructure search is not
> (i may be mistaken though). I recently came across this algorithm, although
> in C, whose performance, i  am impressed with.
> http://amalfi.dis.unina.it/graph/db/vflib-2.0/doc/vflib-30.html
> 
> I have in fact used the same in chemical substructure matching.
> Unfortunately we dont have an open source policy at our company.
> 
> I hope this is of interest to you.
> 
> I have recently spent some time on Helson's Structure Diagram Generator
> paper and I hope some of his wishes can be added in that area. I am
> especially interested in partial cleanup of molecules and retention of
> stereochemistry during cleanup.
> 
> Also i hope you might be interested in writing some kind of combinatorial
> engine that mixes cores and substituents according to some kind of rules. I
> especially think it would be great to work on a standard language for
> defining cores, substitution rules etc, which could be read by a parser and
> acted upon accordingly with external filters that could act in screening for
> specific properties.
> 
> Hope to see more features,
> Best wishes
> 
> - Shyamal
> 
> L. Shyamal, Lead Analyst
> Jubilant Biosys (P) Ltd
> 4th Floor, S.J.M. Towers
> #18 Seshadri Road
> Gandhinagar
> Bangalore 560009
> INDIA
> phone 91-80-2207302 to 2207309 x 1046
> www.jubilantbiosys.com
> 
> 
> 



-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

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