Re: [Rdkit-discuss] SubstructureMatch

[Brian Kelley]

I believe the RDKit uses the vf2 algorithm:
L. P. Cordella, P. Foggia, C. Sansone, and M. Vento. 
An improved algorithm for matching large graphs. 
In: 3rd IAPR-TC15 Workshop on Graph-based Representations in Pattern 
Recognition, pp. 149-159, Cuen, 2001.


If you google search for vf2 substructure search you will find plenty of 
benchmarks


Brian Kelley

> On Jan 9, 2017, at 4:49 AM, Axel Rudling  wrote:
> 
> Hello,
> 
> I've been benchmarking different softwares for substructure searching of 
> molecules. From what I can tell, RDKits substructureMatch appears to do the 
> job. I have been looking around the documentation and this forum for a 
> description of how it actually works. As I understand it, it does the 
> calculation from a molecule object that is created from the smile?
> 
> How does substructureMatch work? Is it still fingerprint based? How accurate 
> is it? Is there a description of some standardised term for what is happening 
> there?
> 
> Best,
> Axel
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[Rdkit-discuss] SubstructureMatch

[Axel Rudling]

Hello,

I've been benchmarking different softwares for substructure searching of
molecules. From what I can tell, RDKits substructureMatch appears to do the
job. I have been looking around the documentation and this forum for a
description of how it actually works. As I understand it, it does the
calculation from a molecule object that is created from the smile?

How does substructureMatch work? Is it still fingerprint based? How
accurate is it? Is there a description of some standardised term for what
is happening there?

Best,
Axel
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