Re: [Cdk-user] Kier Hall topological descriptors, performance

[Rajarshi G. <rg...@in...>]

On Jul 30, 2007, at 8:50 AM, Peter Maas wrote:

> Hi All,
>
> I wanted to use the Kier Hall topological descriptors for a large  
> sdfile but
> it's seems to be very slow. I tested the calculator on a sd-file  
> containing
> 10 (not to complex) structures and it takes over a minute on the  
> following
> platform:
>
> Windows 2000
> Java 1.6.0_02-b06
> Pentium 4 CPU 2.40 GHz
> 1GB RAM
>
> ChiChainDescriptor:	 5 sec.
> ChiPathClusterDescriptor 25 sec.
> ChiClusterDescriptor	 4 sec.
> ChiPathDescriptor:	 46 sec.
>
>
> Can anybody confirm the low performance?
> Is it due to the set-up of the program (query all possible  
> fragments per
> ordered) or am I overlooking something here?

This may be an issue - especially if the molecule is large as it is  
basically doing repeated graph isomorphisms.

I can take a look in more detail next week after I get back to the  
office. Would it be possible to get some example structures?

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Rajarshi Guha  <rg...@in...>
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