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

[Peter M. <Pet...@sp...>]

Dear Chris,

Thank you very much for your fast reply. From the CDK-news 3/3 I assumed
this was the case. Thanks for confirming.

Ciao,

Peter


-----Original Message-----
From: Christoph Steinbeck [mailto:er...@do...] 
Sent: Monday, July 30, 2007 4:42 PM
To: Peter Maas
Cc: cdk...@li...
Subject: Re: [Cdk-user] Kier Hall topological descriptors, performance

Peter,

I don't think you are overlooking something.
The code is very clean but the way the problem is implemented it
catastrophic :-) (This is nothing against the author. At least, he did it!)

The code performs a full substructure search for *every* possible path
(length 2 to 6) instead of recording pathes while performing a
breadth-first-search.

It would be easy to adapt the breadth-first-search output of my cdk
fingerprinter implementation for this purpose, but at the moment, I don't
have time for that.

Cheers,

Chris

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?
> 
> Thanks,
> 
> Peter
> 
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--
PD Dr. Christoph Steinbeck
Lecturer in Chemoinformatics
Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071-29-78978   Fax: (+49/0) 7071-29-5091

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