On 13/04/2012 13:02, Jochen Schreiber wrote:
> Hello everybody,
>
> i have a dataset where i know (form a clustering) which compounds are in
> which cluster.
>
> For example Cluster 55: With 16 Compounds.
>
> Now i want to start a similarity search on each compound in this cluster with
> babel. I will do this with tanimoto 0.7, 0.8 and 0.85 to look for which
> tanimoto i get the best results.
>
> The best result would be that i find with one compound all other 15 compound
> from this cluster.
>
> After i have done this i see that my results are very bad.
The command
obabel Cluster55.sdf -oftp
will show the Tanimotos from the first molecule in Cluster55.sdf to all
the others using FP2 fingerprints
So i want to change the fingerprint. In my first round i use the
standard FP2 fingerprint.
>
> The results for FP3, FP4 oder MACCS are the same. Why is this so? Need i to
> specify something in the txt-files?
>
> My cooperation partner in this projekt uses pipeline pilot with ECFP4. Is
> there a way to use this fingerprint with babel?
OpenBabel does not support this fingerprint.
A paper which compares the effectiveness of 37 different descriptors in
molecular similarity is Bender et al J. Chem. Inf. Model., 2009, 49 (1),
pp 108–119 DOI: 10.1021/ci800249s. But since it is published by ACS I am
not able to read the full text.
Chris
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