Yes it does help -- I don't need the 'fuzziness' so I will stick to
morganbv.
How do you compare RDkit fp and morgan bv is there any particular scenario
where one outdoes the other?
Many Thanks
JP
On 8 March 2011 10:58, Stiefl, Nikolaus <nikolaus.sti...@novartis.com>wrote:
> Hi JeanPaul,
>
>
>
> The difference between featmorganbv and morganbv is that the first one uses
> pharmacophore features for atom descriptions whereas the other one atom
> types (it essentially corresponds to the ECFP descriptors). I would suggest
> to use featmorganbv_fp only if you want to do more fuzzy similarity
> searching (scaffold-hopping and the like).
>
>
>
> RDKit fingerprint is (as stated below) a daylight fingerprint like FP that
> is using hashed molecular subgraphs – it is ok depending on what you want to
> do with it – maybe you have a better in-house descriptor that is optimized
> for substructure searching though.
>
>
>
> Hope that helps
>
> Nik
>
>
>
>
>
> *From:* JP [mailto:jeanpaul.ebe...@inhibox.com]
> *Sent:* Tuesday, March 08, 2011 11:05 AM
> *To:* rdkit-discuss@lists.sourceforge.net
> *Subject:* [Rdkit-discuss] Best practice: which (database) fingerprints to
> use ?
>
>
>
>
>
> Hi there,
>
>
>
> I am storing a ton of molecules (~8M - it would be a ton if you print them
> all out, and hance use all of the trees in Regent's Park) in a database and
> using fingerprints for substructure and similarity searches. The
> fingerprints I am currently using are the ones I took blindly from the
> wikipages documentation (when in doubt, copy) - specifically torsionbv_fp,
> morganbv_fp and atompairbv_fp (from
> http://code.google.com/p/rdkit/wiki/DatabaseCreation2).
>
>
>
> Now I look at the database cartridge documentation -
> http://code.google.com/p/rdkit/wiki/ReferenceDocumentation and I see there
> are others - some of which I have actually heard about:
>
>
>
> *featmorganbv_fp(mol,int) *: returns a bfp which is the bit vector Morgan
> fingerprint for a molecule using chemical-feature invariants. The second
> argument provides the radius. This is an FCFP-like fingerprint.
> *rdkit_fp(mol) *: returns a bfp which is the RDKit fingerprint for a
> molecule. This is a daylight-fingerprint using hashed molecular subgraphs.
>
>
>
> What is the best practice here? Is it to use rdkit_fp ? (I assume this was
> added later - and possibly the original documentation is out of date)
>
> What is the difference between featmorganbv and the one I am using (i.e.
> morganbv_fp) ?
>
> What do you suggest in your experience?
>
> Any ideas will be highly appreciated - as right now I am quite without any
> myself.
>
>
>
> Many Thanks
>
> JP
>
------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
