Hi,
Many applications have multiple definitions of HBA/D from simple heteroatom
counts to sophisticated SMARTS definitions, as long as they are documented and
referenced I’d vote for keeping all definitions. It certainly helps if you want
to go back and try to repeat published work.
Cheers,
Chris
Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
Macs in Chemistry
sw...@mac.com
http://www.macinchem.org
>
> Message: 2
> Date: Tue, 20 Jun 2017 23:52:48 +0800
> From: "Hongbin Yang" <yanyangh...@163.com>
> To: rdkit-discuss <rdkit-discuss@lists.sourceforge.net>
> Subject: [Rdkit-discuss] Definition of HBA differs from pipeline pilot
> Message-ID: <2017062023524801328...@163.com>
> Content-Type: text/plain; charset="gb2312"
>
>
>
>
>
>
>
> Hi, Rdkiters,
> ? ?The definition of HBA in rdkit is (by Lipinski) :
> 32 HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),'
> +
> 33
> '$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' +
> 34 '$([nH0,o,s;+0])]')
>
> ? ? But in pipeline pilot (3.5), there are two HBA definitions, one of which
> is Lipinsk's. I guess the other is the "first edition", which is defined
> as:22 # HAcceptor '[$([!#6;+0]);!$([F,Cl,Br,I]);
> 23 # !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]'
> ? ?Does it mean that we should use the newest edition of HBA and?get rid of
> the default definition in pipeline pilot. These may change the?datasets
> filtered by rules such RO5.
> (I am not sure whether the HBA defined in PP is the same as defined in Line
> 22-23. I made a test.?Abacavir have 7 (current edition) and 6 (old)
> respectively. And in PP, it also returned these two results).
>
> reference:?http://www.rdkit.org/docs/api/rdkit.Chem.Lipinski-pysrc.html#NumHAcceptors?
>
> Hongbin Yang ???
>
> Research: Toxicophore and Chemoinformatics
> Pharmaceutical Science, School of Pharmacy
>
> East China University of Science and Technology?
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
