Dear Jan and Greg,
many thanks for clearing that up.
Best,
Daniel
Von: Greg Landrum [mailto:[email protected]]
Gesendet: Donnerstag, 24. April 2014 05:29
An: [email protected]
Betreff: Re: [Rdkit-discuss] Inconsistency between Cartridge and Python
Hi,
On Wed, Apr 23, 2014 at 5:59 PM, Jan Holst Jensen
<[email protected]<mailto:[email protected]>> wrote:
On 2014-04-23 16:01, Daniel Moser wrote:
Hi all,
I think I found some inconsistent behaviour between the cartridge and python.
At least for “NCO” the cartridge function mol_hbd returns a different value
than Descriptors.NumHDonors.
[...]
I’m seeing this behaviour both with the 2013.09.2 as well as the 2012.12.1
cartridge version. Can anyone confirm this?
I can confirm this difference between Python and the cartridge using a fairly
recent git version.
The cartrige mol_hbd() function calls "calcLipinskiHBD":
MOLDESCR(HBD,RDKit::Descriptors::calcLipinskiHBD,int)
which is
unsigned int calcLipinskiHBD(const ROMol &mol){
unsigned int res=0;
for(ROMol::ConstAtomIterator iter=mol.beginAtoms();
iter!=mol.endAtoms();++iter){
if( ((*iter)->getAtomicNum()==7 || (*iter)->getAtomicNum()==8) ) {
res += (*iter)->getTotalNumHs(true);
}
}
return res;
}
while the Python NumHDonors() is using a SMARTS-based approach as far as I can
tell.
Jan has hit this dead on. The cartridge is using a Lipinski-based definition:
the number of NHs and OHs. The Python version is trying to be more correct and
include only centers that are likely to really be donors.
The somewhat inconsistent naming between the python wrappers and cartridge is
unfortunate (the cartridge should really be "mol_lipinski_hbd"), but since
changing that will break existing code, it would have to be done very carefully.
-greg
The function that the cartridge uses can be accessed via AllChem and then I can
also demonstrate the difference in Python:
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('NCO')
>>> from rdkit.Chem import Descriptors
>>> print Descriptors.NumHDonors(m)
2
>>> from rdkit.Chem import AllChem
>>> print AllChem.CalcNumLipinskiHBD(m)
3
>>>
Cheers
-- Jan
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