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.
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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