Hi Christos, I recently did something like this for a fingerprint, I can't say whether or not the way you proposed works (though if it does it's a shortcut on what I did!)
What I did was
cfac =
ChemicalFeatures.BuildFeatureFactory('/Users/nfirth/Desktop/PythonScripts/ImportantText/featDef.txt')
allRDKitFeats = cfac.GetFeaturesForMol(mol)
for i in allRDKitFeats:
if(i.GetFamily() == 'HBondAcceptor'):
hBondAcceptors.append(i.GetAtomIds()[0])
elif(i.GetFamily() == 'HBondDonor'):
hBondDonors.append(i.GetAtomIds()[0])
elif(i.GetFamily() == 'Aromatic'):
aroAtoms.append(i.GetAtomIds()[0])
Which as you can see is a bit more complicated, but definitely gives the right
results. The contents of the file featDef.txt is as follows:
DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
EndFeature
DefineFeature HAcceptor1 [N,O]
Family HBondAcceptor
Weights 1.0
EndFeature
DefineFeature AromaticAtom [a]
Family Aromatic
Weights 1.0
EndFeature
Hope that helps if your solution doesn't turn out. If it does then thanks for
the shortcut!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
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[cid:image001.gif@01CE053D.51D3C4E0]
On 26 Jul 2013, at 13:54, Christos Kannas
<chriskan...@gmail.com<mailto:chriskan...@gmail.com>> wrote:
Dear RDKiters,
I'm creating a descriptor for estimating water solubility (clogSw) base on the
following article of Delaney (doi:10.1021/ci034243x).
J. S. Delaney, “ESOL: Estimating Aqueous Solubility Directly from Molecular
Structure,” Journal of Chemical Information and Modeling, vol. 44, no. 3, pp.
1000–1005, May 2004.
In this paper he proposes an equation to calculate an estimation of the water
solubility of molecules based on physio-chemical descriptors.
One of the descriptors used is Aromatic Proportion, that is the proportion of
heavy atoms of the molecule that are in aromatic ring.
So in order to find the aromatic heavy atoms I use GetSubstructMatches(...)
with query SMARTS '[a]'. Is that the correct way to find all the aromatic atoms
of a molecule? If not what is the correct SMARTS to use?
@Greg: When I complete this, can we look into adding it as a new descriptor,
clogSw (like clogP), within the RDKit distribution?
Kind Regards,
Christos
--
Christos Kannas
Researcher
Ph.D Student
e-Health Laboratory<http://www.medinfo.cs.ucy.ac.cy/>
kannas.chris...@ucy.ac.cy<mailto:kannas.chris...@ucy.ac.cy>
kannas.chris...@cs.ucy.ac.cy<mailto:kannas.chris...@cs.ucy.ac.cy>
chriskan...@gmail.com<mailto:chriskan...@gmail.com>
Mob: (+357) 99530608
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