Hi All,
The following is a relatively minor point, but IMHO, the Gobbi hydrogen bond
acceptor definition probably should be modified so that only aromatic nitrogen
atoms with two and not three non-hydrogen attachments are considered as
acceptors. For example, the aromatic nitrogen atom pyridine is an acceptor
whereas the nitrogen in indole or N-methylindole is not. Also fluorine atoms
(see https://doi.org/10.1016/0040-4020(96)00749-1
<http://dx.doi.org/10.1016/0040-4020(96)00749-1>) do not appear to be good
acceptors. In addition, thiophenes are very questionable acceptors.
Hence in:
in
~/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py
I have made the following modification:
# Replaced the following line to the next line:
# DefineFeature Acceptor
[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]
DefineFeature Acceptor
[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n;D2;H0;+0]),$([o;+0]]
Cheers,
Konrad
After modifying Gobbi_Pharm2D.py, the following test script gives:
from rdkit import Chem, DataStructs
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
mol = Chem.MolFromSmiles('Cn1ccc2ccccc21’) # N-methylindole
bi = {}
fp = Generate.Gen2DFingerprint(mol,Gobbi_Pharm2D.factory,bitInfo=bi)
onbits = fp.GetOnBits()
for onbit in onbits:
print onbit, Gobbi_Pharm2D.factory.GetBitDescription(onbit), bi[onbit]
output:
77 AR HD |0 0|0 0| [[(3,), (0,)]]
mol = Chem.MolFromSmiles('c1ncccc1C’) # 2-methylpyridine
output:
63 AR BG |0 0|0 0| [[(5,), (1,)]]
70 AR HA |0 0|0 0| [[(5,), (1,)]]
------------------------------------------------------------------------------
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