Hi All,
I’m working with some generated SMARTS and get some errors related to
charges on nitrogens. This following script exemplifies the behavior I did not
expect. Why does the nitrogen charge gets different, depending on if other
SMARTS properties are set for that atom?? m1 has the explicit charge on N, but
not m2
Best Regards
Esben
import rdkit
print(rdkit.__version__)
from rdkit import Chem
m1 = Chem.MolFromSmarts("O=[N+1](-[O-])-[C:2]")
m2 = Chem.MolFromSmarts("O=[N+1;D3](-[O-])-[C:2]")
a = m1.GetAtomWithIdx(1)
print("Smarts 1: N charge %i"%a.GetFormalCharge())
a = m2.GetAtomWithIdx(1)
print("Smarts 2: N charge %i"%a.GetFormalCharge())
print("Smarts 1 as smarts %s"%Chem.MolToSmarts(m1))
print("Smarts 2 as smarts %s"%Chem.MolToSmarts(m2))
print("Smarts 1 as smiles %s"%Chem.MolToSmiles(m1))
print("Smarts 2 as smiles %s"%Chem.MolToSmiles(m2))
Chem.MolFromSmiles(Chem.MolToSmiles(m1))
Chem.MolFromSmarts(Chem.MolToSmarts(m1))
Chem.MolFromSmarts(Chem.MolToSmarts(m2))
#These fails with error: Explicit valence for atom # 1 N, 4, is greater than
permitted
m2.UpdatePropertyCache()
Chem.MolFromSmiles(Chem.MolToSmiles(m2))
2019.03.2
Smarts 1: N charge 1
Smarts 2: N charge 0
Smarts 1 as smarts O=[N&+](-[O&-])-[C:2]
Smarts 2 as smarts O=[N&+&D3](-[O&-])-[C:2]
Smarts 1 as smiles O=[N+]([O-])[CH3:2]
Smarts 2 as smiles O=N([O-])[CH3:2]
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-1-f0121281240c> in <module>
18 Chem.MolFromSmarts(Chem.MolToSmarts(m2))
19 #These fails with error: Explicit valence for atom # 1 N, 4, is greater
than permitted
---> 20 m2.UpdatePropertyCache()
21 Chem.MolFromSmiles(Chem.MolToSmiles(m2))
ValueError: Sanitization error: Explicit valence for atom # 1 N, 4, is greater
than permitted
[ ]:
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