Hi,
I have a molecule that RDKit claims to have 9 rotatable bonds but the
chemists in my office claim to have 6. It's smiles is
CCCCNC(=O)C1CC[NH+](CC(=O)NC(N)=O)CC1
and my colleagues are concerned that the amide and urea groups are being
counted as rotatable incorrectly. Is this a bug, a design decision or a
feature?
The below code snippet shows the problem:
>>> import rdkit
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> mol = Chem.MolFromSmiles('CCCCNC(=O)C1CC[NH+](CC(=O)NC(N)=O)CC1')
>>> print AllChem.CalcNumRotatableBonds(mol)
9
Thanks,
Yours,
Toby Wright
--
InhibOx Ltd
Oxford
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