Re: [Rdkit-discuss] Compound Neutralization

John, Thanks. I meet a couple of problems with the code you suggested. Input smiles: [O-][Cl+3]([O-])([O-])O Output smiles: O[Cl+3](O)(O)O First of, the input smiles is not charged, so the neutralizing function is supposed to do nothing. Could you please help me to know whether there is a f

[Rdkit-discuss] Counting amide groups in rotatable bond counts

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 NC(=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 d

Re: [Rdkit-discuss] Compound Neutralization

Hi Yingfeng, You should use the NeutralisingCompounds on the page Markus linked: http://www.rdkit.org/docs/Cookbook.html. This version has different SMARTS for neutralising Tetrazoles. In the version you linked: # Tetrazoles Chem.MolFromSmarts('[n-]'): Chem.MolFromSm

Re: [Rdkit-discuss] Chem.MolToMolBlock() does not switch to V3000 format as expected, when number of atoms or bonds > 999.

On 2013-12-20 04:57, Greg Landrum wrote: Hi Jan On Thu, Dec 19, 2013 at 11:32 PM, Jan Holst Jensen mailto:j...@biochemfusion.com>> wrote: The first lines of C:/temp/big.mol are: HERCEPTIN FAB (ANTIBODY) - LIGHT CHAIN RDKit 3D 78908023 0 0 0 0