Re: [Rdkit-discuss] Using Chem.WrapLogs()

Yeah, please go ahead and fie a bug for the windows problems. No guarantees that we can fix it, but it's worth at least capturing the problem. -greg On Fri, Sep 8, 2017 at 4:50 PM, Noel O'Boyle wrote: > Thanks Maciek, > > Both of those solutions works on Linux, which is

Re: [Rdkit-discuss] how to output multiple Kekule structures

But keep in mind that the kekulized mols you create with the resonance supplier will not match the SMARTS patterns given. Chem.MolToSmiles(mol2, kekuleSmiles = True) >'C1C=CC=CC=1' mol2.HasSubstructMatch(Chem.MolFromSmarts('[C]=[C]-[C]')) > False

Re: [Rdkit-discuss] how to output multiple Kekule structures

Paolo, Exactly what I was looking for. Very helpful. Thank you. Regards, Jim Metz -Original Message- From: Paolo Tosco To: James T. Metz ; greg.landrum ; rdkit-discuss

Re: [Rdkit-discuss] how to output multiple Kekule structures

Hi Jim, you can indeed enumerate all Kekulè structures for a molecule within the RDKit using Chem.ResonanceMolSupplier(): from rdkit import Chem mol = Chem.MolFromSmiles('c1c1') suppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL) len(suppl) 2 for i in

Re: [Rdkit-discuss] how to output multiple Kekule structures

Greg, Thanks! Yes, very helpful. I will need to digest the detailed information you have provided. I am somewhat familiar with recursive SMARTS. Thanks again. Regards, Jim Metz -Original Message- From: Greg Landrum To: James T. Metz

Re: [Rdkit-discuss] how to output multiple Kekule structures

On Mon, Sep 11, 2017 at 5:55 PM, James T. Metz wrote: > Greg, > > I need to be able to use SMARTS patterns to identify substructures in > molecules > that can be aromatic, and I need to be able to handle cases where there > can be > differences in the way that the

Re: [Rdkit-discuss] how to output multiple Kekule structures

Greg, I need to be able to use SMARTS patterns to identify substructures in molecules that can be aromatic, and I need to be able to handle cases where there can be differences in the way that the molecule was entered or drawn by a user. For example, consider the following

Re: [Rdkit-discuss] how to output multiple Kekule structures

Hi Jim, The code currently has no way to enumerate Kekule structures. I don't recall this coming up in the past and, to be honest, it doesn't seem all that generally useful. Perhaps there's an alternate way to solve the problem; what are you trying to do? -greg On Mon, Sep 11, 2017 at 5:04

[Rdkit-discuss] how to output multiple Kekule structures

Hello, Suppose I read in an aromatic SMILES e.g., for benzene c1c1 I would like to generate the major canonical resonance forms and save the results as two separate molecules. Essentially I am trying to generate m1 = 'C1=CC=CC-C1' m2 = 'C1C=CC=CC1' Can

Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS()

Thanks Greg for this detailed answer. Yes, indeed this helps. From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: Freitag, 8. September 2017 12:10 To: Udvarhelyi, Aniko Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS() Hi Anikó, Both