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 fine for my purposes.
>
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
mol2.HasSubstructMatch(Chem.MolFromSmarts('[c]
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
Sent: Mon, Sep 11, 2017 2:53 pm
Subject: Re: [Rdkit-discuss] how to output multiple Kekule str
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 range(len(suppl)):
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
Cc: RDKit Discuss
Sent: Mon, S
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 molecule was entered or draw
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 alkenyl-subs
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 PM,
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 th
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 func
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