Hi Hongbin,
Thanks for that. It helped me track down part of the solution using
rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition
See https://gist.github.com/tdudgeon/d29dea62540b4eb017d68250bca5d38f
But I'm still not quite there. I have a SMARTS but I want a real SMILES
(see bottom of the notebook).
I think I sort of know how this could be done longhand, but suspect
there's a real simple way!
Tim
On 27/08/2019 03:56, Hongbin Yang wrote:
Hi Tim,
Greg posted a gist on how to generate R-group matrices shortly before.
https://sourceforge.net/p/rdkit/mailman/message/36744886/
Does it help?
Hongbin Yang
*发件人: *Tim Dudgeon <mailto:tdudgeon...@gmail.com>
*发送时间: *2019年8月26日21:08
*收件人: *rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>
*主题: *[Rdkit-discuss] Generating R-group representation
I have a set of molecules that share a common scaffold and differ by
substitution at a small number of sites (typically one or two).
I'd like to generate a generic R-group molecule that summarises the
molecules (e.g. showing the scaffold with the sites of substitution as
R1, R2 etc.).
Finding the MCS of such a set of molecules with RDKit seems straight
forward, but the output of that is a SMARTS expression for the MCS.
Does anyone have any examples (or hints) of using this to generate a
R-group representation?
Tim
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