Re: [Rdkit-discuss] 答复: Generating R-group representation

[Tim Dudgeon]

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 
*发送时间: *2019年8月26日21:08
*收件人: *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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[Rdkit-discuss] 答复: Generating R-group representation

[Hongbin Yang]

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
发送时间: 2019年8月26日 21:08
收件人: 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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