Re: [Rdkit-discuss] Impose conformation of molecule substructure?

[Manish S. <ms...@sa...>]

Hi Kurt,

 

You might find the following scripts helpful for enumerating compounds and
align them to a reference molecule:

 

o RDKitEnumerateCompoundLibrary.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitEnumerateCompoundLibrar
y.html> 

o RDKitPerformPositionalAnalogueScan.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitPerformPositionalAnalog
ueScan.html> 

o RDKitGenerateConstrainedConformers.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitGenerateConstrainedConf
ormers.html> 

o RDKitPerformConstrainedMinimization.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitPerformConstrainedMinim
ization.html> 

 

Let me know of any further questions.

 

Thanks,

Manish

 

 

From: Kurt Thorn <kur...@ar...> 
Sent: Thursday, September 12, 2024 8:50 AM
To: rdk...@li...
Subject: [Rdkit-discuss] Impose conformation of molecule substructure?

 

Hi All -

 

I would like to enumerate a virtual library of a compound family we have a
crystal structure of, where I want to model structures of multiple
substituents at a single site. What I would like to do is enforce that the
constant part of the molecule assume the conformation in the crystal
structure and enumerate just conformers for the new substituent added. Does
anyone have a  suggestion for how to achieve this in rdkit?

 

Thanks,

Kurt

 

 



 Dr Kurt Thorn

Chief Technology Officer

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