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 <[email protected]> Sent: Thursday, September 12, 2024 8:50 AM To: [email protected] 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 +1.609.423.1571 (US Office) +1.415.298.3495 (US Mobile) [email protected] <mailto:[email protected]> www.arrepath.com <http://www.arrepath.com/> ArrePath Inc. 303A College Road East Princeton, NJ 08540 U.S.
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