Thanks Stephen! That code pointed me to the key "coordMap" parameter for fixing atom coordinates.
Kurt ________________________________ From: Stephen Roughley <[email protected]> Sent: Thursday, September 12, 2024 9:40 AM To: Kurt Thorn <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [Rdkit-discuss] Impose conformation of molecule substructure? Hi Kurt, The Vernalis KNIME community contribution has a node "Templated Conformer Generator (RDKit)" (see https://hub.knime.com/n/wK3RJiystQYq5M9w ) which will do exactly this. If you don't want to do it in KNIME, then you can see the relevant bits of the Java source at: https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L441-L465 and in particular at: https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L688-L809 Steve On Thu, 12 Sept 2024 at 17:13, Kurt Thorn <[email protected]<mailto:[email protected]>> wrote: 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 [Logo Description automatically generated] 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. _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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