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 <kurt.th...@arrepath.com> 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 > > > > *[image: Logo Description automatically generated]* > > *Dr Kurt Thorn* > > *Chief Technology Officer* > > +1.609.423.1571 (US Office) > > +1.415.298.3495 (US Mobile) > > kurt.th...@arrepath.com > > www.arrepath.com > > > > *ArrePath Inc.* > > 303A College Road East > > Princeton, NJ 08540 > > U.S. > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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