Thanks Stephen!

That code pointed me to the key "coordMap" parameter for fixing atom 
coordinates.

Kurt
________________________________
From: Stephen Roughley <s.d.rough...@googlemail.com>
Sent: Thursday, September 12, 2024 9:40 AM
To: Kurt Thorn <kurt.th...@arrepath.com>
Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
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 
<kurt.th...@arrepath.com<mailto: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




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