ConstrainedEmbed should be what you need. If it's saying that your molecule doesn't match the core then that's where you need to look. Maybe the core is not an exact substructure? If you still have difficulties you could generate the MCS between the structures and use that as the core. Greg's blog here might help: http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html Tim
On Mon, Jul 27, 2020 at 11:15 PM Rafael da Fonseca Lameiro < rafael.lame...@alumni.usp.br> wrote: > Hello > I'm having a hard time trying to build a 3D structure for a new molecule > (new) based on a reference molecule (ref). > In this case, ref is a substructure of new, and I want the coordinates of > their matching atoms to be exactly the same. > I have tried using: > Chem.rdDepictor.GenerateDepictionMatching3DStructure (only works if both > molecules are the same) > > rdkit.Chem.AllChem.ConstrainedEmbed (I get ValueError: molecule doesn't > match the core) > > AllChem.AlignMol (I need to input a 3D structure for new, which doesn't > match ref) > > I thought about generating a ton of conformers for new using > AllChem.EmbedMultipleConfs and then use the one with the best alignment to > ref, but I figured there should be a better way to do this. I would > appreciate any suggestions. > On a side note, is there a way to convert Chem.rdchem.Conformer objects to > Chem.rdchem.Mol? > > Thank you for the help > > Rafael > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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