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
