It would be a nice idea to have a node which calculates RMSD either in-place or optimally aligned between pairs of structures. The reference structure could be entered in a MOL or PDB block as in the templated conformer generation node, or in a separate column. Performance improvements around checking if one of molecules is a substructure of the other before carrying out MCS would be a good idea, and offering some MCS options (or allow the user to specify an MCS SMARTS column or global input?)
From a forum post at https://forum.knime.com/t/3d-rmsd-of-substructure-vs-larger-molecule/27130/11?u=s.roughley
It would be a nice idea to have a node which calculates RMSD either in-place or optimally aligned between pairs of structures. The reference structure could be entered in a MOL or PDB block as in the templated conformer generation node, or in a separate column. Performance improvements around checking if one of molecules is a substructure of the other before carrying out MCS would be a good idea, and offering some MCS options (or allow the user to specify an MCS SMARTS column or global input?)