I’ve been using the Vernalis MMP nodes to generate all the matched pairs in my dataset. To find the pairs of interest I’ve been filtering first on the L and then on the R fragment. However, it would be nice to be able to filter just once based on the transform itself. I’ve been trying to do that a few different ways, either via the RDKIT SSS node, Schrödinger, and Indigo. So far I haven’t been able to succeed. One of the things I’m running into with the indigo node is that it doesn’t seem to like the structures for either the transform or the fragments from the Vernalis node (invalid index 107 (size = 105) is the error for every single molecule).
Any thoughts on this?