I have recently been looking at using the PaDEL descriptor calculation nodes, but have run into some real problems with the 3D descriptors. Has anyone a success story to share here?
I have been using the BioSolveIT Generate 3D structures node to generate the conformations (under the hood this is powered by Corina), but the mol2 files I write are taking an age to load into the PaDEL compound reader node, and once loaded fail to generate the requested 3D descriptors (only output is NaN).
I thought this might be a peculiarity of the way I generated the molecules, so I tried an SDF generated via RDKit. Again no success.
How should I go about generating 3D structures for this node?