PaDEL descriptors

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?



PaDEL uses CDK, I believe their is a node in CDK for this? Maybe try this one to see if it works.


Have you also trie to PaDEL Molecule to CDK node rather than the compounds reader?





Thanks - turns out that the PaDEL descriptor node doesnt like the mol2 output from the BioSolveIT generate 3D structure node for whatever reason (the SDF output option works fine), which when converted with the PaDEL/Molecule to CDK Node generates the 3D descriptors just fine.