I can reproduce a crash to desktop error when using using a RDKit From Molecule node on a “problematic” mol block record. I am running on Kubuntu 19.01 and an up to date KNIME 4.0.1:
rdkit_cod_rdkitfrommol.knwf (11.8 KB)
(the molecule is saved in the workflow)
If I run KNIME from the terminal, I can see the error causing the crash:
free(): invalid pointer
It looks like that the error comes from these lines right after the bond block:
M STY 1 1 DAT
M SAL 1 1 15
M SDT 1 MRV_IMPLICIT_H
M SDD 1 0.0000 0.0000 DR ALL 0 0
M SED 1 IMPL_H1
Indeed, he error disappears if I replace them with only M END.
Interestingly enough, I can process the mol block directly in Python (RDKit 2019.03.4) without any issue.
Any idea how I could avoid the crashing? It still happens with partial sanitization.
Thanks in advance for your guidance!