Crash to Desktop when converting a molecule to RDKit

[josemanuel]

Dear all,

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
M END

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!

Cheers,
Jose Manuel

[greglandrum]

Hi,

Which version of the RDKit nodes do you have installed?

-greg

[josemanuel]

Hi Greg,

thank you for your reply.

I am using the latest relase of the RDKit nodes:

RDKit KNIME integration 3.8.0.v201906261723

Cheers,
Jose Manuel