RDkit benchmarking

[zizoo]

Hello,
I have a list of peptides that contain missing residues in the middle of their chains. I would like to get from them the RDkit molecular descriptors and/or fingerprints.
Is that possible to get? What is the safest method to deal with these truncated peptides?
Thanks,

[zizoo]

Hi @greglandrum,
Could you please help me with my query above.
Thanks,

[greglandrum]

I’m not quite sure what your input looks like.
Can you please share a sample workflow with one or more of the “truncated peptides”?

[zizoo]

Hi @greglandrum,
I created a new post where I described better the problem with the workflow and the molecule:

Windows version crashes while Linux version works normally with javasnippet

Hello, I used a javasnippet node with a an Rdkit script. One of the users here @josemanuel managed to make it work with Linux version (4.02) but in my version on windows 10 it is not working. Once the snippet is executing, Knime crashes and closes before I can read any error. The snippet worked for me normally with other PDB file but crashes with the one attached here. My analysis of the problem: it worked with other pdb then the script itself and RDkit should be alright. The pdb did not wo…

Thanks,