padelpy hangs with specific peptide sequence

[merritjm]

Hi, novice user here.
when using PaDELpy it works most of the time for me but the following peptide sequence just hangs...and eventually times out.

string = rdkit.Chem.MolToSmiles(rdkit.Chem.MolFromFASTA('GLILVGGYGTR'))
desc = from_smiles(string)

To me i don't see anything obviously wrong with the smiles string that is generated by rdkit.
interesting if i take off the final Arginine (R) it computes fine.

Any ideas?

[tjkessler]

Hey @merritjm,

I'm not too familiar working with peptide sequences - what is the SMILES string that rdkit.Chem.MolToSmiles generates?

Travis

Edit: in other words, what is the value of "string"?

[merritjm]

in the example above GLILVGGYGTR which fails the descriptor calc the smiles is:

GLILVGGYGT which runs fine:

copied pictures since as txt they were causing issues. The smiles can be found in the linked file.

padel smiles testing.txt
4fb1-b132-7ca628389778)