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padelpy hangs with specific peptide sequence #45
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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"? |
in the example above GLILVGGYGTR which fails the descriptor calc the smiles is: copied pictures since as txt they were causing issues. The smiles can be found in the linked file. padel smiles testing.txt |
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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?
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