Hi all, Please be gentle with me! To be honest I am an absolute amateur, at python and RDKit. I'm a trained peptide chemist and trying to convert some peptide sequences with modifications into SMILES codes. I've decided, maybe wrongly, that the best route is via HELM codes to MOL to SMILES using RDKit in Python - mainly since the peptides are quite modified at C-/N-term and branched. I'm a little embarrassed by my code but I have posted it here! https://github.com/grahamsimpson/peptides/blob/master/single_peptide_to_HELM.py <https://github.com/grahamsimpson/peptides/blob/master/single_peptide_to_HELM.py>
The issue I'm having is the RDKit MolFromHELM - Ive been using the HELM Webeditor - http://webeditor.openhelm.org/hwe/examples/App.htm - to validate HELM codes - but the MolFromHELM keeps throwing up an error (resulting in none and subsequently, MolToSequence or MolToSMILES don't work. Traceback (most recent call last): File "test_single_HELM.py", line 34, in <module> Sequence = Chem.MolToSequence(mol) Boost.Python.ArgumentError: Python argument types in rdkit.Chem.rdmolfiles.MolToSequence(NoneType) did not match C++ signature: MolToSequence(RDKit::ROMol mol) The peptides I want are in the form - linear- Ac-ICECREAMAAICECREAMDD-NH2 -branched - (Ac-ICECREAMAA)(Ac-ICECREAMDD)K-NH2 and looking to get the SMILES codes. PEPTIDE1{[ac]}|PEPTIDE2{[am]}|PEPTIDE3{[ac].I.C.E.C.R.E.A.M.A.A.K.D.D.M.A.E.R.C.E.C.I}$PEPTIDE1,PEPTIDE3,1:R2-22:R2|PEPTIDE2,PEPTIDE3,1:R1-12:R3$$$V2.0 or drawn another way PEPTIDE1{[ac].I.C.E.C.R.E.A.M.A.A}|PEPTIDE2{[ac].I.C.E.C.R.E.A.M.D.D.K.[am]}$PEPTIDE2,PEPTIDE1,12:R3-11:R2$$$V2.0 [image: image.png] I would be very grateful for any help you could give me. I'm sure there are more efficient ways of doing this with dictionaries or other approaches. This has been bugging me for a while (but has been a great learning experience!). Please let me know if it there are other places I could post to find the answer to this. Thanks very much in advance, Best wishes, Graham
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