Not recognizing SMILES - Githubissues

oloBion / Retip

Retip - Retention Time prediction for metabolomics

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Not recognizing SMILES #18

Open BasvdVelde opened 2 years ago

BasvdVelde commented 2 years ago

Hi!

Somehow this smile does not work in retip: "C1CN(CCN1CC/C=C\2/C3=CC=CC=C3SC4=C2C=C(C=C4)Cl)CCO"

getRT.smile("C1CN(CCN1CC/C=C\2/C3=CC=CC=C3SC4=C2C=C(C=C4)Cl)CCO",training,model=xgb) Error in eval.desc(mol, descNames) : molecule must be an IAtomContainer In addition: Warning message: In parse.smiles(smile) : 1 out of 1 SMILES were not successfully parsed, resulting in NULLs.

I really don't understand why, because all my other SMILES work just fine.

Thanks again!

Bas

tobigithub commented 2 years ago

Can you check another SMILES notation for the same compound?

OCCN1CCN(CC\C=C/2\c3ccccc3Sc4ccc(Cl)cc24)CC1

Source https://chem.nlm.nih.gov/chemidplus/rn/53772-83-1

The error is related to RCDK, not Retip itself: https://www.google.com/search?q=%22must+be+an+IAtomContainer%22