Thanks for Christoph and John's stimulating replies.

I think I will cope with this problem.


---------- Origin message ----------
>From£º"Christoph Steinbeck" <>
>To£º"¶ÅÓî" <>
>Subject£ºRe: [Cdk-user] Is there any way to filter out peptides from a sdf file?
>Date£º2014-06-05 21:15:51

Dear DuYu,

Ignore the suggestion to remove atoms and bonds. I guess John meant removing peptide substructures from larger molecules. You just want to filter lists of compounds, right.
SMARTS are the way to go. Depending on the type of data you have you might also check for amino acid SMARTS to make sure that you do not filter molecules that have the peptide bond but are not peptides.

Maybe, John’s blog item at
could help with code examples.

Kind regards,


Dr. Christoph Steinbeck
Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK