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 http://efficientbits.blogspot.de/2013/10/all-small-things.html?q=SMARTS could help with code examples. Kind regards, Chris -- 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 Phone +44 1223 49 2640 admin: khol...@ebi.ac.uk https://www.ebi.ac.uk/about/people/christoph-steinbeck What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. On 5 Jun 02014, at 14:36, 杜宇 <y...@student.ecnu.edu.cn> wrote: > Thanks for John May's reply. > > Could I just use the peptide bond as substructure(i.e. SMARTS CC(=O)NC) to > query all the molecules in the sdf file? > But what does the 'removing the atoms and bonds' mean? > > And about the more efficient approach, I don't find the ready-to-use > program. Could you please show some details? > > Yours, > DuYu > > ---------- Origin message ---------- > >From："John May" <john...@ebi.ac.uk> > >To："杜宇" <y...@student.ecnu.edu.cn> > >Subject：Re: [Cdk-user] Is there any way to filter out peptides from a sdf > >file? > >Date：2014-06-05 17:55:48 > > The easiest approach is probably to search for substructures and remove the > atoms and bonds. > > A more efficient approach is described here: > http://www.daylight.com/meetings/mug96/sayle/sayle.html > > On 5 Jun 2014, at 06:47, 杜宇 <y...@student.ecnu.edu.cn> wrote: > > > Dear cdk-user, > > I want to filter out or find out all the peptides from a sdf file. > > Could all birilliant you give some hints on this problem? > > Thanks in > > advance.------------------------------------------------------------------------------ > > Learn Graph Databases - Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases and their > > applications. Written by three acclaimed leaders in the field, > > this first edition is now available. Download your free book today! > > http://p.sf.net/sfu/NeoTech_______________________________________________ > > Cdk-user mailing list > > Cdk-user@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech_______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
