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" <johnmay@ebi.ac.uk>
>To"" <ydu@student.ecnu.edu.cn>
>SubjectRe: [Cdk-user] Is there any way to filter out peptides from a sdf file?
>Date2014-06-05 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, <ydu@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.------------------------------------------------------------------------------
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