Hi Julio, You can use this
https://github.com/asad/SMSD/blob/master/src/org/openscience/smsd/tools/GraphAtomContainer.java IAtomContainer container=new GraphAtomContainer(cdkAtomContainer); Iterable<IAtom> sortedAtoms= container.atoms(); Hope this helps. Asad On 1 Apr 2011, at 13:03, cdk-user-requ...@lists.sourceforge.net wrote: > Send Cdk-user mailing list submissions to > cdk-user@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cdk-user > or, via email, send a message with subject or body 'help' to > cdk-user-requ...@lists.sourceforge.net > > You can reach the person managing the list at > cdk-user-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cdk-user digest..." > > > Today's Topics: > > 1. Sort atom types in IAtomContainer (Julio Peironcely) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 10:15:29 +0200 > From: Julio Peironcely <pey...@gmail.com> > Subject: [Cdk-user] Sort atom types in IAtomContainer > To: cdk-user@lists.sourceforge.net > Message-ID: > <AANLkTimffJ4o_N18rwbkgrHs9s6WHtFwRu3=s_+bf...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > Is there a way of sorting the atoms that are included in an IAtomContainer? > Example: I read into a IAtomContainer a SD file where the first atoms are > oxygens, then carbons, and then nitrogens. I would like that in the > IAtomContainer the atoms are ordered C,O,N, for instance. If I would read a > different SD with atoms ordered N,O,C, the resulting IAtomContainer will > have again C,O,N. > Is there a function in CDK that performs this? > > Cheers, > Julio > > -- > Julio E. Peironcely, PhD student > http://juliopeironcely.com > Leiden/Amsterdam Center for Drug Research || Netherlands Metabolomics Centre > peironc...@chem.leidenuniv.nl || pey...@gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > > > ------------------------------ > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > End of Cdk-user Digest, Vol 59, Issue 1 > ***************************************
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