[Biojava-l] CEAlign > 0 for exact same structures ?

[Andreas Prlic]

Hi Jay,

what are the pdb Ids? When I try this for e.g. 4hhb.A against itself I
am getting an RMSD  of 0.

Use the afpChain.getTotalRmsdOpt() to get the RMSD of the final
alignment. (see also DemoCE.java)

Andreas





On Wed, Jun 22, 2011 at 3:24 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys.. Im finding that two structures that are the same give me non-zero
> RMSD alignments....   There could be a bug in my code, but this is an
> initial notice that I'm pretty sure about.... Any thoughts on the
> performance of CEAlign in ideal cases ?
>
>
>        Atom[] ca1 = GPdbUtils.getAtoms(s1, type);
>        Atom[] ca2 = GPdbUtils.getAtoms(s2, type);
>
>        System.out.println("Aligning two sets of atoms, " + ca1.length
> +","+ca2.length);
>        // get default parameters
>        CeParameters params = new CeParameters();
>
>        // set the maximum gap size to unlimited
>        // params.setMaxGapSize(-1);
>        StructureAlignment algorithm = StructureAlignmentFactory
>                .getAlgorithm(CeMain.algorithmName);
>
>        // The results are stored in an AFPChain object
>        AFPChain afpChain = algorithm.align(ca1, ca2, params);
>        afpChain.setName1("A");
>        afpChain.setName2("B");
>
>        return (float) afpChain.getChainRmsd();
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