Examples of stallone.coordinates.MinimalRMSDistance3D

stallone.coordinates.MinimalRMSDistance3D
Class for a fast calculation of the minimal RMSD between two structures. Based on the fortran implementation of John Chodera and based on the paper Douglas L. Theobald Rapid calculation of RMSDs using a quaternion-based characteristic polynomial Acta Crystallographica Section A, Foundations of Crystallography ISSN 0108-7673 Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA. Correspondence e-mail: theobal@colorado.edu @author Martin Senne - mail@martin-Senne.de @version 1.0

     */
    public double minRMSD(IDoubleArray x1, IDoubleArray x2)
    {
        int N = x1.rows();
        if (minrmsd == null)
            minrmsd = new MinimalRMSDistance3D(N);
        if (minrmsd.getN() != N)
            minrmsd = new MinimalRMSDistance3D(N);
        return minrmsd.distance(x1, x2);
    }

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{
    public ICoordinateTransform transform_minrmsd(final IDoubleArray Xref)
    {
        return new AbstractCoordinateTransform(1)
        {
            MinimalRMSDistance3D minrmsd = new MinimalRMSDistance3D(Xref.rows());


            @Override
            public void transform(IDoubleArray in, IDoubleArray out)
            {
                out.set(0, minrmsd.distance(Xref, in));
            }
        };
    }

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    public IMetric<IDoubleArray> metric(int metricID, int nRows)
    {
        if (metricID == METRIC_MINRMSD)
        {
            return new MinimalRMSDistance3D(nRows);
        }
        if (metricID == METRIC_EUCLIDEAN)
        {
            return new EuclideanDistance();
        }

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        {
            metric = new EuclideanDistance();
        }
        if (metricstring.equalsIgnoreCase("minrmsd"))
        {
            metric = new MinimalRMSDistance3D(data.getSequence(0).dimension() / 3);
        }


        // initial discretization
        if (parser.hasCommand("ninitcluster"))
        {

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Related Classes of stallone.coordinates.MinimalRMSDistance3D

stallone.api.cluster.ClusterFactory

stallone.api.coordinates.CoordinateFactory

stallone.api.coordinates.CoordinateUtilities

stallone.hmm.pmm.AdaptiveDiscretization

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