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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/autoanalyzeCommands.py   Pymol-script-repo(Download)
        for tol in toleranceList:
            print 'clustering at ', tol
            clusterer.make_clustering(tol)
        if outputFile:
            clusterer.write(outputFile)
        for tol in toleranceList:
            print 'clustering at ', tol
            clusterer.make_clustering(tol)
        if outputFile:
            clusterer.write(outputFile)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_wcg_docking.py   Pymol-script-repo(Download)
    cl = Clusterer(d.ch.conformations)
    d.clusterer = cl
    cl.make_clustering(rms_tolerance)
    ref_coords = cl.clustering_dict[rms_tolerance][0][0].getCoords()[:]