Did I find the right examples for you? yes no      Crawl my project      Python Jobs

All Samples(8)  |  Call(8)  |  Derive(0)  |  Import(0)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_docking_directory.py   Pymol-script-repo(Download)
 
    log.info("clustering %s at rms_tol %f" % (docking_name, rms_tolerance))
    d.clusterer.make_clustering(rms_tolerance)
##     d.clusterer.clustering_dict[rms_tolerance].do_stats()
##     d.clusterer.write_summary()

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/compute_rms_between_methods.py   Pymol-script-repo(Download)
    coords = ref_d.ligMol.allAtoms.coords[:]
    ref_d.clusterer.rmsTool = RMSDCalculator(coords)
    ref_d.clusterer.make_clustering(rms_tolerance) 
    clust0 = ref_d.clusterer.clustering_dict[rms_tolerance][0]
    c = clust0[0] #lowest energy overall in reference docking
    #coords = d.ligMol.allAtoms.coords[:]
    d.clusterer.rmsTool = RMSDCalculator(coords)
    d.clusterer.make_clustering(rms_tolerance) 
    clust0 = d.clusterer.clustering_dict[rms_tolerance][0]
    c = clust0[0]

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_largest_cluster_ligand.py   Pymol-script-repo(Download)
        d.readDlg(dlg)
    d.clusterer.rmsTool = RMSDCalculator(d.ligMol.allAtoms.coords[:])
    d.clusterer.make_clustering(rms_tolerance)
    clustering = d.clusterer.clustering_dict[rms_tolerance]
    largest = clustering[0]

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_clustering_histogram_postscript.py   Pymol-script-repo(Download)
    d.clusterer.rmsToolRef = '0'   # for ADT only?
    #d.clusterer_dict['ats_binding'] = d.clusterer #for ADT only??
    d.clusterer.make_clustering(rms_tolerance) 
    s = d.ch.conformations
    elist = []

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results4.py   Pymol-script-repo(Download)
            refCoords = coords[:]
    d.clusterer.rmsTool = RMSDCalculator(coords)
    d.clusterer.make_clustering(rms_tolerance) 
    mode = 'w'
    first = True

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results.py   Pymol-script-repo(Download)
    d.clusterer.rmsTool = RMSDCalculator(coords)
 
    d.clusterer.make_clustering(rms_tolerance) 
 
    # for building hydrogen bonds or reporting energy breakdown

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_docking.py   Pymol-script-repo(Download)
            refCoords = coords[:]
    d.clusterer.rmsTool = RMSDCalculator(coords)
    d.clusterer.make_clustering(rms_tolerance) 
    mode = 'w'
    first = True