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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/autoanalyzeCommands.py   Pymol-script-repo(Download)
            else:
                d = Docking()
            d.readDlg(resultsFile)
        elif ext=='.res' or ext=='.results':
            if addToPrevious and isinstance(self.vf.docked.parser,EntropiaParser):

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/compute_rms_between_methods.py   Pymol-script-repo(Download)
    ref_d = Docking()
    for dlg in ref_dlg_list:
        ref_d.readDlg(dlg)
    #setup rmsd tool
    coords = ref_d.ligMol.allAtoms.coords[:]
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)
    #setup rmsd tool
    #coords = d.ligMol.allAtoms.coords[:]

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_vs_hits.py   Pymol-script-repo(Download)
        #create a docking
        d = Docking()
        d.readDlg(dlgFN)
        #set ligand to lowest energy conformation LE
        cluD = d.clusterer.clustering_dict

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_lowest_energy_ligand.py   Pymol-script-repo(Download)
 
    d = Docking()
    d.readDlg(dlgfilename)
 
    if verbose: print 'read ', dlgfilename

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

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_conformations_from_dlg.py   Pymol-script-repo(Download)
 
    d = Docking()
    d.readDlg(docking_filename)
    lines = d.ligMol.parser.allLines
    for i in range(len(lines)):

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_clustering_histogram_postscript.py   Pymol-script-repo(Download)
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)
        if len(d.ch.conformations)>=50:
            print 'stop reading dlgs at', len(d.ch.conformations)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_all_complexes.py   Pymol-script-repo(Download)
 
    d = Docking()
    d.readDlg(docking_filename)
    receptor_stem = os.path.splitext(os.path.basename(receptor_filename))[0]
    print "receptor_stem =", receptor_stem

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results4.py   Pymol-script-repo(Download)
        #code contributed by S.Forli
        try:  
            d.readDlg(dlg)
        except:
            print "Error reading the file \"%s\""  % dlg

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results.py   Pymol-script-repo(Download)
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)
 
    #setup rmsd tool

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