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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/compute_rms_between_methods.py   Pymol-script-repo(Download)
    clust0 = ref_d.clusterer.clustering_dict[rms_tolerance][0]
    c = clust0[0] #lowest energy overall in reference docking
    ref_d.ch.set_conformation(c)
    ref_LE_coords = ref_d.ligMol.allAtoms.coords[:]
    ref_largest = clust0
            if verbose: print "resetting largest clust: now len=", len(clust)
            ref_largest = clust
    ref_d.ch.set_conformation(ref_largest[0])
    ref_LC_coords = ref_d.ligMol.allAtoms.coords[:]
 
    c = clust0[0]
    #SET d.ligMol to LOWEST ENERGY conf
    d.ch.set_conformation(c)
    LE_coords = d.ligMol.allAtoms.coords[:]
    # lowest energy in test v. lowest energy in ref
    conf_LC = largest[0]  #lowest energy conformation in largest cluster
    #SET d.ligMol to LARGEST CLUSTER's LOWEST ENERGY conf
    d.ch.set_conformation(conf_LC)
    LC_coords = d.ligMol.allAtoms.coords[:]
    # largest cluster lowest energy in test v. lowest energy in ref

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_wcg_docking.py   Pymol-script-repo(Download)
        #update the coords if you need to
        if build_hydrogen_bonds or report_energy_breakdown:
            d.ch.set_conformation(c)
        if report_energy_breakdown:
            ms.set_coords(1, c.getCoords()[:])
            score_list = []
            if build_hydrogen_bonds or report_energy_breakdown:
                d.ch.set_conformation(c)
            if report_energy_breakdown:
                ms.set_coords(1, c.getCoords()[:])

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_vs_hits.py   Pymol-script-repo(Download)
        rms_tol = cluD.keys()[0]
        LE = cluD[rms_tol][0][0]
        d.ch.set_conformation(LE)
        #get coordinates of LE conformation
        crds = d.ligMol.allAtoms.coords[:]

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_lowest_energy_ligand.py   Pymol-script-repo(Download)
    key0 = d.clusterer.clustering_dict.keys()[0]
    conf0 = d.clusterer.clustering_dict[key0][0][0]
    d.ch.set_conformation(conf0)
    parser = d.ligMol.parser
    lines = []

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_largest_cluster_ligand.py   Pymol-script-repo(Download)
            largest = clust
    #update the coordinates with those of conf with lowest energy in this largest cluster
    d.ch.set_conformation(largest[0])
    parser = d.ligMol.parser
    lines = []

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_all_complexes.py   Pymol-script-repo(Download)
        output_stem = receptor_stem + '_' + d.ligMol.name
    for ix, conf in enumerate(confs):
        d.ch.set_conformation(conf)
        if write_best_only:
            ind = 0

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results4.py   Pymol-script-repo(Download)
            fptr.write(ostr)
            if build_hydrogen_bonds or report_energy_breakdown:
                d.ch.set_conformation(c)
            be = c.binding_energy
            if subtract_internal_energy:

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_results.py   Pymol-script-repo(Download)
            if build_hydrogen_bonds or report_energy_breakdown:
                if verbose: print "setting conf to ", id(c)
                d.ch.set_conformation(c)
            de = c.docking_energy
            ostr = "%3d,% 8.4f,% 8.4f" %(len(clust), de, c.getRMSD(refCoords=refCoords))

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_docking.py   Pymol-script-repo(Download)
            fptr.write(ostr)
            if build_hydrogen_bonds or report_energy_breakdown:
                d.ch.set_conformation(c)
            be = c.binding_energy
            if subtract_internal_energy: