m_atoms = model.get_atoms() print "\n\n\nAFTER FILTERING!!!\n\n\n" for a in m_atoms: print "Res:{} Atom:{} x:{} y:{} z:{}".format(a.get_parent().get_resname(), a.get_name(), a.get_coord()[0], a.get_coord()[1], a.get_coord()[2]) t_residues = target.get_residues() i = 0 for t_res in t_residues: rand_res = t_res if i == 10: break i = i + 1 print "!!! !!!" sph = Sphere(m_ch, t_ch) pr = sph.processResRadius(rand_res, 300.0) print "Before swap: rmsd:{}|frac:{}".format(pr[0], pr[1]) sph.swapAmbiguousAtomLabels() pr = sph.processResRadius(rand_res, 300.0) print "After swap: rmsd:{}|frac:{}".format(pr[0], pr[1]) # # SphereGrinder engine sph = Sphere(m_ch, t_ch) sph.swapAmbiguousAtomLabels() data = sph.process(radii, caOnly) # # output results to file outdir = os.path.dirname(outf) if not os.path.exists(outdir): os.makedirs(outdir) if not os.path.isdir(outdir): raise OSError("Can't make dir {}".format(outdir)) try: