How to use the chempy.models.Indexed function in chempy

from chempy import fragments, feedback, models

    cycles, state, quiet = int(cycles), int(state), int(quiet)

    # suppress feedback for model merging
    feedback['actions'] = False

    # work with named selection
    namedsele = cmd.get_unused_name('_')
    cmd.select(namedsele, '{} & present'.format(selection), 0)

    identifiers = []
    cmd.iterate(namedsele + ' and polymer and guide and alt +A',
            'identifiers.append([segi,chain,resi,resv,resn])', space=locals())

    model = models.Indexed()
    for (segi,chain,resi,resv,resn) in identifiers:
        try:
            fname = resn.lower() if resn != 'MSE' else 'met'
            frag = fragments.get(fname)
        except IOError:
            print(' Warning: unknown residue: ' + resn)
            continue

        for a in frag.atom:
            a.segi = segi
            a.chain = chain
            a.resi = resi
            a.resi_number = resv
            a.resn = resn

        model.merge(frag)

def _create_molecule(n, mydata, resolution, created):
    model = models.Indexed()
    name = _get_molecule_name(n.get_name(), resolution)
    if name in created:
        name = name + "-2"
    print n, name, resolution
    th = RMF.TraverseHelper(n, name, resolution)
    created[name] = (th, model)
    print "creating molecule", name
    cgol = []
    _create_atoms(th, mydata, model, cgol, created)
    frame = n.get_file().get_current_frame().get_index() + 1

    if len(cgol) > 0:
        print cgol
        cmd.load_cgo(cgol, name + "-graphics", frame)

continue
        elif byte <= 0x7f:
            # LABEL
            read_label()
            xyz = read_xyz()
            survey.label(xyz, byte & 0x3f)
        elif byte <= 0xbf:
            # LINE
            read_label()
            xyz = read_xyz()
            survey.line(xyz)
        elif byte <= 0xff:
            # Reserved
            continue

    model = models.Indexed()
    for (xyz,s) in survey.items():
        l0, _, l1 = s.labels[0].rpartition('.')
        resi, name = l1[:5], l1[5:]
        segi, chain, resn = l0[-8:-4], l0[-4:-3], l0[-3:]
        atom = Atom()
        atom.coord = [i/100.0 for i in xyz]
        atom.segi = segi
        atom.chain = chain
        atom.resn = resn
        atom.name = name
        atom.resi = resi
        atom.b = atom.coord[2]
        atom.label = s.labels[0]
        if s.lrud is not None:
            atom.vdw = sum(s.lrud)/400.0
        model.add_atom(atom)

# jen to zaskrtnute
            generatedString = ""
            for key in self.s:
                if self.s[key].get() == 1:
                    # pak pouzit do vyberu:
                    if key == "AA":
                        generatedString = generatedString + "+" + self.stdamString
                    else:
                        generatedString = generatedString + "+" + key

            generatedString = generatedString[1:]
            print("Checked: " + generatedString)

            mmodel = cmd.get_model(self.whichModelSelect)
            print(self.whichModelSelect + " asize: " + str(len(mmodel.atom)))
            newmodel = Indexed()
            for matom in mmodel.atom:
                if generatedString.find(matom.resn) > -1:
                    # print matom.resn
                    newmodel.atom.append(matom)
            cmd.load_model(newmodel, "tmpCaverModel")
            # cmd.label("example","name")
            # fix outdir slashes
            outdir = outdir.replace("\\", "/")
            if (outdir.endswith("/")):
                outdir = outdir[:-1]
            input = "%s/out.pdb" % (outdir)
            # cmd.save(input, self.whichModelSelect) # to by ulozilo cely model whichModelSelect.
            cmd.save(input, "tmpCaverModel")
            cmd.delete("tmpCaverModel")
            cesta = os.getcwd()
            # set ignore waters to false -- the model is already filtered by input model and aminos

atmap = dict()
    if method in ['bahar1996', '1', 1]:
        modelAll = cmd.get_model('(%s) and resn %s' % (selection, '+'.join(sidechaincenteratoms)))
        for at in modelAll.atom:
            if at.name in sidechaincenteratoms[at.resn]:
                atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
    elif method in ['centroid', '2', 2]:
        modelAll = cmd.get_model('(%s) and polymer and not (hydro or name C+N+O)' % selection)
        for at in modelAll.atom:
            atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
    else:
        print('Error: unknown method:', method)
        raise CmdException

    model = models.Indexed()
    for centeratoms in atmap.values():
        center = cpv.get_null()
        for at in centeratoms:
            center = cpv.add(center, at.coord)
        center = cpv.scale(center, 1./len(centeratoms))
        atom = Atom()
        atom.coord = center
        atom.index = model.nAtom + 1
        atom.name = name
        for key in ['resn','chain','resi','resi_number','hetatm','ss','segi']:
            atom.__dict__[key] = at.__dict__[key]
        model.add_atom(atom)
    model.update_index()
    if object in cmd.get_object_list():
        cmd.delete(object)
    cmd.load_model(model, object)

def removewater(self, selection='(all)'):
        seloutwater = Indexed()
        for a in selection.atom:
            if (a.resn != "HOH") and (a.resn != "H2O") and (a.resn != "WAT"):
                seloutwater.atom.append(a)
        return seloutwater