How to use the prody.LOGGER.progress function in ProDy

ags, headers = results
    ags, headers = list(ags), list(headers)

    if model == 0:
        LOGGER.info('only header is requested and returned')
        return results

    if header:
        results = (ags, headers)
    else:
#        ags = results
#        ags = list(ags)
        results = ags

    LOGGER.progress('Extracting Pfam domains...', len(ags))
    comma_splitter = re.compile(r'\s*,\s*').split
    no_info = []
    for i, ag in enumerate(ags):
        LOGGER.update(i)
        data_dict = data_dicts[i]
        pfamRange = data_dict['UniprotResnumRange'].split('-')
        uniprotAcc = data_dict['UniprotAcc']
        try:
            uniData = queryUniprot(uniprotAcc)
        except:
            LOGGER.warn('No Uniprot record found for {0}'.format(data_dict['PBD_ID']))
            continue

        resrange = None
        found = False
        for key, value in uniData.items():

pass
        try:
            ndim, shape = coordsets.ndim, coordsets.shape
        except:
            raise TypeError('coordsets must be a Numpy array or a ProDy '
                            'object with `getCoordsets` method')
        if ndim != 3 or shape[0] == 1:
            raise ValueError('coordsets must contain multiple sets')
        msf = var(coordsets, 0).sum(1)
    else:
        nfi = coordsets.nextIndex()
        natoms = coordsets.numSelected()
        total = zeros((natoms, 3))
        sqsum = zeros((natoms, 3))

        LOGGER.progress('Evaluating {0} frames from {1}:'
                        .format(ncsets, str(coordsets)), ncsets,
                        '_prody_calcMSF')
        ncsets = 0
        coordsets.reset()
        for frame in coordsets:
            frame.superpose()
            coords = frame._getCoords()
            total += coords
            sqsum += coords ** 2
            ncsets += 1
            LOGGER.update(ncsets, label='_prody_calcMSF')
        LOGGER.finish(label='_prody_calcMSF')
        msf = (sqsum/ncsets - (total/ncsets)**2).sum(1)
        coordsets.goto(nfi)
    return msf

# initialize a PDBEnsemble with reference atoms and coordinates
    if isinstance(ref, PDBEnsemble):
        ensemble = ref
    else:
        # select the subset of reference beforehand for the sake of efficiency
        if subset != 'all':
            target = target.select(subset)
        ensemble = PDBEnsemble(title)
        ensemble.setAtoms(target)
        ensemble.setCoords(target.getCoords())
    
    # build the ensemble
    if unmapped is None: unmapped = []

    LOGGER.progress('Building the ensemble...', len(atomics), '_prody_buildPDBEnsemble')
    for i, atoms in enumerate(atomics):
        if atoms is None:
            unmapped.append(labels[i])
            continue

        LOGGER.update(i, 'Mapping %s to the reference...'%atoms.getTitle(), 
                      label='_prody_buildPDBEnsemble')
        try:
            atoms.getHierView()
        except AttributeError:
            raise TypeError('atomics must be a list of instances having the access to getHierView')
        
        if subset != 'all':
            atoms = atoms.select(subset)

        # find the mapping of chains of atoms to those of target

select = None
    if ensemble.isSelected():
        select = atoms
        atoms = ensemble.getAtoms(selected=False)

    ori_coords = atoms.getCoords()
        
    labels = ensemble.getLabels()

    ### ENMs ###
    ## ENM for every conf
    enms = []
    n_confs = ensemble.numConfs()

    str_modes = 'all' if n_modes is None else str(n_modes)
    LOGGER.progress('Calculating {0} {1} modes for {2} conformations...'
                    .format(str_modes, model_type, n_confs), n_confs, '_prody_calcEnsembleENMs')

    for i in range(n_confs):
        LOGGER.update(i, label='_prody_calcEnsembleENMs')
        coords = ensemble.getCoordsets(i, selected=False)
        nodes = coords[0, :, :]
        if atoms is not None:
            atoms.setCoords(nodes)
            nodes = atoms
        enm, _ = calcENM(nodes, select, model=model, trim=trim, 
                            n_modes=n_modes, title=labels[i], **kwargs)
        enms.append(enm)

        #lbl = labels[i] if labels[i] != '' else '%d-th conformation'%(i+1)
    LOGGER.finish()

tar_com = tar[ref]

            tar_org = (tar - tar_com)
            mob_org = zeros(tar_org.shape, dtype=mobs.dtype)
            tar_org = tar_org.T
        else:
            weights_sum = weights.sum()
            weights_dot = dot(weights.T, weights)
            if ref is None:
                tar_com = (tar * weights).sum(axis=0) / weights_sum
            else:
                tar_com = (tar[ref] * weights[ref]).sum(axis=0) / sum(weights[ref])
            tar_org = (tar - tar_com)
            mob_org = zeros(tar_org.shape, dtype=mobs.dtype)

        LOGGER.progress('Superposing ', len(mobs), '_prody_ensemble')
        for i, mob in enumerate(mobs):
            if idx:
                mob = mob[indices]
            if weights is None:
                mob_com = mob.mean(0)
                matrix = dot(tar_org, subtract(mob, mob_com, mob_org))
            else:
                mob_com = (mob * weights).sum(axis=0) / weights_sum
                subtract(mob, mob_com, mob_org)
                matrix = dot((tar_org * weights).T,
                             (mob_org * weights)) / weights_dot

            U, s, Vh = svd(matrix)
            Id = array([[1, 0, 0], [0, 1, 0], [0, 0, sign(det(matrix))]])
            rotation = dot(Vh.T, dot(Id, U.T))

pdb = pdb[0]
            n_pdb = len(pdb)
            
    if n_pdb == 1:
        return _parsePDB(pdb[0], **kwargs)
    else:
        results = []
        lstkwargs = {}
        for key in kwargs:
            argval = kwargs.get(key)
            if np.isscalar(argval):
                argval = [argval]*n_pdb
            lstkwargs[key] = argval

        start = time.time()
        LOGGER.progress('Retrieving {0} PDB structures...'
                    .format(n_pdb), n_pdb, '_prody_parsePDB')
        for i, p in enumerate(pdb):
            kwargs = {}
            for key in lstkwargs:
                kwargs[key] = lstkwargs[key][i]
            c = kwargs.get('chain','')
            LOGGER.update(i, 'Retrieving {0}...'.format(p+c), 
                          label='_prody_parsePDB')
            result = _parsePDB(p, **kwargs)
            if not isinstance(result, tuple):
                if isinstance(result, dict):
                    result = (None, result)
                else:
                    result = (result, None)
            results.append(result)

n_fixed = trajectory.numFixed()
    else:
        isTrajectory = False
        unitcell = False
        if isinstance(trajectory, Ensemble):
            frame = trajectory[0]
        else:
            frame = trajectory
            acsi = trajectory.getACSIndex()
        timestep = 1
        first_ts = 0
        framefreq = 1
        n_fixed = 0

    dcd = DCDFile(filename, mode='w')
    LOGGER.progress('Writing DCD', len(irange), '_prody_writeDCD')
    prev = -1
    uc = None
    time_ = time()
    for j, i in enumerate(irange):
        diff = i - prev
        if diff > 1:
            trajectory.skip(diff-1)
        prev = i
        if isTrajectory:
            frame = next(trajectory)
            if frame is None:
                break
            if unitcell:
                uc = frame._getUnitcell()
                uc[3:] = np.sin((PISQUARE/90) * (90-uc[3:]))
                uc = uc[[0,3,1,4,5,2]]

pass
        try:
            ndim, shape = coordsets.ndim, coordsets.shape
        except:
            raise TypeError('coordsets must be a Numpy array or a ProDy '
                            'object with `getCoordsets` method')
        if ndim != 3 or shape[0] == 1:
            raise ValueError('coordsets must contain multiple sets')
        msf = var(coordsets, 0).sum(1)
    else:
        nfi = coordsets.nextIndex()
        natoms = coordsets.numSelected()
        total = zeros((natoms, 3))
        sqsum = zeros((natoms, 3))

        LOGGER.progress('Evaluating {0} frames from {1}:'
                        .format(ncsets, str(coordsets)), ncsets,
                        '_prody_calcMSF')
        ncsets = 0
        coordsets.reset()
        for frame in coordsets:
            frame.superpose()
            coords = frame._getCoords()
            total += coords
            sqsum += coords ** 2
            ncsets += 1
            LOGGER.update(ncsets, label='_prody_calcMSF')
        LOGGER.finish()
        msf = (sqsum/ncsets - (total/ncsets)**2).sum(1)
        coordsets.goto(nfi)
    return msf