How to use the prody.SETTINGS function in ProDy

if not isinstance(chain, str):
            raise TypeError('chain must be a string')
        elif len(chain) == 0:
            raise ValueError('chain must not be an empty string')
        title_suffix = chain + title_suffix
    ag = kwargs.pop('ag', None)
    if ag is not None:
        if not isinstance(ag, AtomGroup):
            raise TypeError('ag must be an AtomGroup instance')
        n_csets = ag.numCoordsets()
    elif model != 0:
        ag = AtomGroup(str(kwargs.get('title', 'Unknown')) + title_suffix)
        n_csets = 0

    biomol = kwargs.get('biomol', False)
    auto_secondary = SETTINGS.get('auto_secondary')
    secondary = kwargs.get('secondary', auto_secondary)
    split = 0
    hd = None
    if model != 0:
        LOGGER.timeit()
        try:
            lines = stream.readlines()
        except AttributeError as err:
            try:
                lines = stream.read().split('\n')
            except AttributeError:
                raise err
        if not len(lines):
            raise ValueError('empty PDB file or stream')
        if header or biomol or secondary:
            hd, split = getHeaderDict(lines)

the current folder, pass an invalid path, e.g. ``folder=''``.

    If *divided* is **True**, the divided folder structure of wwPDB servers
    will be assumed when reading from and writing to the local folder.  For
    example, a structure with identifier **1XYZ** will be present as
    :file:`pdblocalfolder/yz/pdb1xyz.pdb.gz`.

    If *divided* is **False**, a plain folder structure will be expected and
    adopted when saving files.  For example, the same structure will be
    present as :file:`pdblocalfolder/1xyz.pdb.gz`.

    Finally, in either case, lower case letters will be used and compressed
    files will be stored."""

    if folder is None:
        folder = SETTINGS.get('pdb_local_folder')
        if folder:
            if isdir(folder):
                return folder, SETTINGS.get('pdb_local_divided', True)
            else:
                LOGGER.warn('PDB local folder {0} is not a accessible.'
                            .format(repr(folder)))
    else:
        if isdir(folder):
            folder = abspath(folder)
            LOGGER.info('Local PDB folder is set: {0}'.format(repr(folder)))
            if divided:
                LOGGER.info('wwPDB divided folder structure will be assumed.')
            else:
                LOGGER.info('A plain folder structure will be assumed.')
            SETTINGS['pdb_local_folder'] = folder
            SETTINGS['pdb_local_divided'] = bool(divided)

matrix, format=kwargs.get('numformat', '%12g'))

        if heatmap:
            writeHeatmap(prefix + suffix + '.hm', matrix,
                         title = msa.getTitle() + tuffix, **hmargs)

        if kwargs.get('figcoevol'):
            try:
                import matplotlib.pyplot as plt
            except ImportError:
                LOGGER.warn('Matplotlib could not be imported, '
                            'figures are not saved.')
            else:
                cmin = kwargs.get('cmin', matrix.min())
                cmax = kwargs.get('cmax', matrix.max())
                prody.SETTINGS['auto_show'] = False
                width = kwargs.get('figwidth', 8)
                height = kwargs.get('figheight', 6)
                xlabel = kwargs.get('xlabel')
                title = kwargs.get('title')
                figure = plt.figure(figsize=(width, height))
                show = showMutinfoMatrix(matrix, msa=msa, clim=(cmin, cmax),
                                         xlabel=xlabel, title=title)

                format = kwargs.get('figformat', 'pdf')
                figure.savefig(prefix + suffix + '.' + format, format=format,
                            dpi=kwargs.get('figdpi', 300))

def getWWPDBFTPServer():
    """Return a tuple containing name, host, and path of the currently 
    set `wwPDB `_ FTP server."""
    
    server = SETTINGS.get('wwpdb_ftp', None)
    if server is None:
        LOGGER.warning('A wwPDB FTP server is not set, default FTP server '
                       'RCSB PDB is used. Use `setWWPDBFTPServer` function '
                       'to set a server close to your location.')
        return _WWPDB_RCSB
    else:
        if server[2].endswith('data/structures/divided/pdb/'):
            return (server[0], server[1], 
                    server[2][:-len('data/structures/divided/pdb/')])
        else:
            return server

Following ProDy functions are for visualizing Hi-C data:

  * :func:`.showMap` - show Hi-C contact map
  * :func:`.showDomains` - show Hi-C structural domains

Save/load HiC class
-------------------

    * :func:`.saveHiC`
    * :func:`.loadHiC`

"""

import prody
LOGGER = prody.LOGGER
SETTINGS = prody.SETTINGS

__all__ = []

from . import hic
from .hic import *
__all__.extend(hic.__all__)

from . import norm
from .norm import *
__all__.extend(norm.__all__)

from . import cluster
from .cluster import *
__all__.extend(cluster.__all__)

from . import functions

url = 'http://files.rcsb.org/ligands/download/{0}.xml'.format(cci.upper())
        if not xml:
            #'http://www.pdb.org/pdb/files/ligand/{0}.xml'
            try:
                inp = openURL(url)
            except IOError:
                raise IOError('XML file for ligand {0} is not found online'
                              .format(cci))
            else:
                xml = inp.read()
                inp.close()
            if filename:
                out = openFile(filename, mode='w', folder=folder)
                out.write(xml)
                out.close()
            if SETTINGS.get('ligand_xml_save'):
                with openFile(xmlgz, 'w') as out:
                    out.write(xml)

    import xml.etree.cElementTree as ET

    root = ET.XML(xml)
    if (root.get('{http://www.w3.org/2001/XMLSchema-instance}'
                 'schemaLocation') !=
            'http://pdbml.pdb.org/schema/pdbx-v40.xsd pdbx-v40.xsd'):
        LOGGER.warn('XML is not in PDBx/PDBML v 4.0 format, resulting '
                    'dictionary may not contain all data fields')
    ns = root.tag[:root.tag.rfind('}')+1]
    len_ns = len(ns)
    dict_ = {'url': url, 'path': path}

    for child in list(root.find(ns + 'chem_compCategory')[0]):

'macro name'.format(repr(name)))
    elif not (name.isalpha() and name.islower()):
        raise ValueError('macro names must be all lower case letters, {0} '
                         'is not a valid macro name'.format(repr(name)))

    LOGGER.info('Testing validity of selection string.')
    try:
        ATOMGROUP.select(selstr)
    except SelectionError:
        LOGGER.warn('{0} is not a valid selection string, macro {1} is not'
                    'defined.'.format(repr(selstr), repr(name)))
    else:
        LOGGER.info("Macro {0} is defined as {1}."
                    .format(repr(name), repr(selstr)))
        MACROS[name] = selstr
        SETTINGS['selection_macros'] = MACROS
        SETTINGS.save()

SETTINGS.pop(NONSTANDARD_KEY, None)
        SETTINGS[TIMESTAMP_KEY] = int(time())
        SETTINGS.save()
        updateDefinitions()
    elif flag == 'nonstdaa':
        SETTINGS.pop(NONSTANDARD_KEY, None)
        SETTINGS[TIMESTAMP_KEY] = int(time())
        SETTINGS.save()
        updateDefinitions()
    else:
        try:
            SETTINGS.pop(DEFINITIONS_KEY, {}).pop(flag)
        except KeyError:
            pass
        else:
            SETTINGS[TIMESTAMP_KEY] = int(time())
            SETTINGS.save()
            updateDefinitions()

"""

    V = _getEigvecs(V, row_norm=True)
    try:
        from scipy.cluster.hierarchy import linkage, dendrogram
    except ImportError:
        raise ImportError('Use of this function (showLinkage) requires the '
                          'installation of scipy.')
    
    method = kwargs.pop('method', 'single')
    metric = kwargs.pop('metric', 'euclidean')
    Z = linkage(V, method=method, metric=metric)

    no_labels = kwargs.pop('no_labels', True)
    dendrogram(Z, no_labels=no_labels, **kwargs)
    if SETTINGS['auto_show']:
        showFigure()
    return Z