How to use the prody.SETTINGS.get function in ProDy

"""Rename *filename* with *backup_ext* appended to its name for backup
    purposes, if *backup* is **True** or if automatic backups is turned on
    using :func:`.confProDy`.  Default extension :file:`.BAK` is used when
    one is not set using :func:`.confProDy`.  If *filename* does not exist,
    no action will be taken and *filename* will be returned.  If file is
    successfully renamed, new filename will be returned."""

    try:
        exists = isfile(filename)
    except Exception as err:
        raise TypeError('filename must be a string ({0})'.format(str(err)))

    from prody import SETTINGS
    if exists and (backup or SETTINGS.get('backup', False)):
        if backup_ext == '.BAK':
            backup_ext = SETTINGS.get('backup_ext', '.BAK')
        bak = filename + backup_ext
        if isfile(bak):
            try:
                os.remove(bak)
            except Exception as err:
                pass
        try:
            os.rename(filename, bak)
        except Exception as err:
            pass
        return bak
    else:
        return filename

structures.  Use one of the following keywords for setting a server:

    +---------------------------+-----------------------------+
    | wwPDB FTP server          | *Key* (case insensitive)    |
    +===========================+=============================+
    | RCSB PDB (USA) (default)  | RCSB, USA, US               |
    +---------------------------+-----------------------------+
    | PDBe (Europe)             | PDBe, Europe, Euro, EU      |
    +---------------------------+-----------------------------+
    | PDBj (Japan)              | PDBj, Japan, Jp             |
    +---------------------------+-----------------------------+

    .. _wwPDB: http://www.wwpdb.org/"""

    if not key:
        return SETTINGS.get('wwpdb', None)
    elif len(key) == 1:
        try:
            key = key[0].lower()
        except AttributeError:
            raise TypeError('key must be a string')
        if key in WWPDB_FTP_SERVERS:
            SETTINGS['wwpdb'] = key
            SETTINGS.save()
            LOGGER.info('wwPDB server is set to {}.'
                        .format(WWPDB_FTP_SERVERS[key][0]))
        else:
            raise ValueError('{0} is not a valid wwPDB server identifier'
                             .format(repr(key)))
    else:
        raise TypeError('one wwPDB server identifier is expected, {0} given'
                        .format(len(key)))

def backupFile(filename, backup=None, backup_ext='.BAK', **kwargs):
    """Rename *filename* with *backup_ext* appended to its name for backup
    purposes, if *backup* is **True** or if automatic backups is turned on
    using :func:`.confProDy`.  Default extension :file:`.BAK` is used when
    one is not set using :func:`.confProDy`.  If *filename* does not exist,
    no action will be taken and *filename* will be returned.  If file is
    successfully renamed, new filename will be returned."""

    try:
        exists = isfile(filename)
    except Exception as err:
        raise TypeError('filename must be a string ({0})'.format(str(err)))

    from prody import SETTINGS
    if exists and (backup or SETTINGS.get('backup', False)):
        if backup_ext == '.BAK':
            backup_ext = SETTINGS.get('backup_ext', '.BAK')
        bak = filename + backup_ext
        if isfile(bak):
            try:
                os.remove(bak)
            except Exception as err:
                pass
        try:
            os.rename(filename, bak)
        except Exception as err:
            pass
        return bak
    else:
        return filename

def changeDefinitions(**kwargs):

    defs = SETTINGS.get(DEFINITIONS_KEY, {})
    defs.update(kwargs)
    SETTINGS[DEFINITIONS_KEY] = defs
    SETTINGS[TIMESTAMP_KEY] = int(time())
    SETTINGS.save()
    updateDefinitions()

def updateDefinitions():
    """Update definitions and set some global variables.  This function must be
    called at the end of the module."""

    global DEFINITIONS, AMINOACIDS, BACKBONE, TIMESTAMP
    DEFINITIONS = {}
    user = SETTINGS.get('flag_definitions', {})

    # nucleics
    nucleic = set()
    for key in ['nucleobase', 'nucleoside', 'nucleotide']:
        aset = set(user.get(key, DEFAULTS[key]))
        nucleic.update(aset)
        DEFINITIONS[key] = aset
    DEFINITIONS['nucleic'] = nucleic

    # heteros
    for key in ['water', 'lipid', 'ion', 'sugar', 'heme',
                'at', 'cg', 'purine', 'pyrimidine']:
        DEFINITIONS[key] = set(user.get(key, DEFAULTS[key]))

    DEFINITIONS['backbone'] = DEFINITIONS['bb'] = set(user.get(key,
                                                      DEFAULTS['bb']))

DEFINITIONS['charged'].update(DEFINITIONS['basic'])

        for resi, props in nonstd.items():
            for prop in props:
                DEFINITIONS[prop].add(resi)

    DEFINITIONS['stdaa'] = DEFAULTS['stdaa']
    DEFINITIONS['nonstdaa'] = set(nonstd)
    AMINOACIDS = set(DEFINITIONS['stdaa'])
    AMINOACIDS.update(DEFINITIONS['nonstdaa'])
    DEFINITIONS['protein'] = DEFINITIONS['aminoacid'] = AMINOACIDS

    BACKBONE = DEFINITIONS['bb']

    global TIMESTAMP
    TIMESTAMP = SETTINGS.get(TIMESTAMP_KEY, 0)

def debug(sel, loc, *args):

    if DEBUG:
        print('')
        if args:
            print(args[0], args[1:])
        print(repr(sel))
        print(' ' * (loc + 1) + '^')

__all__ = ['Select', 'SelectionError', 'SelectionWarning',
           'defSelectionMacro', 'delSelectionMacro', 'getSelectionMacro',
           'isSelectionMacro']

ATOMGROUP = None

MACROS = SETTINGS.get('selection_macros', {})
MACROS_REGEX = None


def isSelectionMacro(word):
    """Returns **True** if *word* is a user defined selection macro."""

    try:
        return word in MACROS
    except:
        return False


def defSelectionMacro(name, selstr):
    """Define selection macro *selstr* with name *name*.  Both *name* and
    *selstr* must be string.  An existing keyword cannot be used as a macro
    name. If a macro with given *name* exists, it will be overwritten.

def listNonstdAAProps(resname):
    """Returns properties of non-standard amino acid *resname*.

    .. ipython:: python

       listNonstdAAProps('PTR')"""

    try:
        alist = list(SETTINGS.get(NONSTANDARD_KEY, NONSTANDARD)[resname])
    except KeyError:
        raise ValueError('{0} is not a non-standard residue name'
                         .format(repr(resname)))
    else:
        alist.sort()
        return alist