Example #1
0
File: goa.py Project: nffaruk/ProDy
def parseOBO(**kwargs):
    """Parse a GO OBO file containing the GO itself.
    See `OBO`_ for more information on the file format.

    .. _OBO: http://owlcollab.github.io/oboformat/doc/obo-syntax.html
    """
    try:
        from goatools import obo_parser
    except:
        raise ImportError('GOATools needs to be installed to use parseOBO')

    go_obo_url = kwargs.get('go_obo_url', None)
    if go_obo_url is None:
        go_obo_url = 'http://purl.obolibrary.org/obo/go/go-basic.obo'

    data_folder = kwargs.get('data_folder', None)
    if data_folder is None:
        data_folder = os.getcwd() + '/Data'

    # Check if we have the ./data directory already
    if (not os.path.isfile(data_folder)):
        # Emulate mkdir -p (no error if folder exists)
        try:
            os.mkdir(data_folder)
        except OSError as e:
            if (e.errno != 17):
                raise e
    else:
        raise Exception(
            'Data path (' + data_folder + ') exists as a file. '
            'Please rename, remove or change the desired location of the data path.'
        )

    # Check if the file exists already
    if (not os.path.isfile(data_folder + '/go-basic.obo')):
        try:
            handle = openURL(go_obo_url)
        except Exception as err:
            LOGGER.warn('{0} download failed ({1}).'.format(
                go_obo_url, str(err)))
        else:
            data = handle.read()
            if len(data):
                filename = data_folder + '/go-basic.obo'

                with open(filename, 'w+b') as obofile:
                    obofile.write(data)

                LOGGER.debug('{0} downloaded ({1})'.format(
                    go_obo_url, sympath(filename)))
            else:
                LOGGER.warn(
                    '{0} download failed, reason unknown.'.format(go_obo_url))

    else:
        go_obo = data_folder + '/go-basic.obo'

    return obo_parser.GODag(go_obo)
Example #2
0
File: goa.py Project: prody/ProDy
def parseOBO(**kwargs):
    """Parse a GO OBO file containing the GO itself.
    See `OBO`_ for more information on the file format.

    .. _OBO: http://owlcollab.github.io/oboformat/doc/obo-syntax.html
    """
    try:
        from goatools import obo_parser
    except:
        raise ImportError('GOATools needs to be installed to use parseOBO')

    go_obo_url = kwargs.get('go_obo_url', None)
    if go_obo_url is None:
        go_obo_url = 'http://purl.obolibrary.org/obo/go/go-basic.obo'

    data_folder = kwargs.get('data_folder', None)
    if data_folder is None:
        data_folder = os.getcwd() + '/Data'

    # Check if we have the ./data directory already
    if(not os.path.isfile(data_folder)):
        # Emulate mkdir -p (no error if folder exists)
        try:
            os.mkdir(data_folder)
        except OSError as e:
            if(e.errno != 17):
                raise e
    else:
        raise Exception('Data path (' + data_folder + ') exists as a file. '
                        'Please rename, remove or change the desired location of the data path.')

    # Check if the file exists already
    if(not os.path.isfile(data_folder+'/go-basic.obo')):
        try:
            handle = openURL(go_obo_url)
        except Exception as err:
            LOGGER.warn('{0} download failed ({1}).'.format(
                go_obo_url, str(err)))
        else:
            data = handle.read()
            if len(data):
                filename = data_folder+'/go-basic.obo'

                with open(filename, 'w+b') as obofile:
                    obofile.write(data)

                LOGGER.debug('{0} downloaded ({1})'
                             .format(go_obo_url, sympath(filename)))
            else:
                LOGGER.warn('{0} download failed, reason unknown.'
                            .format(go_obo_url))

    else:
        go_obo = data_folder+'/go-basic.obo'

    return obo_parser.GODag(go_obo)
Example #3
0
def fetchPDB(*pdb, **kwargs):
    """Returns path(s) to PDB file(s) for specified *pdb* identifier(s).  Files
    will be sought in user specified *folder* or current working director, and
    then in local PDB folder and mirror, if they are available.  If *copy*
    is set **True**, files will be copied into *folder*.  If *compressed* is
    **False**, all files will be decompressed.  See :func:`pathPDBFolder` and
    :func:`pathPDBMirror` for managing local resources, :func:`.fetchPDBviaFTP`
    and :func:`.fetchPDBviaFTP` for downloading files from PDB servers."""

    if len(pdb) == 1 and isinstance(pdb[0], list):
        pdb = pdb[0]

    if 'format' in kwargs and kwargs.get('format') != 'pdb':
        return fetchPDBviaFTP(*pdb, **kwargs)

    identifiers = checkIdentifiers(*pdb)

    folder = kwargs.get('folder', '.')
    compressed = kwargs.get('compressed')

    # check *folder* specified by the user, usually pwd ('.')
    filedict = findPDBFiles(folder, compressed=compressed)

    filenames = []
    not_found = []
    exists = 0
    for i, pdb in enumerate(identifiers):
        if pdb is None:
            filenames.append(None)
        elif pdb in filedict:
            filenames.append(filedict[pdb])
            exists += 1
        else:
            filenames.append(None)
            not_found.append((i, pdb))

    if not not_found:
        if len(filenames) == 1:
            filenames = filenames[0]
            if exists:
                LOGGER.debug(
                    'PDB file is found in working directory ({0}).'.format(
                        sympath(filenames)))
        return filenames

    if not isWritable(folder):
        raise IOError('permission to write in {0} is denied, please '
                      'specify another folder'.format(folder))

    if compressed is not None and not compressed:
        filedict = findPDBFiles(folder, compressed=True)
        not_found, decompress = [], not_found
        for i, pdb in decompress:
            if pdb in filedict:
                fn = filedict[pdb]
                filenames[i] = gunzip(fn, splitext(fn)[0])
            else:
                not_found.append((i, pdb))

    if not not_found:
        return filenames[0] if len(identifiers) == 1 else filenames

    local_folder = pathPDBFolder()
    copy = kwargs.setdefault('copy', False)
    if local_folder:
        local_folder, is_divided = local_folder
        temp, not_found = not_found, []
        for i, pdb in temp:
            if is_divided:
                fn = join(local_folder, pdb[1:3], 'pdb' + pdb + '.pdb.gz')
            else:
                fn = join(local_folder, pdb + '.pdb.gz')
            if isfile(fn):
                if copy or not compressed and compressed is not None:
                    if compressed:
                        fn = copyFile(fn, join(folder, pdb + 'pdb.gz'))
                    else:
                        fn = gunzip(fn, join(folder, pdb + '.pdb'))
                filenames[i] = normpath(fn)
            else:
                not_found.append((i, pdb))

    if not not_found:
        if len(identifiers) == 1:
            fn = filenames[0]
            items = fn.split(pathsep)
            if len(items) > 5:
                fndisp = pathsep.join(items[:3] + ['...'] + items[-1:])
            else:
                fndisp = relpath(fn)
            LOGGER.debug(
                'PDB file is found in the local folder ({0}).'.format(fndisp))
            return fn
        else:
            return filenames

    if kwargs['copy'] or (compressed is not None and not compressed):
        kwargs['folder'] = folder

    downloads = [pdb for i, pdb in not_found]
    fns = None

    try:
        fns = fetchPDBfromMirror(*downloads, **kwargs)
    except IOError:
        pass
    else:
        if len(downloads) == 1: fns = [fns]
        temp, not_found = not_found, []
        for i, fn in enumerate(fns):
            if fn is None:
                not_found.append(temp[i])
            else:
                i, _ = temp[i]
                filenames[i] = fn

    if not not_found:
        return filenames[0] if len(identifiers) == 1 else filenames

    if fns:
        downloads = [pdb for i, pdb in not_found]

    fns = None

    tp = kwargs.pop('tp', None)
    if tp is not None:
        tp = tp.lower()

    if tp == 'http':
        try:
            fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
        except Exception as err:
            LOGGER.warn('Downloading PDB files via HTTP failed '
                        '({0}).'.format(str(err)))
    elif tp == 'ftp':
        try:
            fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
        except Exception as err:
            LOGGER.warn('Downloading PDB files via FTP failed '
                        '({0}).'.format(str(err)))
    else:
        tryHTTP = False
        try:
            fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
        except Exception as err:
            tryHTTP = True

        if fns is None or isinstance(fns, list) and None in fns:
            tryHTTP = True
        elif isinstance(fns, list):
            downloads = [
                not_found[i][1] for i in range(len(fns)) if fns[i] is None
            ]
            if len(downloads) > 0:
                tryHTTP = True
        if tryHTTP:
            LOGGER.info('Downloading PDB files via FTP failed, '
                        'trying HTTP.')
            try:
                fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
            except Exception as err:
                LOGGER.warn('Downloading PDB files via HTTP also failed '
                            '({0}).'.format(str(err)))

    if len(downloads) == 1: fns = [fns]
    if fns:
        for i, fn in zip([i for i, pdb in not_found], fns):
            filenames[i] = fn

    return filenames[0] if len(identifiers) == 1 else filenames
Example #4
0
def fetchPDBfromMirror(*pdb, **kwargs):
    """Returns path(s) to PDB (default), PDBML, or mmCIF file(s) for specified
    *pdb* identifier(s).  If a *folder* is specified, files will be copied
    into this folder.  If *compressed* is **False**, files will decompressed.
    *format* argument can be used to get `PDBML <http://pdbml.pdb.org/>`_ and
    `mmCIF <http://mmcif.pdb.org/>`_ files: ``format='cif'`` will fetch an
    mmCIF file, and ``format='xml'`` will fetch a PDBML file.  If PDBML header
    file is desired, ``noatom=True`` argument will do the job."""

    mirror = pathPDBMirror()
    if mirror is None:
        raise IOError('no mirror path is set')

    try:
        mirror, mirror_format = mirror
    except ValueError:
        mirror_format = None

    format = str(kwargs.pop('format', 'pdb')).lower()

    if kwargs.get('check', True):
        identifiers = checkIdentifiers(*pdb)
    else:
        identifiers = list(pdb)

    if format == 'pdb':
        ftp_divided = 'data/structures/divided/pdb'
        ftp_pdbext = '.ent.gz'
        ftp_prefix = 'pdb'
        extension = '.pdb'
    elif format == 'xml':
        if bool(kwargs.pop('noatom', False)):
            ftp_divided = 'data/structures/divided/XML-noatom'
            ftp_pdbext = '-noatom.xml.gz'
            extension = '-noatom.xml'
        else:
            ftp_divided = 'data/structures/divided/XML'
            ftp_pdbext = '.xml.gz'
            extension = '.xml'
        ftp_prefix = ''
    elif format == 'cif':
        ftp_divided = 'data/structures/divided/mmCIF'
        ftp_pdbext = '.cif.gz'
        ftp_prefix = ''
        extension = '.cif'
    else:
        if format:
            raise ValueError('{0} is not a recognized format'.format(
                repr(format)))
        else:
            raise ValueError('please specify a valid format')

    if mirror_format:
        if mirror_format.lower() != format:
            raise IOError('mirror contains only ' + mirror_format + ' files')
        ftp_divided = ''
    else:
        ftp_divided = join(*ftp_divided.split('/'))
    folder = kwargs.get('folder')
    compressed = kwargs.get('compressed', True)
    filenames = []
    append = filenames.append
    success = 0
    failure = 0
    for pdb in identifiers:
        if pdb is None:
            append(None)
            continue
        fn = join(mirror, ftp_divided, pdb[1:3], ftp_prefix + pdb + ftp_pdbext)
        if isfile(fn):
            if folder or not compressed:
                if compressed:
                    fn = copyFile(fn,
                                  join(folder or '.', pdb + extension + '.gz'))
                else:
                    fn = gunzip(fn, join(folder or '.', pdb + extension))
            append(normpath(fn))
            success += 1
        else:
            append(None)
            failure += 1

    if len(identifiers) == 1:
        fn = filenames[0]
        if success:
            LOGGER.debug('PDB file is found in the local mirror ({0}).'.format(
                sympath(fn)))
        return fn
    else:
        LOGGER.debug('PDB files found in the local mirror ({0} found, '
                     '{1} missed).'.format(success, failure))
        return filenames
Example #5
0
def fetchPDB(*pdb, **kwargs):
    """Returns path(s) to PDB file(s) for specified *pdb* identifier(s).  Files
    will be sought in user specified *folder* or current working director, and
    then in local PDB folder and mirror, if they are available.  If *copy*
    is set **True**, files will be copied into *folder*.  If *compressed* is
    **False**, all files will be decompressed.  See :func:`pathPDBFolder` and
    :func:`pathPDBMirror` for managing local resources, :func:`.fetchPDBviaFTP`
    and :func:`.fetchPDBviaFTP` for downloading files from PDB servers."""

    if len(pdb) == 1 and isinstance(pdb[0], list):
        pdb = pdb[0]

    if 'format' in kwargs and kwargs.get('format') != 'pdb':
        return fetchPDBviaFTP(*pdb, **kwargs)

    identifiers = checkIdentifiers(*pdb)

    folder = kwargs.get('folder', '.')
    compressed = kwargs.get('compressed')

    # check *folder* specified by the user, usually pwd ('.')
    filedict = findPDBFiles(folder, compressed=compressed)

    filenames = []
    not_found = []
    exists = 0
    for i, pdb in enumerate(identifiers):
        if pdb is None:
            filenames.append(None)
        elif pdb in filedict:
            filenames.append(filedict[pdb])
            exists += 1
        else:
            filenames.append(None)
            not_found.append((i, pdb))

    if not not_found:
        if len(filenames) == 1:
            filenames = filenames[0]
            if exists:
                LOGGER.debug('PDB file is found in working directory ({0}).'
                             .format(sympath(filenames)))
        return filenames

    if not isWritable(folder):
        raise IOError('permission to write in {0} is denied, please '
                      'specify another folder'.format(folder))

    if compressed is not None and not compressed:
        filedict = findPDBFiles(folder, compressed=True)
        not_found, decompress = [], not_found
        for i, pdb in decompress:
            if pdb in filedict:
                fn = filedict[pdb]
                filenames[i] = gunzip(fn, splitext(fn)[0])
            else:
                not_found.append((i, pdb))

    if not not_found:
        return filenames[0] if len(identifiers) == 1 else filenames

    local_folder = pathPDBFolder()
    copy = kwargs.setdefault('copy', False)
    if local_folder:
        local_folder, is_divided = local_folder
        temp, not_found = not_found, []
        for i, pdb in temp:
            if is_divided:
                fn = join(local_folder, pdb[1:3], 'pdb' + pdb + '.pdb.gz')
            else:
                fn = join(local_folder, pdb + '.pdb.gz')
            if isfile(fn):
                if copy or not compressed and compressed is not None:
                    if compressed:
                        fn = copyFile(fn, join(folder, pdb + 'pdb.gz'))
                    else:
                        fn = gunzip(fn, join(folder, pdb + '.pdb'))
                filenames[i] = normpath(fn)
            else:
                not_found.append((i, pdb))

    if not not_found:
        if len(identifiers) == 1:
            fn = filenames[0]
            if kwargs.get('report', True):
                items = fn.split(pathsep)
                if len(items) > 5:
                    fndisp = pathsep.join(items[:3] + ['...'] + items[-1:])
                else:
                    fndisp = relpath(fn)
                LOGGER.debug('PDB file is found in the local folder ({0}).'
                             .format(fndisp))
            return fn
        else:
            return filenames

    if kwargs['copy'] or (compressed is not None and not compressed):
        kwargs['folder'] = folder

    downloads = [pdb for i, pdb in not_found]
    fns = None

    try:
        fns = fetchPDBfromMirror(*downloads, **kwargs)
    except IOError:
        pass
    else:
        if len(downloads) == 1: fns = [fns]
        temp, not_found = not_found, []
        for i, fn in enumerate(fns):
            if fn is None:
                not_found.append(temp[i])
            else:
                i, _ = temp[i]
                filenames[i] = fn

    if not not_found:
        return filenames[0] if len(identifiers) == 1 else filenames

    if fns:
        downloads = [pdb for i, pdb in not_found]
    fns = None
    try:
        fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
    except Exception as err:
        LOGGER.warn('Downloading PDB files via FTP failed ({0}), '
                    'trying HTTP.'.format(str(err)))
        try:
            fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
        except Exception as err:
            LOGGER.warn('Downloading PDB files via HTTP also failed '
                        '({0}).'.format(str(err)))
    if len(downloads) == 1: fns = [fns]
    if fns:
        for i, fn in zip([i for i, pdb in not_found], fns):
            filenames[i] = fn

    return filenames[0] if len(identifiers) == 1 else filenames
Example #6
0
def fetchPDBfromMirror(*pdb, **kwargs):
    """Returns path(s) to PDB (default), PDBML, or mmCIF file(s) for specified
    *pdb* identifier(s).  If a *folder* is specified, files will be copied
    into this folder.  If *compressed* is **False**, files will decompressed.
    *format* argument can be used to get `PDBML <http://pdbml.pdb.org/>`_ and
    `mmCIF <http://mmcif.pdb.org/>`_ files: ``format='cif'`` will fetch an
    mmCIF file, and ``format='xml'`` will fetch a PDBML file.  If PDBML header
    file is desired, ``noatom=True`` argument will do the job."""

    mirror = pathPDBMirror()
    if mirror is None:
        raise IOError('no mirror path is set')


    try:
        mirror, mirror_format = mirror
    except ValueError:
        mirror_format = None

    format = str(kwargs.pop('format', 'pdb')).lower()

    if kwargs.get('check', True):
        identifiers = checkIdentifiers(*pdb)
    else:
        identifiers = list(pdb)

    if format == 'pdb':
        ftp_divided = 'data/structures/divided/pdb'
        ftp_pdbext = '.ent.gz'
        ftp_prefix = 'pdb'
        extension = '.pdb'
    elif format == 'xml':
        if bool(kwargs.pop('noatom', False)):
            ftp_divided = 'data/structures/divided/XML-noatom'
            ftp_pdbext = '-noatom.xml.gz'
            extension = '-noatom.xml'
        else:
            ftp_divided = 'data/structures/divided/XML'
            ftp_pdbext = '.xml.gz'
            extension = '.xml'
        ftp_prefix = ''
    elif format == 'cif':
        ftp_divided = 'data/structures/divided/mmCIF'
        ftp_pdbext = '.cif.gz'
        ftp_prefix = ''
        extension = '.cif'
    else:
        if format:
            raise ValueError('{0} is not a recognized format'
                             .format(repr(format)))
        else:
            raise ValueError('please specify a valid format')

    if mirror_format:
        if mirror_format.lower() != format:
            raise IOError('mirror contains only ' + mirror_format + ' files')
        ftp_divided = ''
    else:
        ftp_divided = join(*ftp_divided.split('/'))
    folder = kwargs.get('folder')
    compressed = kwargs.get('compressed', True)
    filenames = []
    append = filenames.append
    success = 0
    failure = 0
    for pdb in identifiers:
        if pdb is None:
            append(None)
            continue
        fn = join(mirror, ftp_divided, pdb[1:3],
                  ftp_prefix + pdb + ftp_pdbext)
        if isfile(fn):
            if folder or not compressed:
                if compressed:
                    fn = copyFile(fn, join(folder or '.',
                                             pdb + extension + '.gz'))
                else:
                    fn = gunzip(fn, join(folder or '.', pdb + extension))
            append(normpath(fn))
            success += 1
        else:
            append(None)
            failure += 1

    if len(identifiers) == 1:
        fn = filenames[0]
        if kwargs.get('report', True):
            if success:
                LOGGER.debug('PDB file is found in the local mirror ({0}).'
                             .format(sympath(fn)))
        return fn
    else:
        if kwargs.get('report', True):
            LOGGER.debug('PDB files found in the local mirror ({0} found, '
                         '{1} missed).'.format(success, failure))
        return filenames
Example #7
0
def fetchPDBviaHTTP(*pdb, **kwargs):
    """Retrieve PDB file(s) for specified *pdb* identifier(s) and return
    path(s).  Downloaded files will be stored in local PDB folder, if one
    is set using :meth:`.pathPDBFolder`, and copied into *folder*, if
    specified by the user.  If no destination folder is specified, files
    will be saved in the current working directory.  If *compressed* is
    **False**, decompressed files will be copied into *folder*."""

    if kwargs.get('check', True):
        identifiers = checkIdentifiers(*pdb)
    else:
        identifiers = list(pdb)

    output_folder = kwargs.pop('folder', None)
    compressed = bool(kwargs.pop('compressed', True))

    extension = '.pdb'
    local_folder = pathPDBFolder()
    if local_folder:
        local_folder, is_divided = local_folder
        if is_divided:
            getPath = lambda pdb: join(makePath(join(local_folder, pdb[1:3])),
                                       'pdb' + pdb + '.pdb.gz')
        else:
            getPath = lambda pdb: join(local_folder, pdb + '.pdb.gz')
        if output_folder is None:
            second = lambda filename, pdb: filename
        else:
            if compressed:
                second = lambda filename, pdb: (copyFile(filename,
                            join(output_folder, pdb + extension + '.gz')))
            else:
                second = lambda filename, pdb: gunzip(filename,
                            join(output_folder, pdb + extension))

    else:
        if output_folder is None:
            output_folder = getcwd()
        if compressed:
            getPath = lambda pdb: join(output_folder, pdb + extension + '.gz')
            second = lambda filename, pdb: filename
        else:
            getPath = lambda pdb: join(output_folder, pdb + extension)
            second = lambda filename, pdb: gunzip(getPath(pdb), getPath(pdb))


    getURL = WWPDB_HTTP_URL[wwPDBServer() or 'us']

    success = 0
    failure = 0
    filenames = []
    for pdb in identifiers:
        if pdb is None:
            filenames.append(None)
            continue
        try:
            handle = openURL(getURL(pdb))
        except Exception as err:
            LOGGER.warn('{0} download failed ({1}).'.format(pdb, str(err)))
            failure += 1
            filenames.append(None)
        else:
            data = handle.read()
            if len(data):
                filename = getPath(pdb)

                with open(filename, 'w+b') as pdbfile:
                    pdbfile.write(data)

                filename = normpath(relpath(second(filename, pdb)))
                LOGGER.debug('{0} downloaded ({1})'
                             .format(pdb, sympath(filename)))
                success += 1
                filenames.append(filename)
            else:
                LOGGER.warn('{0} download failed, reason unknown.'
                            .format(pdb))
                failure += 1
                filenames.append(None)
    LOGGER.debug('PDB download via HTTP completed ({0} downloaded, '
                 '{1} failed).'.format(success, failure))
    if len(identifiers) == 1:
        return filenames[0]
    else:
        return filenames
Example #8
0
def fetchPDBviaFTP(*pdb, **kwargs):
    """Retrieve PDB (default), PDBML, mmCIF, or EMD file(s) for specified *pdb*
    identifier(s) and return path(s).  Downloaded files will be stored in
    local PDB folder, if one is set using :meth:`.pathPDBFolder`, and copied
    into *folder*, if specified by the user.  If no destination folder is
    specified, files will be saved in the current working directory.  If
    *compressed* is **False**, decompressed files will be copied into
    *folder*.  *format* keyword argument can be used to retrieve
    `PDBML <http://pdbml.pdb.org/>`_, `mmCIF <http://mmcif.pdb.org/>`_
    and `PDBML <ftp://ftp.wwpdb.org/pub/emdb/doc/Map-format/current/EMDB_map_format.pdf>`_ 
    files: ``format='cif'`` will fetch an mmCIF file, ``format='emd'`` will fetch an EMD file,
    and ``format='xml'`` will fetch a PDBML file. 
    If PDBML header file is desired, ``noatom=True`` argument will do the job."""

    if kwargs.get('check', True):
        identifiers = checkIdentifiers(*pdb)
    else:
        identifiers = list(pdb)

    output_folder = kwargs.pop('folder', None)
    compressed = bool(kwargs.pop('compressed', True))
    format = str(kwargs.pop('format', 'pdb')).lower()
    noatom = bool(kwargs.pop('noatom', False))

    if format == 'pdb':
        ftp_divided = 'pdb/data/structures/divided/pdb'
        ftp_pdbext = '.ent.gz'
        ftp_prefix = 'pdb'
        extension = '.pdb'
    elif format == 'xml':
        if noatom:
            ftp_divided = 'pdb/data/structures/divided/XML-noatom'
            ftp_pdbext = '-noatom.xml.gz'
            extension = '-noatom.xml'
        else:
            ftp_divided = 'pdb/data/structures/divided/XML'
            ftp_pdbext = '.xml.gz'
            extension = '.xml'
        ftp_prefix = ''
    elif format == 'cif':
        ftp_divided = 'pdb/data/structures/divided/mmCIF'
        ftp_pdbext = '.cif.gz'
        ftp_prefix = ''
        extension = '.cif'
    elif format == 'emd' or format == 'map':
        ftp_divided = 'emdb/structures'
        ftp_pdbext = '.map.gz'
        ftp_prefix = 'emd_'
        extension = '.map'
    else:
        raise ValueError(repr(format) + ' is not valid format')

    local_folder = pathPDBFolder()

    if format == 'pdb' and local_folder:
        local_folder, is_divided = local_folder
        if is_divided:
            getPath = lambda pdb: join(makePath(join(local_folder, pdb[1:3])),
                                       'pdb' + pdb + '.pdb.gz')
        else:
            getPath = lambda pdb: join(local_folder, pdb + '.pdb.gz')
        if output_folder is None:
            second = lambda filename, pdb: filename
        else:
            if compressed:
                second = lambda filename, pdb: (copyFile(filename,
                            join(output_folder, pdb + extension + '.gz')))
            else:
                second = lambda filename, pdb: gunzip(filename,
                            join(output_folder, pdb + extension))

    else:
        if output_folder is None:
            output_folder = getcwd()
        if compressed:
            getPath = lambda pdb: join(output_folder, pdb + extension + '.gz')
            second = lambda filename, pdb: filename
        else:
            getPath = lambda pdb: join(output_folder, pdb + extension)
            second = lambda filename, pdb: gunzip(getPath(pdb), getPath(pdb))


    ftp_name, ftp_host, ftp_path = WWPDB_FTP_SERVERS[wwPDBServer() or 'us']
    LOGGER.debug('Connecting wwPDB FTP server {0}.'.format(ftp_name))

    from ftplib import FTP
    try:
        ftp = FTP(ftp_host)
    except Exception as error:
        raise type(error)('FTP connection problem, potential reason: '
                          'no internet connectivity')
    else:
        success = 0
        failure = 0
        filenames = []
        ftp.login('')
        for pdb in identifiers:
            if pdb is None:
                filenames.append(None)
                continue
            data = []
            ftp_fn = ftp_prefix + pdb + ftp_pdbext
            try:
                ftp.cwd(ftp_path)
                ftp.cwd(ftp_divided)
                if format == 'emd':
                    ftp.cwd('EMD-{0}/map'.format(pdb))
                else:
                    ftp.cwd(pdb[1:3])
                ftp.retrbinary('RETR ' + ftp_fn, data.append)
            except Exception as error:
                if ftp_fn in ftp.nlst():
                    LOGGER.warn('{0} download failed ({1}). It is '
                                'possible that you do not have rights to '
                                'download .gz files in the current network.'
                                .format(pdb, str(error)))
                else:
                    LOGGER.info('{0} download failed. {1} does not exist '
                                'on {2}.'.format(ftp_fn, pdb, ftp_host))
                failure += 1
                filenames.append(None)
            else:
                if len(data):
                    filename = getPath(pdb)

                    with open(filename, 'w+b') as pdbfile:
                        write = pdbfile.write
                        [write(block) for block in data]

                    filename = normpath(relpath(second(filename, pdb)))
                    LOGGER.debug('{0} downloaded ({1})'
                                 .format(pdb, sympath(filename)))
                    success += 1
                    filenames.append(filename)
                else:
                    LOGGER.warn('{0} download failed, reason unknown.'
                                .format(pdb))
                    failure += 1
                    filenames.append(None)

        ftp.quit()

    LOGGER.debug('PDB download via FTP completed ({0} downloaded, '
                 '{1} failed).'.format(success, failure))
    if len(identifiers) == 1:
        return filenames[0]
    else:
        return filenames