How to use pyEMMA - 10 common examples

itraj : int
            trajectory index
        stride : int
            return value is the number of frames in the trajectory when
            running through it with a step size of `stride`.
        skip: int or None
            skip n frames.

        Returns
        -------
        int : length of trajectory
        """
        if itraj >= self.ntraj:
            raise IndexError("given index (%s) exceeds number of data sets (%s)."
                             " Zero based indexing!" % (itraj, self.ntraj))
        if not IteratorState.is_uniform_stride(stride):
            selection = stride[stride[:, 0] == itraj][:, 0]
            return 0 if itraj not in selection else len(selection)
        else:
            res = max((self._lengths[itraj] - skip - 1) // int(stride) + 1, 0)
            return res

xtcs.append(these_trajs)
            if struct is None:
                struct = '%s-%u-protein.pdb'%(proj,ii)
                struct_already = True
                struct = os.path.join(subdir, struct)
                struct = sorted(glob(struct))

            elif isinstance(struct, str) and not struct_already:
                struct = os.path.join(subdir,struct)
                struct = sorted(glob(struct))

            if isinstance(struct,list):
                struct=struct[0]
            ii += 1

    src = _source(xtcs, top=struct)

    return src, xtcs

def loadclass(module_and_name):
    """Loads the module and returns the class.

    >>> cls = loadclass('datetime.datetime')
    >>> cls.__name__
    'datetime'

    >>> loadclass('does.not.exist')

    >>> loadclass('__builtin__.int')()
    0

    """
    try:
        module, name = module_and_name.rsplit('.', 1)
        module = util.untranslate_module_name(module)
        __import__(module)
        return getattr(sys.modules[module], name)
    except:
        return None

def partial_fit(self, X):
        """ incrementally update the estimates

        Parameters
        ----------
        X: array, list of arrays, PyEMMA reader
            input data.
        """
        from pyemma.coordinates import source

        self._estimate(source(X), partial_fit=True)
        self._estimated = True

        return self

def _resolve(self):
        module = _import_module(self.mod)
        return getattr(module, self.attr)


class _MovedItems(types.ModuleType):
    """Lazy loading of moved objects"""


_moved_attributes = [
    MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
    MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
    MovedAttribute("filterfalse", "itertools", "itertools", "ifilterfalse", "filterfalse"),
    MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
    MovedAttribute("map", "itertools", "builtins", "imap", "map"),
    MovedAttribute("range", "__builtin__", "builtins", "xrange", "range"),
    MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
    MovedAttribute("reduce", "__builtin__", "functools"),
    MovedAttribute("StringIO", "StringIO", "io"),
    MovedAttribute("UserString", "UserString", "collections"),
    MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
    MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
    MovedAttribute("zip_longest", "itertools", "itertools", "izip_longest", "zip_longest"),

    MovedModule("builtins", "__builtin__"),
    MovedModule("configparser", "ConfigParser"),
    MovedModule("copyreg", "copy_reg"),
    MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
    MovedModule("http_cookies", "Cookie", "http.cookies"),
    MovedModule("html_entities", "htmlentitydefs", "html.entities"),
    MovedModule("html_parser", "HTMLParser", "html.parser"),

]
for attr in _moved_attributes:
    setattr(_MovedItems, attr.name, attr)
del attr

moves = sys.modules[__name__ + ".moves"] = _MovedItems(__name__ + ".moves")


class Module_six_moves_urllib_parse(types.ModuleType):
    """Lazy loading of moved objects in six.moves.urllib_parse"""


_urllib_parse_moved_attributes = [
    MovedAttribute("ParseResult", "urlparse", "urllib.parse"),
    MovedAttribute("parse_qs", "urlparse", "urllib.parse"),
    MovedAttribute("parse_qsl", "urlparse", "urllib.parse"),
    MovedAttribute("urldefrag", "urlparse", "urllib.parse"),
    MovedAttribute("urljoin", "urlparse", "urllib.parse"),
    MovedAttribute("urlparse", "urlparse", "urllib.parse"),
    MovedAttribute("urlsplit", "urlparse", "urllib.parse"),
    MovedAttribute("urlunparse", "urlparse", "urllib.parse"),
    MovedAttribute("urlunsplit", "urlparse", "urllib.parse"),
    MovedAttribute("quote", "urllib", "urllib.parse"),
    MovedAttribute("quote_plus", "urllib", "urllib.parse"),
    MovedAttribute("unquote", "urllib", "urllib.parse"),
    MovedAttribute("unquote_plus", "urllib", "urllib.parse"),
    MovedAttribute("urlencode", "urllib", "urllib.parse"),
]
for attr in _urllib_parse_moved_attributes:
    setattr(Module_six_moves_urllib_parse, attr.name, attr)
del attr

MovedAttribute("HTTPPasswordMgr", "urllib2", "urllib.request"),
    MovedAttribute("HTTPPasswordMgrWithDefaultRealm", "urllib2", "urllib.request"),
    MovedAttribute("AbstractBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("AbstractDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPSHandler", "urllib2", "urllib.request"),
    MovedAttribute("FileHandler", "urllib2", "urllib.request"),
    MovedAttribute("FTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("CacheFTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("UnknownHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPErrorProcessor", "urllib2", "urllib.request"),
    MovedAttribute("urlretrieve", "urllib", "urllib.request"),
    MovedAttribute("urlcleanup", "urllib", "urllib.request"),
    MovedAttribute("URLopener", "urllib", "urllib.request"),
    MovedAttribute("FancyURLopener", "urllib", "urllib.request"),
]
for attr in _urllib_request_moved_attributes:
    setattr(Module_six_moves_urllib_request, attr.name, attr)
del attr

sys.modules[__name__ + ".moves.urllib_request"] = Module_six_moves_urllib_request(__name__ + ".moves.urllib_request")
sys.modules[__name__ + ".moves.urllib.request"] = Module_six_moves_urllib_request(__name__ + ".moves.urllib.request")


class Module_six_moves_urllib_response(types.ModuleType):
    """Lazy loading of moved objects in six.moves.urllib_response"""

_urllib_parse_moved_attributes = [
    MovedAttribute("ParseResult", "urlparse", "urllib.parse"),
    MovedAttribute("parse_qs", "urlparse", "urllib.parse"),
    MovedAttribute("parse_qsl", "urlparse", "urllib.parse"),
    MovedAttribute("urldefrag", "urlparse", "urllib.parse"),
    MovedAttribute("urljoin", "urlparse", "urllib.parse"),
    MovedAttribute("urlparse", "urlparse", "urllib.parse"),
    MovedAttribute("urlsplit", "urlparse", "urllib.parse"),
    MovedAttribute("urlunparse", "urlparse", "urllib.parse"),
    MovedAttribute("urlunsplit", "urlparse", "urllib.parse"),
    MovedAttribute("quote", "urllib", "urllib.parse"),
    MovedAttribute("quote_plus", "urllib", "urllib.parse"),
    MovedAttribute("unquote", "urllib", "urllib.parse"),
    MovedAttribute("unquote_plus", "urllib", "urllib.parse"),
    MovedAttribute("urlencode", "urllib", "urllib.parse"),
]
for attr in _urllib_parse_moved_attributes:
    setattr(Module_six_moves_urllib_parse, attr.name, attr)
del attr

sys.modules[__name__ + ".moves.urllib_parse"] = Module_six_moves_urllib_parse(__name__ + ".moves.urllib_parse")
sys.modules[__name__ + ".moves.urllib.parse"] = Module_six_moves_urllib_parse(__name__ + ".moves.urllib.parse")


class Module_six_moves_urllib_error(types.ModuleType):
    """Lazy loading of moved objects in six.moves.urllib_error"""


_urllib_error_moved_attributes = [
    MovedAttribute("URLError", "urllib2", "urllib.error"),

MovedAttribute("HTTPRedirectHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPCookieProcessor", "urllib2", "urllib.request"),
    MovedAttribute("ProxyHandler", "urllib2", "urllib.request"),
    MovedAttribute("BaseHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPPasswordMgr", "urllib2", "urllib.request"),
    MovedAttribute("HTTPPasswordMgrWithDefaultRealm", "urllib2", "urllib.request"),
    MovedAttribute("AbstractBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("AbstractDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPSHandler", "urllib2", "urllib.request"),
    MovedAttribute("FileHandler", "urllib2", "urllib.request"),
    MovedAttribute("FTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("CacheFTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("UnknownHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPErrorProcessor", "urllib2", "urllib.request"),
    MovedAttribute("urlretrieve", "urllib", "urllib.request"),
    MovedAttribute("urlcleanup", "urllib", "urllib.request"),
    MovedAttribute("URLopener", "urllib", "urllib.request"),
    MovedAttribute("FancyURLopener", "urllib", "urllib.request"),
]
for attr in _urllib_request_moved_attributes:
    setattr(Module_six_moves_urllib_request, attr.name, attr)
del attr

sys.modules[__name__ + ".moves.urllib_request"] = Module_six_moves_urllib_request(__name__ + ".moves.urllib_request")
sys.modules[__name__ + ".moves.urllib.request"] = Module_six_moves_urllib_request(__name__ + ".moves.urllib.request")

MovedAttribute("Request", "urllib2", "urllib.request"),
    MovedAttribute("OpenerDirector", "urllib2", "urllib.request"),
    MovedAttribute("HTTPDefaultErrorHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPRedirectHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPCookieProcessor", "urllib2", "urllib.request"),
    MovedAttribute("ProxyHandler", "urllib2", "urllib.request"),
    MovedAttribute("BaseHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPPasswordMgr", "urllib2", "urllib.request"),
    MovedAttribute("HTTPPasswordMgrWithDefaultRealm", "urllib2", "urllib.request"),
    MovedAttribute("AbstractBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyBasicAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("AbstractDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("ProxyDigestAuthHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPSHandler", "urllib2", "urllib.request"),
    MovedAttribute("FileHandler", "urllib2", "urllib.request"),
    MovedAttribute("FTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("CacheFTPHandler", "urllib2", "urllib.request"),
    MovedAttribute("UnknownHandler", "urllib2", "urllib.request"),
    MovedAttribute("HTTPErrorProcessor", "urllib2", "urllib.request"),
    MovedAttribute("urlretrieve", "urllib", "urllib.request"),
    MovedAttribute("urlcleanup", "urllib", "urllib.request"),
    MovedAttribute("URLopener", "urllib", "urllib.request"),
    MovedAttribute("FancyURLopener", "urllib", "urllib.request"),
]
for attr in _urllib_request_moved_attributes:
    setattr(Module_six_moves_urllib_request, attr.name, attr)
del attr

sys.modules[__name__ + ".moves.urllib_request"] = Module_six_moves_urllib_request(__name__ + ".moves.urllib_request")