Code stringlengths 103 85.9k | Summary listlengths 0 94 |
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Please provide a description of the function:def requires_user(fn):
@functools.wraps(fn)
def wrap(*args, **kwargs):
subject = Yosai.get_current_subject()
if subject.identifiers is None:
msg = ("Attempting to perform a user-only operation. The "
... | [
"\n Requires that the calling Subject be *either* authenticated *or* remembered\n via RememberMe services before allowing access.\n\n This method essentially ensures that subject.identifiers IS NOT None\n\n :raises UnauthenticatedException: indicating that the decorated method is\n ... |
Please provide a description of the function:def requires_permission(permission_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
subject = Yosai.get_current_subject()
subject.check_permission(per... | [
"\n Requires that the calling Subject be authorized to the extent that is\n required to satisfy the permission_s specified and the logical operation\n upon them.\n\n :param permission_s: the permission(s) required\n :type permission_s: a List of Strings or List of Permission in... |
Please provide a description of the function:def requires_dynamic_permission(permission_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
newperms = [perm.format(**kwargs) for perm in permission_s]
... | [
"\n This method requires that the calling Subject be authorized to the extent\n that is required to satisfy the dynamic permission_s specified and the logical\n operation upon them. Unlike ``requires_permission``, which uses statically\n defined permissions, this function derives a perm... |
Please provide a description of the function:def requires_role(role_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
subject = Yosai.get_current_subject()
subject.check_role(role_s, logical_oper... | [
"\n Requires that the calling Subject be authorized to the extent that is\n required to satisfy the role_s specified and the logical operation\n upon them.\n\n :param role_s: a collection of the role(s) required, specified by\n identifiers (such as a role name... |
Please provide a description of the function:def create_manager(self, yosai, settings, session_attributes):
mgr_settings = SecurityManagerSettings(settings)
attributes = mgr_settings.attributes
realms = self._init_realms(settings, attributes['realms'])
session_attributes = sel... | [
"\n Order of execution matters. The sac must be set before the cache_handler is\n instantiated so that the cache_handler's serialization manager instance\n registers the sac.\n "
] |
Please provide a description of the function:def resolve_realms(self, attributes):
realms = []
for realm, realm_attributes in attributes['realms'].items():
realm_cls = maybe_resolve(realm)
account_store_cls = maybe_resolve(realm_attributes['account_store'])
... | [
"\n The format of realm settings is:\n {'name_of_realm':\n {'cls': 'location to realm class',\n 'account_store': 'location to realm account_store class'}}\n\n - 'name of realm' is a label used for internal tracking\n - 'cls' and 'account_store' ... |
Please provide a description of the function:def init_realms(self, realms):
# this eliminates the need for an authorizing_realms attribute:
self.realms = tuple(realm for realm in realms
if isinstance(realm, realm_abcs.AuthorizingRealm))
self.register_cache_cl... | [
"\n :type realms: tuple\n "
] |
Please provide a description of the function:def _has_role(self, identifiers, role_s):
for realm in self.realms:
# the realm's has_role returns a generator
yield from realm.has_role(identifiers, role_s) | [
"\n :type identifiers: subject_abcs.IdentifierCollection\n :type role_s: Set of String(s)\n "
] |
Please provide a description of the function:def _is_permitted(self, identifiers, permission_s):
for realm in self.realms:
# the realm's is_permitted returns a generator
yield from realm.is_permitted(identifiers, permission_s) | [
"\n :type identifiers: subject_abcs.IdentifierCollection\n\n :param permission_s: a collection of 1..N permissions\n :type permission_s: List of permission string(s)\n "
] |
Please provide a description of the function:def is_permitted(self, identifiers, permission_s, log_results=True):
self.assert_realms_configured()
results = collections.defaultdict(bool) # defaults to False
is_permitted_results = self._is_permitted(identifiers, permission_s)
... | [
"\n Yosai differs from Shiro in how it handles String-typed Permission\n parameters. Rather than supporting *args of String-typed Permissions,\n Yosai supports a list of Strings. Yosai remains true to Shiro's API\n while determining permissions a bit more pythonically. This may\n ... |
Please provide a description of the function:def is_permitted_collective(self, identifiers,
permission_s, logical_operator):
self.assert_realms_configured()
# interim_results is a set of tuples:
interim_results = self.is_permitted(identifiers, permission... | [
"\n :param identifiers: a collection of Identifier objects\n :type identifiers: subject_abcs.IdentifierCollection\n\n :param permission_s: a collection of 1..N permissions\n :type permission_s: List of Permission object(s) or String(s)\n\n :param logical_operator: indicates whet... |
Please provide a description of the function:def check_permission(self, identifiers, permission_s, logical_operator):
self.assert_realms_configured()
permitted = self.is_permitted_collective(identifiers,
permission_s,
... | [
"\n like Yosai's authentication process, the authorization process will\n raise an Exception to halt further authz checking once Yosai determines\n that a Subject is unauthorized to receive the requested permission\n\n :param identifiers: a collection of identifiers\n :type identi... |
Please provide a description of the function:def has_role(self, identifiers, role_s, log_results=True):
self.assert_realms_configured()
results = collections.defaultdict(bool) # defaults to False
for role, has_role in self._has_role(identifiers, role_s):
# checkrole expec... | [
"\n :param identifiers: a collection of identifiers\n :type identifiers: subject_abcs.IdentifierCollection\n\n :param role_s: a collection of 1..N Role identifiers\n :type role_s: Set of String(s)\n\n :param log_results: states whether to log results (True) or allow the\n ... |
Please provide a description of the function:def has_role_collective(self, identifiers, role_s, logical_operator):
self.assert_realms_configured()
# interim_results is a set of tuples:
interim_results = self.has_role(identifiers, role_s, log_results=False)
results = logical_op... | [
"\n :param identifiers: a collection of identifiers\n :type identifiers: subject_abcs.IdentifierCollection\n\n :param role_s: a collection of 1..N Role identifiers\n :type role_s: Set of String(s)\n\n :param logical_operator: indicates whether all or at least one\n ... |
Please provide a description of the function:def check_role(self, identifiers, role_s, logical_operator):
self.assert_realms_configured()
has_role_s = self.has_role_collective(identifiers,
role_s, logical_operator)
if not has_role_s:
... | [
"\n :param identifiers: a collection of identifiers\n :type identifiers: subject_abcs.IdentifierCollection\n\n :param role_s: 1..N role identifiers\n :type role_s: a String or Set of Strings\n\n :param logical_operator: indicates whether all or at least one\n ... |
Please provide a description of the function:def add_collection(self, identifier_collection):
try:
new_source_identifiers = identifier_collection.source_identifiers
self.source_identifiers.update(new_source_identifiers)
except AttributeError:
msg = "Invalid i... | [
"\n :type identifier_collection: a SimpleIdentifierCollection\n "
] |
Please provide a description of the function:def by_type(self, identifier_class):
myidentifiers = set()
for identifier in self.source_identifiers.values():
if (isinstance(identifier, identifier_class)):
myidentifiers.update([identifier])
return set(myidentifi... | [
"\n returns all unique instances of a type of identifier\n\n :param identifier_class: the class to match identifier with\n :returns: a tuple\n "
] |
Please provide a description of the function:def create(self, session):
sessionid = super().create(session) # calls _do_create and verify
self._cache(session, sessionid)
return sessionid | [
"\n caches the session and caches an entry to associate the cached session\n with the subject\n "
] |
Please provide a description of the function:def is_timed_out(self):
if (self.is_expired):
return True
try:
if (not self.last_access_time):
msg = ("session.last_access_time for session with id [" +
str(self.session_id) + "] is null... | [
"\n determines whether a Session has been inactive/idle for too long a time\n OR exceeds the absolute time that a Session may exist\n ",
"\n Calculate at what time a session would have been last accessed\n for it to be expired at this point. In other words, subtract\n... |
Please provide a description of the function:def _retrieve_session(self, session_key):
session_id = session_key.session_id
if (session_id is None):
msg = ("Unable to resolve session ID from SessionKey [{0}]."
"Returning null to indicate a session could not be "
... | [
"\n :type session_key: SessionKey\n :returns: SimpleSession\n "
] |
Please provide a description of the function:def do_get_session(self, session_key):
session_id = session_key.session_id
msg = ("do_get_session: Attempting to retrieve session with key " +
str(session_id))
logger.debug(msg)
session = self._retrieve_session(session... | [
"\n :type session_key: SessionKey\n :returns: SimpleSession\n "
] |
Please provide a description of the function:def on_expiration(self, session, expired_session_exception=None,
session_key=None):
if (expired_session_exception and session_key):
try:
self.on_change(session)
msg = "Session with id [{0}] ha... | [
"\n This method overloaded for now (java port). TBD\n Two possible scenarios supported:\n 1) All three arguments passed = session + ese + session_key\n 2) Only session passed as an argument\n "
] |
Please provide a description of the function:def notify_event(self, session_info, topic):
try:
self.event_bus.sendMessage(topic, items=session_info)
except AttributeError:
msg = "Could not publish {} event".format(topic)
raise AttributeError(msg) | [
"\n :type identifiers: SimpleIdentifierCollection\n "
] |
Please provide a description of the function:def start(self, session_context):
# is a SimpleSesson:
session = self._create_session(session_context)
self.session_handler.on_start(session, session_context)
mysession = session_tuple(None, session.session_id)
self.notify_e... | [
"\n unlike shiro, yosai does not apply session timeouts from within the\n start method of the SessionManager but rather defers timeout settings\n responsibilities to the SimpleSession, which uses session_settings\n "
] |
Please provide a description of the function:def create_exposed_session(self, session, key=None, context=None):
# shiro ignores key and context parameters
return DelegatingSession(self, SessionKey(session.session_id)) | [
"\n :type session: SimpleSession\n "
] |
Please provide a description of the function:def get_session(self, key):
# a SimpleSession:
session = self.session_handler.do_get_session(key)
if (session):
return self.create_exposed_session(session, key)
else:
return None | [
"\n :returns: DelegatingSession\n "
] |
Please provide a description of the function:def _lookup_required_session(self, key):
session = self.session_handler.do_get_session(key)
if (not session):
msg = ("Unable to locate required Session instance based "
"on session_key [" + str(key) + "].")
... | [
"\n :returns: SimpleSession\n "
] |
Please provide a description of the function:def set_attributes(self, session_key, attributes):
session = self._lookup_required_session(session_key)
session.set_attributes(attributes)
self.session_handler.on_change(session) | [
"\n :type attributes: dict\n "
] |
Please provide a description of the function:def remove_attributes(self, session_key, attribute_keys):
session = self._lookup_required_session(session_key)
removed = session.remove_attributes(attribute_keys)
if removed:
self.session_handler.on_change(session)
return ... | [
"\n :type attribute_keys: a list of strings\n "
] |
Please provide a description of the function:def resolve_reference(ref):
if not isinstance(ref, str) or ':' not in ref:
return ref
modulename, rest = ref.split(':', 1)
try:
obj = import_module(modulename)
except ImportError as e:
raise LookupError(
'error resolv... | [
"\n Return the object pointed to by ``ref``.\n If ``ref`` is not a string or does not contain ``:``, it is returned as is.\n References must be in the form <modulename>:<varname> where <modulename> is the fully\n qualified module name and varname is the path to the variable inside that module.\n For... |
Please provide a description of the function:def qualified_name(obj):
try:
module = obj.__module__
qualname = obj.__qualname__
except AttributeError:
type_ = type(obj)
module = type_.__module__
qualname = type_.__qualname__
return qualname if module in ('typing'... | [
"Return the qualified name (e.g. package.module.Type) for the given object."
] |
Please provide a description of the function:def add_item(session, item, quantity=1):
shopping_cart = session.get_attribute('shopping_cart')
if shopping_cart:
shopping_cart.add_item(item, quantity)
else:
shopping_cart = ShoppingCart()
shopping_cart.ad... | [
"\n :param item: a ShoppingCartItem namedtuple\n "
] |
Please provide a description of the function:def first_realm_successful_strategy(authc_attempt):
authc_token = authc_attempt.authentication_token
realm_errors = []
account = None
for realm in authc_attempt.realms:
if (realm.supports(authc_token)):
try:
account = ... | [
"\n The FirstRealmSuccessfulStrategy will iterate over the available realms\n and invoke Realm.authenticate_account(authc_token) on each one. The moment\n that a realm returns an Account without raising an Exception, that account\n is returned immediately and all subsequent realms ignored entirely\n... |
Please provide a description of the function:def _setup(self, name=None):
envvar = self.__dict__['env_var']
if envvar:
settings_file = os.environ.get(envvar)
else:
settings_file = self.__dict__['file_path']
if not settings_file:
msg = ("Reque... | [
"\n Load the settings module referenced by env_var. This environment-\n defined configuration process is called during the settings\n configuration process.\n "
] |
Please provide a description of the function:def _get_subject(self):
web_registry = WebYosai.get_current_webregistry()
subject_context = WebSubjectContext(yosai=self,
security_manager=self.security_manager,
... | [
"\n Returns the currently accessible Subject available to the calling code\n depending on runtime environment.\n\n :param web_registry: The WebRegistry instance that knows how to interact\n with the web application's request and response APIs\n\n :returns: t... |
Please provide a description of the function:def requires_authentication(fn):
@functools.wraps(fn)
def wrap(*args, **kwargs):
subject = WebYosai.get_current_subject()
if not subject.authenticated:
msg = "The current Subject is not authenticated. ACCESS... | [
"\n Requires that the calling Subject be authenticated before allowing access.\n "
] |
Please provide a description of the function:def requires_user(fn):
@functools.wraps(fn)
def wrap(*args, **kwargs):
subject = WebYosai.get_current_subject()
if subject.identifiers is None:
msg = ("Attempting to perform a user-only operation. The "
... | [
"\n Requires that the calling Subject be *either* authenticated *or* remembered\n via RememberMe services before allowing access.\n\n This method essentially ensures that subject.identifiers IS NOT None\n "
] |
Please provide a description of the function:def requires_permission(permission_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
subject = WebYosai.get_current_subject()
try:
... | [
"\n Requires that the calling Subject be authorized to the extent that is\n required to satisfy the permission_s specified and the logical operation\n upon them.\n\n :param permission_s: the permission(s) required\n :type permission_s: a List of Strings or List of Permission in... |
Please provide a description of the function:def requires_dynamic_permission(permission_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
params = WebYosai.get_current_webregistry().resource_params
... | [
"\n This method requires that the calling Subject be authorized to the extent\n that is required to satisfy the dynamic permission_s specified and the logical\n operation upon them. Unlike ``requires_permission``, which uses statically\n defined permissions, this function derives a perm... |
Please provide a description of the function:def requires_role(role_s, logical_operator=all):
def outer_wrap(fn):
@functools.wraps(fn)
def inner_wrap(*args, **kwargs):
subject = WebYosai.get_current_subject()
try:
subject.che... | [
"\n Requires that the calling Subject be authorized to the extent that is\n required to satisfy the role_s specified and the logical operation\n upon them.\n\n :param role_s: a collection of the role(s) required, specified by\n identifiers (such as a role name... |
Please provide a description of the function:def do_create_subject(self, subject_context):
if not isinstance(subject_context, web_subject_abcs.WebSubjectContext):
return super().do_create_subject(subject_context=subject_context)
security_manager = subject_context.resolve_security_m... | [
"\n By the time this method is invoked, all possible\n ``SubjectContext`` data (session, identifiers, et. al.) has been made\n accessible using all known heuristics.\n\n :returns: a Subject instance reflecting the data in the specified\n SubjectContext data map\n ... |
Please provide a description of the function:def remember_encrypted_identity(self, subject, encrypted):
try:
# base 64 encode it and store as a cookie:
encoded = base64.b64encode(encrypted).decode('utf-8')
subject.web_registry.remember_me = encoded
except Att... | [
"\n Base64-encodes the specified serialized byte array and sets that\n base64-encoded String as the cookie value.\n\n The ``subject`` instance is expected to be a ``WebSubject`` instance\n with a web_registry handle so that an HTTP cookie may be set on an\n outgoing response. If ... |
Please provide a description of the function:def get_remembered_encrypted_identity(self, subject_context):
if (self.is_identity_removed(subject_context)):
if not isinstance(subject_context, web_subject_abcs.WebSubjectContext):
msg = ("SubjectContext argument is not an HTTP-a... | [
"\n Returns a previously serialized identity byte array or None if the byte\n array could not be acquired.\n\n This implementation retrieves an HTTP cookie, Base64-decodes the cookie\n value, and returns the resulting byte array.\n\n The ``subject_context`` instance is expected to... |
Please provide a description of the function:def read_raw_temp(self):
self._device.write8(BMP085_CONTROL, BMP085_READTEMPCMD)
time.sleep(0.005) # Wait 5ms
raw = self._device.readU16BE(BMP085_TEMPDATA)
self._logger.debug('Raw temp 0x{0:X} ({1})'.format(raw & 0xFFFF, raw))
... | [
"Reads the raw (uncompensated) temperature from the sensor."
] |
Please provide a description of the function:def read_raw_pressure(self):
self._device.write8(BMP085_CONTROL, BMP085_READPRESSURECMD + (self._mode << 6))
if self._mode == BMP085_ULTRALOWPOWER:
time.sleep(0.005)
elif self._mode == BMP085_HIGHRES:
time.sleep(0.014)... | [
"Reads the raw (uncompensated) pressure level from the sensor."
] |
Please provide a description of the function:def read_altitude(self, sealevel_pa=101325.0):
# Calculation taken straight from section 3.6 of the datasheet.
pressure = float(self.read_pressure())
altitude = 44330.0 * (1.0 - pow(pressure / sealevel_pa, (1.0/5.255)))
self._logger.d... | [
"Calculates the altitude in meters."
] |
Please provide a description of the function:def read_sealevel_pressure(self, altitude_m=0.0):
pressure = float(self.read_pressure())
p0 = pressure / pow(1.0 - altitude_m/44330.0, 5.255)
self._logger.debug('Sealevel pressure {0} Pa'.format(p0))
return p0 | [
"Calculates the pressure at sealevel when given a known altitude in\n meters. Returns a value in Pascals."
] |
Please provide a description of the function:def login_open_sheet(email, password, spreadsheet):
try:
gc = gspread.login(email, password)
worksheet = gc.open(spreadsheet).sheet1
return worksheet
except:
print 'Unable to login and get spreadsheet. Check email, password, spreadsheet name.'
sys.exit(1) | [
"Connect to Google Docs spreadsheet and return the first worksheet."
] |
Please provide a description of the function:def _get_settings_class():
if not hasattr(django_settings, "AUTH_ADFS"):
msg = "The configuration directive 'AUTH_ADFS' was not found in your Django settings"
raise ImproperlyConfigured(msg)
cls = django_settings.AUTH_ADFS.get('SETTINGS_CLASS', D... | [
"\n Get the AUTH_ADFS setting from the Django settings.\n "
] |
Please provide a description of the function:def build_authorization_endpoint(self, request, disable_sso=None):
self.load_config()
redirect_to = request.GET.get(REDIRECT_FIELD_NAME, None)
if not redirect_to:
redirect_to = django_settings.LOGIN_REDIRECT_URL
redirect_t... | [
"\n This function returns the ADFS authorization URL.\n\n Args:\n request(django.http.request.HttpRequest): A django Request object\n disable_sso(bool): Whether to disable single sign-on and force the ADFS server to show a login prompt.\n\n Returns:\n str: The r... |
Please provide a description of the function:def vote(self, request, pk=None):
choice = self.get_object()
choice.vote()
serializer = self.get_serializer(choice)
return Response(serializer.data) | [
"\n post:\n A description of the post method on the custom action.\n "
] |
Please provide a description of the function:def create_user(self, claims):
# Create the user
username_claim = settings.USERNAME_CLAIM
usermodel = get_user_model()
user, created = usermodel.objects.get_or_create(**{
usermodel.USERNAME_FIELD: claims[username_claim]
... | [
"\n Create the user if it doesn't exist yet\n\n Args:\n claims (dict): claims from the access token\n\n Returns:\n django.contrib.auth.models.User: A Django user\n "
] |
Please provide a description of the function:def update_user_attributes(self, user, claims):
required_fields = [field.name for field in user._meta.fields if field.blank is False]
for field, claim in settings.CLAIM_MAPPING.items():
if hasattr(user, field):
if claim ... | [
"\n Updates user attributes based on the CLAIM_MAPPING setting.\n\n Args:\n user (django.contrib.auth.models.User): User model instance\n claims (dict): claims from the access token\n "
] |
Please provide a description of the function:def update_user_groups(self, user, claims):
if settings.GROUPS_CLAIM is not None:
# Update the user's group memberships
django_groups = [group.name for group in user.groups.all()]
if settings.GROUPS_CLAIM in claims:
... | [
"\n Updates user group memberships based on the GROUPS_CLAIM setting.\n\n Args:\n user (django.contrib.auth.models.User): User model instance\n claims (dict): Claims from the access token\n "
] |
Please provide a description of the function:def update_user_flags(self, user, claims):
if settings.GROUPS_CLAIM is not None:
if settings.GROUPS_CLAIM in claims:
access_token_groups = claims[settings.GROUPS_CLAIM]
if not isinstance(access_token_groups, list):... | [
"\n Updates user boolean attributes based on the BOOLEAN_CLAIM_MAPPING setting.\n\n Args:\n user (django.contrib.auth.models.User): User model instance\n claims (dict): Claims from the access token\n "
] |
Please provide a description of the function:def get(self, request):
code = request.GET.get("code")
if not code:
# Return an error message
return render(request, 'django_auth_adfs/login_failed.html', {
'error_message': "No authorization code was provided... | [
"\n Handles the redirect from ADFS to our site.\n We try to process the passed authorization code and login the user.\n\n Args:\n request (django.http.request.HttpRequest): A Django Request object\n "
] |
Please provide a description of the function:def authenticate(self, request):
auth = get_authorization_header(request).split()
if not auth or auth[0].lower() != b'bearer':
return None
if len(auth) == 1:
msg = 'Invalid authorization header. No credentials provid... | [
"\n Returns a `User` if a correct access token has been supplied\n in the Authorization header. Otherwise returns `None`.\n "
] |
Please provide a description of the function:def molecular_orbital(coords, mocoeffs, gbasis):
'''Return a molecular orbital given the nuclei coordinates, as well as
molecular orbital coefficients and basis set specification as given by the cclib library.
The molecular orbital is represented as a func... | [] |
Please provide a description of the function:def getbfs(coords, gbasis):
sym2powerlist = {
'S' : [(0,0,0)],
'P' : [(1,0,0),(0,1,0),(0,0,1)],
'D' : [(2,0,0),(0,2,0),(0,0,2),(1,1,0),(0,1,1),(1,0,1)],
'F' : [(3,0,0),(2,1,0),(2,0,1),(1,2,0),(1,1,1),(1,0,2),
(0,3,0),(... | [
"Convenience function for both wavefunction and density based on PyQuante Ints.py."
] |
Please provide a description of the function:def S(a,b):
if b.contracted:
return sum(cb*S(pb,a) for (cb,pb) in b)
elif a.contracted:
return sum(ca*S(b,pa) for (ca,pa) in a)
return a.norm*b.norm*overlap(a.exponent,a.powers,
a.origin,b.exponent,b.powers,b.... | [
"\n Simple interface to the overlap function.\n >>> from pyquante2 import pgbf,cgbf\n >>> s = pgbf(1)\n >>> isclose(S(s,s),1.0)\n True\n >>> sc = cgbf(exps=[1],coefs=[1])\n >>> isclose(S(sc,sc),1.0)\n True\n\n >>> sc = cgbf(exps=[1],coefs=[1])\n >>> isclose(S(sc,s),1.0)\n True\n ... |
Please provide a description of the function:def T(a,b):
if b.contracted:
return sum(cb*T(pb,a) for (cb,pb) in b)
elif a.contracted:
return sum(ca*T(b,pa) for (ca,pa) in a)
return a.norm*b.norm*kinetic(a.exponent,a.powers,a.origin,
b.exponent,b.powers,b.... | [
"\n Simple interface to the kinetic function.\n >>> from pyquante2 import pgbf,cgbf\n >>> from pyquante2.basis.pgbf import pgbf\n >>> s = pgbf(1)\n >>> isclose(T(s,s),1.5)\n True\n\n >>> sc = cgbf(exps=[1],coefs=[1])\n >>> isclose(T(sc,sc),1.5)\n True\n\n >>> sc = cgbf(exps=[1],coefs=[... |
Please provide a description of the function:def V(a,b,C):
if b.contracted:
return sum(cb*V(pb,a,C) for (cb,pb) in b)
elif a.contracted:
return sum(ca*V(b,pa,C) for (ca,pa) in a)
return a.norm*b.norm*nuclear_attraction(a.exponent,a.powers,a.origin,
... | [
"\n Simple interface to the nuclear attraction function.\n >>> from pyquante2 import pgbf,cgbf\n >>> s = pgbf(1)\n >>> isclose(V(s,s,(0,0,0)),-1.595769)\n True\n\n >>> sc = cgbf(exps=[1],coefs=[1])\n >>> isclose(V(sc,sc,(0,0,0)),-1.595769)\n True\n\n >>> sc = cgbf(exps=[1],coefs=[1])\n ... |
Please provide a description of the function:def overlap(alpha1,lmn1,A,alpha2,lmn2,B):
l1,m1,n1 = lmn1
l2,m2,n2 = lmn2
rab2 = norm2(A-B)
gamma = alpha1+alpha2
P = gaussian_product_center(alpha1,A,alpha2,B)
pre = pow(pi/gamma,1.5)*exp(-alpha1*alpha2*rab2/gamma)
wx = overlap1d(l1,l2,P[0... | [
"\n Full form of the overlap integral. Taken from THO eq. 2.12\n >>> isclose(overlap(1,(0,0,0),array((0,0,0),'d'),1,(0,0,0),array((0,0,0),'d')),1.968701)\n True\n "
] |
Please provide a description of the function:def overlap1d(l1,l2,PAx,PBx,gamma):
total = 0
for i in range(1+int(floor(0.5*(l1+l2)))):
total += binomial_prefactor(2*i,l1,l2,PAx,PBx)* \
fact2(2*i-1)/pow(2*gamma,i)
return total | [
"\n The one-dimensional component of the overlap integral. Taken from THO eq. 2.12\n >>> isclose(overlap1d(0,0,0,0,1),1.0)\n True\n "
] |
Please provide a description of the function:def gaussian_product_center(alpha1,A,alpha2,B):
return (alpha1*A+alpha2*B)/(alpha1+alpha2) | [
"\n The center of the Gaussian resulting from the product of two Gaussians:\n >>> gaussian_product_center(1,array((0,0,0),'d'),1,array((0,0,0),'d'))\n array([ 0., 0., 0.])\n "
] |
Please provide a description of the function:def binomial_prefactor(s,ia,ib,xpa,xpb):
total= 0
for t in range(s+1):
if s-ia <= t <= ib:
total += binomial(ia,s-t)*binomial(ib,t)* \
pow(xpa,ia-s+t)*pow(xpb,ib-t)
return total | [
"\n The integral prefactor containing the binomial coefficients from Augspurger and Dykstra.\n >>> binomial_prefactor(0,0,0,0,0)\n 1\n "
] |
Please provide a description of the function:def kinetic(alpha1,lmn1,A,alpha2,lmn2,B):
l1,m1,n1 = lmn1
l2,m2,n2 = lmn2
term0 = alpha2*(2*(l2+m2+n2)+3)*\
overlap(alpha1,(l1,m1,n1),A,\
alpha2,(l2,m2,n2),B)
term1 = -2*pow(alpha2,2)*\
(overlap(alpha1,(... | [
"\n The full form of the kinetic energy integral\n >>> isclose(kinetic(1,(0,0,0),array((0,0,0),'d'),1,(0,0,0),array((0,0,0),'d')),2.953052)\n True\n "
] |
Please provide a description of the function:def nuclear_attraction(alpha1,lmn1,A,alpha2,lmn2,B,C):
l1,m1,n1 = lmn1
l2,m2,n2 = lmn2
gamma = alpha1+alpha2
P = gaussian_product_center(alpha1,A,alpha2,B)
rab2 = norm2(A-B)
rcp2 = norm2(C-P)
dPA = P-A
dPB = P-B
dPC = P-C
Ax = ... | [
"\n Full form of the nuclear attraction integral\n >>> isclose(nuclear_attraction(1,(0,0,0),array((0,0,0),'d'),1,(0,0,0),array((0,0,0),'d'),array((0,0,0),'d')),-3.141593)\n True\n "
] |
Please provide a description of the function:def A_term(i,r,u,l1,l2,PAx,PBx,CPx,gamma):
return pow(-1,i)*binomial_prefactor(i,l1,l2,PAx,PBx)*\
pow(-1,u)*factorial(i)*pow(CPx,i-2*r-2*u)*\
pow(0.25/gamma,r+u)/factorial(r)/factorial(u)/factorial(i-2*r-2*u) | [
"\n THO eq. 2.18\n\n >>> A_term(0,0,0,0,0,0,0,0,1)\n 1.0\n >>> A_term(0,0,0,0,1,1,1,1,1)\n 1.0\n >>> A_term(1,0,0,0,1,1,1,1,1)\n -1.0\n >>> A_term(0,0,0,1,1,1,1,1,1)\n 1.0\n >>> A_term(1,0,0,1,1,1,1,1,1)\n -2.0\n >>> A_term(2,0,0,1,1,1,1,1,1)\n 1.0\n >>> A_term(2,0,1,1,1,1,... |
Please provide a description of the function:def A_array(l1,l2,PA,PB,CP,g):
Imax = l1+l2+1
A = [0]*Imax
for i in range(Imax):
for r in range(int(floor(i/2)+1)):
for u in range(int(floor((i-2*r)/2)+1)):
I = i-2*r-u
A[I] = A[I] + A_term(i,r,u,l1,l2,PA,P... | [
"\n THO eq. 2.18 and 3.1\n\n >>> A_array(0,0,0,0,0,1)\n [1.0]\n >>> A_array(0,1,1,1,1,1)\n [1.0, -1.0]\n >>> A_array(1,1,1,1,1,1)\n [1.5, -2.5, 1.0]\n "
] |
Please provide a description of the function:def mesh(self,xyzs):
I,J,K = self.powers
d = np.asarray(xyzs,'d')-self.origin
# Got help from stackoverflow user @unutbu with this.
# See: http://stackoverflow.com/questions/17391052/compute-square-distances-from-numpy-array
d... | [
"\n Evaluate basis function on a mesh of points *xyz*.\n "
] |
Please provide a description of the function:def _normalize(self):
"Normalize basis function. From THO eq. 2.2"
l,m,n = self.powers
self.norm = np.sqrt(pow(2,2*(l+m+n)+1.5)*
pow(self.exponent,l+m+n+1.5)/
fact2(2*l-1)/fact2(2*m-1)/
... | [] |
Please provide a description of the function:def select(self, selections):
'''Make a selection in this
representation. BallAndStickRenderer support selections of
atoms and bonds.
To select the first atom and the first bond you can use the
following code::
... | [] |
Please provide a description of the function:def hide(self, selections):
'''Hide objects in this representation. BallAndStickRepresentation
support selections of atoms and bonds.
To hide the first atom and the first bond you can use the
following code::
from chemlab.mviewer... | [] |
Please provide a description of the function:def scale(self, selections, factor):
'''Scale the objects represented by *selections* up to a
certain *factor*.
'''
if 'atoms' in selections:
atms = selections['atoms'].mask
if factor is None:
self.... | [] |
Please provide a description of the function:def change_radius(self, selections, value):
'''Change the radius of each atom by a certain value
'''
if 'atoms' in selections:
atms = selections['atoms'].mask
if value is None:
self.radii_state.array[at... | [] |
Please provide a description of the function:def change_color(self, selections, value):
'''Change the color of each atom by a certain value. *value*
should be a tuple.
'''
if 'atoms' in selections:
atms = selections['atoms'].mask
if value is None:
... | [] |
Please provide a description of the function:def paintGL(self):
'''GL function called each time a frame is drawn'''
if self.post_processing:
# Render to the first framebuffer
glBindFramebuffer(GL_FRAMEBUFFER, self.fb0)
glViewport(0, 0, self.width(), self.height())
... | [] |
Please provide a description of the function:def toimage(self, width=None, height=None):
'''Return the current scene as a PIL Image.
**Example**
You can build your molecular viewer as usual and dump an image
at any resolution supported by the video card (up to the
memory limits... | [] |
Please provide a description of the function:def sto(zeta,N=1,L=0,M=0,origin=(0,0,0)):
nlm2powers = {
(1,0,0) : (0,0,0,0), # x,y,z,r
(2,0,0) : (0,0,0,1),
(3,0,0) : (0,0,0,2),
(2,1,0) : (1,0,0,0),
(2,1,1) : (0,1,0,0),
(2,1,-1) : (0,0,1,0),
(3,1,0) : (1,0... | [
"\n Use Stewarts STO-6G fits to create a contracted Gaussian approximation to a\n Slater function. Fits of other expansion lengths (1G, 3G, etc) are in the paper.\n\n Reference: RF Stewart, JCP 52, 431 (1970)\n\n >>> s = sto(1)\n >>> np.isclose(s(0,0,0),0.530121)\n True\n "
] |
Please provide a description of the function:def mesh(self,xyzs):
return sum(c*p.mesh(xyzs) for c,p in self) | [
"\n Evaluate basis function on a mesh of points *xyz*.\n "
] |
Please provide a description of the function:def _real(coords1, charges1, coords2, charges2, rcut, alpha, box):
n = coords1.shape[0]
m = coords2.shape[0]
# Unit vectors
a = box[0]
b = box[1]
c = box[2]
# This is helpful to add the correct number of boxes
l_max = int(np.cei... | [
"Calculate ewald real part. Box has to be a cuboidal box you should\n transform any other box shape to a cuboidal box before using this.\n \n "
] |
Please provide a description of the function:def _reciprocal(coords1, charges1, coords2, charges2, kmax, kappa, box):
n = coords1.shape[0]
m = coords2.shape[0]
result = np.zeros(n, dtype=np.float64)
need_self = np.zeros(n, dtype=np.uint8)
# Reciprocal unit vectors
g1, g2, g3 = reciprocal_v... | [
"Calculate ewald reciprocal part. Box has to be a cuboidal box you should\n transform any other box shape to a cuboidal box before using this.\n \n "
] |
Please provide a description of the function:def update_bounds(self, bounds):
'''Update cylinders start and end positions
'''
starts = bounds[:,0,:]
ends = bounds[:,1,:]
self.bounds = bounds
self.lengths = np.sqrt(((ends - starts)**2).sum(axis=1))
ver... | [] |
Please provide a description of the function:def make_trajectory(first, filename, restart=False):
'''Factory function to easily create a trajectory object'''
mode = 'w'
if restart:
mode = 'a'
return Trajectory(first, filename, mode) | [] |
Please provide a description of the function:def compileShader( source, shaderType ):
if isinstance(source, str):
source = [source]
elif isinstance(source, bytes):
source = [source.decode('utf-8')]
shader = glCreateShader(shaderType)
glShaderSource(shader, source)
glCompile... | [
"Compile shader source of given type\n \n source -- GLSL source-code for the shader\n shaderType -- GLenum GL_VERTEX_SHADER, GL_FRAGMENT_SHADER, etc,\n \n returns GLuint compiled shader reference\n raises RuntimeError when a compilation failure occurs\n ",
"Shader compile failure (%s): %s"
] |
Please provide a description of the function:def has_key(self, key):
k = self._lowerOrReturn(key)
return k in self.data | [
"Case insensitive test whether 'key' exists."
] |
Please provide a description of the function:def update(self, dict):
for k,v in dict.items():
self[k] = v | [
"Copy (key,value) pairs from 'dict'."
] |
Please provide a description of the function:def update_positions(self, positions):
'''Update the sphere positions.
'''
sphs_verts = self.sphs_verts_radii.copy()
sphs_verts += positions.reshape(self.n_spheres, 1, 3)
self.tr.update_vertices(sphs_verts)
self.poslist = posi... | [] |
Please provide a description of the function:def query_ball_point(self, x, r, p=2., eps=0):
x = np.asarray(x).astype(np.float)
if x.shape[-1] != self.m:
raise ValueError("Searching for a %d-dimensional point in a " \
"%d-dimensional KDTree" % (x.shape[-1... | [
"\n Find all points within distance r of point(s) x.\n\n Parameters\n ----------\n x : array_like, shape tuple + (self.m,)\n The point or points to search for neighbors of.\n r : positive float\n The radius of points to return.\n p : float, optional\n ... |
Please provide a description of the function:def isnamedtuple(obj):
return isinstance(obj, tuple) \
and hasattr(obj, "_fields") \
and hasattr(obj, "_asdict") \
and callable(obj._asdict) | [
"Heuristic check if an object is a namedtuple."
] |
Please provide a description of the function:def display_molecule(mol, style='ball-and-stick'):
'''Display the molecule *mol* with the default viewer.
'''
v = QtViewer()
if style == 'ball-and-stick':
bs = v.add_renderer(BallAndStickRenderer,
mol.r_array,
... | [] |
Please provide a description of the function:def display_system(sys, style='vdw'):
'''Display the system *sys* with the default viewer.
'''
v = QtViewer()
#v.add_post_processing(FXAAEffect)
v.add_post_processing(SSAOEffect)
if style == 'vdw':
sr = v.add_renderer(AtomRende... | [] |
Please provide a description of the function:def display_trajectory(sys, times, coords_list, box_vectors=None,
style='spheres'):
'''Display the the system *sys* and instrument the trajectory
viewer with frames information.
.. image:: /_static/display_trajectory.png
**Par... | [] |
Please provide a description of the function:def running_coordination_number(coordinates_a, coordinates_b, periodic,
binsize=0.002, cutoff=1.5):
x, y = rdf(coordinates_a,
coordinates_b,
periodic=periodic,
normalize=False,
... | [
"This is the cumulative radial distribution \n function, also called running coordination number"
] |
Please provide a description of the function:def update_colors(self, colors):
colors = np.array(colors, dtype=np.uint8)
self._vbo_c.set_data(colors)
self._vbo_c.unbind() | [
"Update the colors"
] |
Please provide a description of the function:def trajectory(start=None, stop=None, step=None):
'''Useful command to iterate on the trajectory frames by time (in
ns). It is meant to be used in a for loop::
for i in trajectory(0, 10, 0.1):
coords = current_frame()
t = current_time... | [] |
Please provide a description of the function:def frames(skip=1):
'''Useful command to iterate on the trajectory frames. It can be
used in a for loop.
::
for i in frames():
coords = current_trajectory()[i]
# Do operation on coords
You can use the option *skip* to ta... | [] |
Please provide a description of the function:def display_system(system, autozoom=True):
'''Display a `~chemlab.core.System` instance at screen'''
viewer.clear()
viewer.add_representation(BallAndStickRepresentation, system)
if autozoom:
autozoom_()
viewer.update()
msg(str(system)) | [] |
Please provide a description of the function:def display_molecule(mol, autozoom=True):
'''Display a `~chemlab.core.Molecule` instance in the viewer.
This function wraps the molecule in a system before displaying
it.
'''
s = System([mol])
display_system(s, autozoom=True) | [] |
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