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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.create_subject | def create_subject(self,
authc_token=None,
account_id=None,
existing_subject=None,
subject_context=None):
"""
Creates a ``Subject`` instance for the user represented by the given method
arguments.
... | python | def create_subject(self,
authc_token=None,
account_id=None,
existing_subject=None,
subject_context=None):
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Creates a ``Subject`` instance for the user represented by the given method
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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.login | def login(self, subject, authc_token):
"""
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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.ensure_security_manager | def ensure_security_manager(self, subject_context):
"""
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will have access to a ``SecurityManager`` during Subject construction.
... | python | def ensure_security_manager(self, subject_context):
"""
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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.resolve_session | def resolve_session(self, subject_context):
"""
This method attempts to resolve any associated session based on the
context and returns a context that represents this resolved Session to
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that performs actual... | python | def resolve_session(self, subject_context):
"""
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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.resolve_identifiers | def resolve_identifiers(self, subject_context):
"""
ensures that a subject_context has identifiers and if it doesn't will
attempt to locate them using heuristics
"""
session = subject_context.session
identifiers = subject_context.resolve_identifiers(session)
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"""
ensures that a subject_context has identifiers and if it doesn't will
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"""
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YosaiProject/yosai | yosai/core/mgt/mgt.py | NativeSecurityManager.logout | def logout(self, subject):
"""
Logs out the specified Subject from the system.
Note that most application developers should not call this method unless
they have a good reason for doing so. The preferred way to logout a
Subject is to call ``Subject.logout()``, not by calling ``... | python | def logout(self, subject):
"""
Logs out the specified Subject from the system.
Note that most application developers should not call this method unless
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YosaiProject/yosai | yosai/core/realm/realm.py | AccountStoreRealm.is_permitted | def is_permitted(self, identifiers, permission_s):
"""
If the authorization info cannot be obtained from the accountstore,
permission check tuple yields False.
:type identifiers: subject_abcs.IdentifierCollection
:param permission_s: a collection of one or more permissions, re... | python | def is_permitted(self, identifiers, permission_s):
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YosaiProject/yosai | yosai/core/realm/realm.py | AccountStoreRealm.has_role | def has_role(self, identifiers, required_role_s):
"""
Confirms whether a subject is a member of one or more roles.
If the authorization info cannot be obtained from the accountstore,
role check tuple yields False.
:type identifiers: subject_abcs.IdentifierCollection
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Confirms whether a subject is a member of one or more roles.
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YosaiProject/yosai | yosai/web/session/session.py | WebSessionHandler.on_start | def on_start(self, session, session_context):
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Stores the Session's ID, usually as a Cookie, to associate with future
requests.
:param session: the session that was just ``createSession`` created
"""
session_id = session.session_id
web_registry = session_conte... | python | def on_start(self, session, session_context):
"""
Stores the Session's ID, usually as a Cookie, to associate with future
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YosaiProject/yosai | yosai/web/session/session.py | WebSessionStorageEvaluator.is_session_storage_enabled | def is_session_storage_enabled(self, subject=None):
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YosaiProject/yosai | yosai/core/serialize/marshalling.py | default_marshaller | def default_marshaller(obj):
"""
Retrieve the state of the given object.
Calls the ``__getstate__()`` method of the object if available, otherwise returns the
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:param obj: the object to marshal
:return: the marshalled object state
"""
if hasattr(obj, '__gets... | python | def default_marshaller(obj):
"""
Retrieve the state of the given object.
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:param obj: the object to marshal
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YosaiProject/yosai | yosai/core/serialize/marshalling.py | default_unmarshaller | def default_unmarshaller(instance, state):
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YosaiProject/yosai | yosai/core/authc/authc.py | DefaultAuthenticator.do_authenticate_account | def do_authenticate_account(self, authc_token):
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YosaiProject/yosai | yosai/core/logging/formatters.py | JSONFormatter.extra_from_record | def extra_from_record(self, record):
"""Returns `extra` dict you passed to logger.
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"""
return {
attr_name: record.__dict__[attr_name]
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... | python | def extra_from_record(self, record):
"""Returns `extra` dict you passed to logger.
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return {
attr_name: record.__dict__[attr_name]
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YosaiProject/yosai | yosai/core/session/session.py | CachingSessionStore.create | def create(self, session):
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YosaiProject/yosai | yosai/core/session/session.py | NativeSessionManager.start | def start(self, session_context):
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YosaiProject/yosai | yosai/web/mgt/mgt.py | CookieRememberMeManager.remember_encrypted_identity | def remember_encrypted_identity(self, subject, encrypted):
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jobec/django-auth-adfs | django_auth_adfs/config.py | _get_settings_class | def _get_settings_class():
"""
Get the AUTH_ADFS setting from the Django settings.
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cls = django_settings.AUTH_ADFS.g... | python | def _get_settings_class():
"""
Get the AUTH_ADFS setting from the Django settings.
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jobec/django-auth-adfs | django_auth_adfs/config.py | ProviderConfig.build_authorization_endpoint | def build_authorization_endpoint(self, request, disable_sso=None):
"""
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Args:
request(django.http.request.HttpRequest): A django Request object
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jobec/django-auth-adfs | django_auth_adfs/backend.py | AdfsBaseBackend.create_user | def create_user(self, claims):
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claims (dict): claims from the access token
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"""
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claims (dict): claims from the access token
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jobec/django-auth-adfs | django_auth_adfs/backend.py | AdfsBaseBackend.update_user_attributes | def update_user_attributes(self, user, claims):
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user (django.contrib.auth.models.User): User model instance
claims (dict): claims from the access token
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required_fields = [field.nam... | python | def update_user_attributes(self, user, claims):
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Updates user attributes based on the CLAIM_MAPPING setting.
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claims (dict): claims from the access token
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jobec/django-auth-adfs | django_auth_adfs/backend.py | AdfsBaseBackend.update_user_groups | def update_user_groups(self, user, claims):
"""
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user (django.contrib.auth.models.User): User model instance
claims (dict): Claims from the access token
"""
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jobec/django-auth-adfs | django_auth_adfs/backend.py | AdfsBaseBackend.update_user_flags | def update_user_flags(self, user, claims):
"""
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Args:
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claims (dict): Claims from the access token
"""
if settings.GROUPS... | python | def update_user_flags(self, user, claims):
"""
Updates user boolean attributes based on the BOOLEAN_CLAIM_MAPPING setting.
Args:
user (django.contrib.auth.models.User): User model instance
claims (dict): Claims from the access token
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"""
Handles the redirect from ADFS to our site.
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Args:
request (django.http.request.HttpRequest): A Django Request object
"""
code = request.GET.get("code")
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Handles the redirect from ADFS to our site.
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"""
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"""
auth = get_authorization_header(request).split()
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Returns a `User` if a correct access token has been supplied
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chemlab/chemlab | chemlab/qc/wavefunction.py | molecular_orbital | 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.
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chemlab/chemlab | chemlab/qc/wavefunction.py | getbfs | def getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
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)... | python | def getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
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)],
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chemlab/chemlab | chemlab/qc/one.py | A_term | def A_term(i,r,u,l1,l2,PAx,PBx,CPx,gamma):
"""
THO eq. 2.18
>>> A_term(0,0,0,0,0,0,0,0,1)
1.0
>>> A_term(0,0,0,0,1,1,1,1,1)
1.0
>>> A_term(1,0,0,0,1,1,1,1,1)
-1.0
>>> A_term(0,0,0,1,1,1,1,1,1)
1.0
>>> A_term(1,0,0,1,1,1,1,1,1)
-2.0
>>> A_term(2,0,0,1,1,1,1,1,1)
1... | python | def A_term(i,r,u,l1,l2,PAx,PBx,CPx,gamma):
"""
THO eq. 2.18
>>> A_term(0,0,0,0,0,0,0,0,1)
1.0
>>> A_term(0,0,0,0,1,1,1,1,1)
1.0
>>> A_term(1,0,0,0,1,1,1,1,1)
-1.0
>>> A_term(0,0,0,1,1,1,1,1,1)
1.0
>>> A_term(1,0,0,1,1,1,1,1,1)
-2.0
>>> A_term(2,0,0,1,1,1,1,1,1)
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chemlab/chemlab | chemlab/qc/one.py | A_array | def A_array(l1,l2,PA,PB,CP,g):
"""
THO eq. 2.18 and 3.1
>>> A_array(0,0,0,0,0,1)
[1.0]
>>> A_array(0,1,1,1,1,1)
[1.0, -1.0]
>>> A_array(1,1,1,1,1,1)
[1.5, -2.5, 1.0]
"""
Imax = l1+l2+1
A = [0]*Imax
for i in range(Imax):
for r in range(int(floor(i/2)+1)):
... | python | def A_array(l1,l2,PA,PB,CP,g):
"""
THO eq. 2.18 and 3.1
>>> A_array(0,0,0,0,0,1)
[1.0]
>>> A_array(0,1,1,1,1,1)
[1.0, -1.0]
>>> A_array(1,1,1,1,1,1)
[1.5, -2.5, 1.0]
"""
Imax = l1+l2+1
A = [0]*Imax
for i in range(Imax):
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chemlab/chemlab | chemlab/qc/pgbf.py | pgbf._normalize | def _normalize(self):
"Normalize basis function. From THO eq. 2.2"
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self.norm = np.sqrt(pow(2,2*(l+m+n)+1.5)*
pow(self.exponent,l+m+n+1.5)/
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fact2(2*n-1)/pow(np.pi,1.5... | python | def _normalize(self):
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l,m,n = self.powers
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chemlab/chemlab | chemlab/mviewer/representations/ballandstick.py | BallAndStickRepresentation.hide | 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.state import Selection
represent... | python | def hide(self, selections):
'''Hide objects in this representation. BallAndStickRepresentation
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chemlab/chemlab | chemlab/mviewer/representations/ballandstick.py | BallAndStickRepresentation.change_radius | 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[atms] = [vdw_radii.get(t) * 0.3 for t in self.... | python | def change_radius(self, selections, value):
'''Change the radius of each atom by a certain value
'''
if 'atoms' in selections:
atms = selections['atoms'].mask
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chemlab/chemlab | chemlab/graphics/qt/qchemlabwidget.py | QChemlabWidget.paintGL | def paintGL(self):
'''GL function called each time a frame is drawn'''
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# Render to the first framebuffer
glBindFramebuffer(GL_FRAMEBUFFER, self.fb0)
glViewport(0, 0, self.width(), self.height())
status = glCheckFramebufferStatus(... | python | def paintGL(self):
'''GL function called each time a frame is drawn'''
if self.post_processing:
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glBindFramebuffer(GL_FRAMEBUFFER, self.fb0)
glViewport(0, 0, self.width(), self.height())
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chemlab/chemlab | chemlab/graphics/qt/qchemlabwidget.py | QChemlabWidget.toimage | 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)::
v = QtViewer()
... | python | def toimage(self, width=None, height=None):
'''Return the current scene as a PIL Image.
**Example**
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chemlab/chemlab | chemlab/md/ewald.py | _real | def _real(coords1, charges1, coords2, charges2, rcut, alpha, box):
"""Calculate ewald real part. Box has to be a cuboidal box you should
transform any other box shape to a cuboidal box before using this.
"""
n = coords1.shape[0]
m = coords2.shape[0]
# Unit vectors
a = box[0]
b = box... | python | def _real(coords1, charges1, coords2, charges2, rcut, alpha, box):
"""Calculate ewald real part. Box has to be a cuboidal box you should
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chemlab/chemlab | chemlab/md/ewald.py | _reciprocal | def _reciprocal(coords1, charges1, coords2, charges2, kmax, kappa, box):
"""Calculate ewald reciprocal part. Box has to be a cuboidal box you should
transform any other box shape to a cuboidal box before using this.
"""
n = coords1.shape[0]
m = coords2.shape[0]
result = np.zeros(n, dtype=np... | python | def _reciprocal(coords1, charges1, coords2, charges2, kmax, kappa, box):
"""Calculate ewald reciprocal part. Box has to be a cuboidal box you should
transform any other box shape to a cuboidal box before using this.
"""
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chemlab/chemlab | chemlab/graphics/renderers/cylinder.py | CylinderRenderer.update_bounds | def update_bounds(self, bounds):
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ends = bounds[:,1,:]
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chemlab/chemlab | chemlab/graphics/renderers/sphere.py | SphereRenderer.update_positions | def update_positions(self, positions):
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'''
sphs_verts = self.sphs_verts_radii.copy()
sphs_verts += positions.reshape(self.n_spheres, 1, 3)
self.tr.update_vertices(sphs_verts)
self.poslist = positions | python | def update_positions(self, positions):
'''Update the sphere positions.
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sphs_verts = self.sphs_verts_radii.copy()
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chemlab/chemlab | chemlab/md/analysis.py | running_coordination_number | def running_coordination_number(coordinates_a, coordinates_b, periodic,
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chemlab/chemlab | chemlab/graphics/renderers/line.py | LineRenderer.update_colors | def update_colors(self, colors):
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"""Update the colors"""
colors = np.array(colors, dtype=np.uint8)
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chemlab/chemlab | chemlab/mviewer/api/core.py | frames | def frames(skip=1):
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::
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chemlab/chemlab | chemlab/mviewer/api/display.py | display_system | 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)) | python | def display_system(system, autozoom=True):
'''Display a `~chemlab.core.System` instance at screen'''
viewer.clear()
viewer.add_representation(BallAndStickRepresentation, system)
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chemlab/chemlab | chemlab/mviewer/api/display.py | display_molecule | def display_molecule(mol, autozoom=True):
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it.
'''
s = System([mol])
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chemlab/chemlab | chemlab/mviewer/api/display.py | load_molecule | def load_molecule(name, format=None):
'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name, format=format).read('molecule')
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'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
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mol = datafile(name, format=format).read('molecule')
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chemlab/chemlab | chemlab/mviewer/api/display.py | write_system | def write_system(filename, format=None):
'''Write the system currently displayed to a file.'''
datafile(filename, format=format, mode='w').write('system',
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'''Write the system currently displayed to a file.'''
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chemlab/chemlab | chemlab/mviewer/api/display.py | write_molecule | def write_molecule(filename, format=None):
'''Write the system displayed in a file as a molecule.'''
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chemlab/chemlab | chemlab/mviewer/api/display.py | load_trajectory | def load_trajectory(name, skip=1, format=None):
'''Load a trajectory file into chemlab. You should call this
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load_system or load_remote_system.
'''
df = datafile(name, format=format)
dt, coords = df.read('trajectory', skip=skip)
boxes ... | python | def load_trajectory(name, skip=1, format=None):
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load_system or load_remote_system.
'''
df = datafile(name, format=format)
dt, coords = df.read('trajectory', skip=skip)
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chemlab/chemlab | chemlab/core/system.py | System.from_arrays | def from_arrays(cls, **kwargs):
'''Initialize a System from its constituent arrays. It is the
fastest way to initialize a System, well suited for
reading one or more big System from data files.
**Parameters**
The following parameters are required:
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'''Initialize a System from its constituent arrays. It is the
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chemlab/chemlab | chemlab/core/system.py | System.minimum_image | def minimum_image(self):
"""Align the system according to the minimum image convention"""
if self.box_vectors is None:
raise ValueError('No periodic vectors defined')
else:
self.r_array = minimum_image(self.r_array, self.box_vectors.diagonal())
return sel... | python | def minimum_image(self):
"""Align the system according to the minimum image convention"""
if self.box_vectors is None:
raise ValueError('No periodic vectors defined')
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self.r_array = minimum_image(self.r_array, self.box_vectors.diagonal())
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chemlab/chemlab | chemlab/core/system.py | System.where | def where(self, within_of=None, inplace=False, **kwargs):
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chemlab/chemlab | chemlab/qc/utils.py | _gser | def _gser(a,x):
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assert(x>=0),'x < 0 in gser'
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chemlab/chemlab | chemlab/qc/utils.py | _gcf | def _gcf(a,x):
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b=x+1.-a
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for i in range(1,ITMAX+1):
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chemlab/chemlab | chemlab/qc/utils.py | dmat | def dmat(c,nocc):
"Form the density matrix from the first nocc orbitals of c"
return np.dot(c[:,:nocc],c[:,:nocc].T) | python | def dmat(c,nocc):
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chemlab/chemlab | chemlab/qc/utils.py | geigh | def geigh(H,S):
"Solve the generalized eigensystem Hc = ESc"
A = cholorth(S)
E,U = np.linalg.eigh(simx(H,A))
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chemlab/chemlab | chemlab/utils/neighbors.py | _check_periodic | def _check_periodic(periodic):
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'''Validate periodic input'''
periodic = np.array(periodic)
# If it is a matrix
if len(periodic.shape) == 2:
assert periodic.shape[0] == periodic.shape[1], 'periodic shoud be a square matrix or a flat array'
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chemlab/chemlab | chemlab/utils/neighbors.py | count_neighbors | def count_neighbors(coordinates_a, coordinates_b, periodic, r):
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:param np.ndarray coordinates_a: Either an array of coordinates of shape (N,3)
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chemlab/chemlab | chemlab/mviewer/api/appeareance.py | change_default_radii | def change_default_radii(def_map):
"""Change the default radii
"""
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rep = current_representation()
rep.radii_state.default = [def_map[t] for t in s.type_array]
rep.radii_state.reset() | python | def change_default_radii(def_map):
"""Change the default radii
"""
s = current_system()
rep = current_representation()
rep.radii_state.default = [def_map[t] for t in s.type_array]
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chemlab/chemlab | chemlab/mviewer/api/appeareance.py | add_post_processing | def add_post_processing(effect, **options):
"""Apply a post processing effect.
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effect: string
The effect to be applied, choose between ``ssao``,
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**options:
Options used to initialize the effect, check the
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"""Apply a post processing effect.
**Parameters**
effect: string
The effect to be applied, choose between ``ssao``,
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chemlab/chemlab | chemlab/core/spacegroup/cell.py | unit_vector | def unit_vector(x):
"""Return a unit vector in the same direction as x."""
y = np.array(x, dtype='float')
return y/norm(y) | python | def unit_vector(x):
"""Return a unit vector in the same direction as x."""
y = np.array(x, dtype='float')
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chemlab/chemlab | chemlab/core/spacegroup/cell.py | angle | def angle(x, y):
"""Return the angle between vectors a and b in degrees."""
return arccos(dot(x, y)/(norm(x)*norm(y)))*180./pi | python | def angle(x, y):
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chemlab/chemlab | chemlab/core/spacegroup/cell.py | metric_from_cell | def metric_from_cell(cell):
"""Calculates the metric matrix from cell, which is given in the
Cartesian system."""
cell = np.asarray(cell, dtype=float)
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"""Calculates the metric matrix from cell, which is given in the
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cell = np.asarray(cell, dtype=float)
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chemlab/chemlab | chemlab/io/datafile.py | add_default_handler | def add_default_handler(ioclass, format, extension=None):
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chemlab/chemlab | chemlab/utils/pbc.py | minimum_image | def minimum_image(coords, pbc):
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Wraps a vector collection of atom positions into the central periodic
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Parameters
----------
pos : :class:`numpy.ndarray`, (Nx3)
Vector collection of atom positions.
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-------
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"""
Wraps a vector collection of atom positions into the central periodic
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----------
pos : :class:`numpy.ndarray`, (Nx3)
Vector collection of atom positions.
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chemlab/chemlab | chemlab/utils/pbc.py | subtract_vectors | def subtract_vectors(a, b, periodic):
'''Returns the difference of the points vec_a - vec_b subject
to the periodic boundary conditions.
'''
r = a - b
delta = np.abs(r)
sign = np.sign(r)
return np.where(delta > 0.5 * periodic, sign * (periodic - delta), r) | python | def subtract_vectors(a, b, periodic):
'''Returns the difference of the points vec_a - vec_b subject
to the periodic boundary conditions.
'''
r = a - b
delta = np.abs(r)
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'''Returns the sum of the points vec_a - vec_b subject
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chemlab/chemlab | chemlab/utils/pbc.py | geometric_center | def geometric_center(coords, periodic):
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eps = np.cos(theta) * max_vals / (2 * np.pi)
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'''Geometric center taking into account periodic boundaries'''
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theta = 2 * np.pi * (coords / max_vals)
eps = np.cos(theta) * max_vals / (2 * np.pi)
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chemlab/chemlab | chemlab/utils/pbc.py | radius_of_gyration | def radius_of_gyration(coords, periodic):
'''Calculate the square root of the mean distance squared from the center of gravity.
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'''Calculate the square root of the mean distance squared from the center of gravity.
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gc = geometric_center(coords, periodic)
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chemlab/chemlab | chemlab/libs/chemspipy.py | find | def find(query):
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chemlab/chemlab | chemlab/libs/chemspipy.py | Compound.imageurl | def imageurl(self):
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self._imageurl = 'http://www.chemspider.com/ImagesHandler.ashx?id=%s' % self.csid
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""" Return the URL of a png image of the 2D structure """
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chemlab/chemlab | chemlab/libs/chemspipy.py | Compound.loadextendedcompoundinfo | def loadextendedcompoundinfo(self):
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""" Load extended compound info from the Mass Spec API """
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chemlab/chemlab | chemlab/libs/chemspipy.py | Compound.image | def image(self):
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response = urlopen(apiurl)
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""" Return string containing PNG binary image data of 2D structure image """
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chemlab/chemlab | chemlab/libs/chemspipy.py | Compound.mol | def mol(self):
""" Return record in MOL format """
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response = urlopen(apiurl)
tree = ET.parse(response)
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""" Return record in MOL format """
if self._mol is None:
apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetRecordMol?csid=%s&calc3d=false&token=%s' % (self.csid,TOKEN)
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chemlab/chemlab | chemlab/libs/chemspipy.py | Compound.mol3d | def mol3d(self):
""" Return record in MOL format with 3D coordinates calculated """
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response = urlopen(apiurl)
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chemlab/chemlab | chemlab/graphics/renderers/ballandstick.py | BallAndStickRenderer.update_positions | def update_positions(self, r_array):
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self.ar.update_positions(r_array)
if self.has_bonds:
self.br.update_positions(r_array) | python | def update_positions(self, r_array):
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chemlab/chemlab | chemlab/core/base.py | concatenate_attributes | def concatenate_attributes(attributes):
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attr = InstanceAttribute(tpl.name, tpl.shape,
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chemlab/chemlab | chemlab/core/base.py | normalize_index | def normalize_index(index):
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.to_dict | def to_dict(self):
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] | c8730966316d101e24f39ac3b96b51282aba0abe | https://github.com/chemlab/chemlab/blob/c8730966316d101e24f39ac3b96b51282aba0abe/chemlab/core/base.py#L105-L114 | train |
chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.from_json | def from_json(cls, string):
"""Create a ChemicalEntity from a json string
"""
exp_dict = json_to_data(string)
version = exp_dict.get('version', 0)
if version == 0:
return cls.from_dict(exp_dict)
elif version == 1:
return cls.from_dict(exp_dict)
... | python | def from_json(cls, string):
"""Create a ChemicalEntity from a json string
"""
exp_dict = json_to_data(string)
version = exp_dict.get('version', 0)
if version == 0:
return cls.from_dict(exp_dict)
elif version == 1:
return cls.from_dict(exp_dict)
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.copy | def copy(self):
"""Create a copy of this ChemicalEntity
"""
inst = super(type(self), type(self)).empty(**self.dimensions)
# Need to copy all attributes, fields, relations
inst.__attributes__ = {k: v.copy() for k, v in self.__attributes__.items()}
inst.__... | python | def copy(self):
"""Create a copy of this ChemicalEntity
"""
inst = super(type(self), type(self)).empty(**self.dimensions)
# Need to copy all attributes, fields, relations
inst.__attributes__ = {k: v.copy() for k, v in self.__attributes__.items()}
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.copy_from | def copy_from(self, other):
"""Copy properties from another ChemicalEntity
"""
# Need to copy all attributes, fields, relations
self.__attributes__ = {k: v.copy() for k, v in other.__attributes__.items()}
self.__fields__ = {k: v.copy() for k, v in other.__fields__.items(... | python | def copy_from(self, other):
"""Copy properties from another ChemicalEntity
"""
# Need to copy all attributes, fields, relations
self.__attributes__ = {k: v.copy() for k, v in other.__attributes__.items()}
self.__fields__ = {k: v.copy() for k, v in other.__fields__.items(... | [
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.update | def update(self, dictionary):
"""Update the current chemical entity from a dictionary of attributes"""
allowed_attrs = list(self.__attributes__.keys())
allowed_attrs += [a.alias for a in self.__attributes__.values()]
for k in dictionary:
# We only update existing attributes
... | python | def update(self, dictionary):
"""Update the current chemical entity from a dictionary of attributes"""
allowed_attrs = list(self.__attributes__.keys())
allowed_attrs += [a.alias for a in self.__attributes__.values()]
for k in dictionary:
# We only update existing attributes
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.subentity | def subentity(self, Entity, index):
"""Return child entity"""
dim = Entity.__dimension__
entity = Entity.empty()
if index >= self.dimensions[dim]:
raise ValueError('index {} out of bounds for dimension {} (size {})'
.format(index, dim, se... | python | def subentity(self, Entity, index):
"""Return child entity"""
dim = Entity.__dimension__
entity = Entity.empty()
if index >= self.dimensions[dim]:
raise ValueError('index {} out of bounds for dimension {} (size {})'
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.sub_dimension | def sub_dimension(self, index, dimension, propagate=True, inplace=False):
"""Return a ChemicalEntity sliced through a dimension.
If other dimensions depend on this one those are updated accordingly.
"""
filter_ = self._propagate_dim(index, dimension, propagate)
return se... | python | def sub_dimension(self, index, dimension, propagate=True, inplace=False):
"""Return a ChemicalEntity sliced through a dimension.
If other dimensions depend on this one those are updated accordingly.
"""
filter_ = self._propagate_dim(index, dimension, propagate)
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.expand_dimension | def expand_dimension(self, newdim, dimension, maps={}, relations={}):
''' When we expand we need to provide new maps and relations as those
can't be inferred '''
for name, attr in self.__attributes__.items():
if attr.dim == dimension:
newattr = attr.copy()
... | python | def expand_dimension(self, newdim, dimension, maps={}, relations={}):
''' When we expand we need to provide new maps and relations as those
can't be inferred '''
for name, attr in self.__attributes__.items():
if attr.dim == dimension:
newattr = attr.copy()
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.concat | def concat(self, other, inplace=False):
'''Concatenate two ChemicalEntity of the same kind'''
# Create new entity
if inplace:
obj = self
else:
obj = self.copy()
# Stitch every attribute
for name, attr in obj.__attributes__.items()... | python | def concat(self, other, inplace=False):
'''Concatenate two ChemicalEntity of the same kind'''
# Create new entity
if inplace:
obj = self
else:
obj = self.copy()
# Stitch every attribute
for name, attr in obj.__attributes__.items()... | [
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chemlab/chemlab | chemlab/core/base.py | ChemicalEntity.sub | def sub(self, inplace=False, **kwargs):
"""Return a entity where the conditions are met"""
filter_ = self.where(**kwargs)
return self.subindex(filter_, inplace) | python | def sub(self, inplace=False, **kwargs):
"""Return a entity where the conditions are met"""
filter_ = self.where(**kwargs)
return self.subindex(filter_, inplace) | [
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chemlab/chemlab | chemlab/core/attributes.py | InstanceArray.sub | def sub(self, index):
"""Return a sub-attribute"""
index = np.asarray(index)
if index.dtype == 'bool':
index = index.nonzero()[0]
if self.size < len(index):
raise ValueError('Can\'t subset "{}": index ({}) is bigger than the number of elements ({})'.forma... | python | def sub(self, index):
"""Return a sub-attribute"""
index = np.asarray(index)
if index.dtype == 'bool':
index = index.nonzero()[0]
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chemlab/chemlab | chemlab/libs/cirpy.py | resolve | def resolve(input, representation, resolvers=None, **kwargs):
""" Resolve input to the specified output representation """
resultdict = query(input, representation, resolvers, **kwargs)
result = resultdict[0]['value'] if resultdict else None
if result and len(result) == 1:
result = result[0]
... | python | def resolve(input, representation, resolvers=None, **kwargs):
""" Resolve input to the specified output representation """
resultdict = query(input, representation, resolvers, **kwargs)
result = resultdict[0]['value'] if resultdict else None
if result and len(result) == 1:
result = result[0]
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chemlab/chemlab | chemlab/libs/cirpy.py | query | def query(input, representation, resolvers=None, **kwargs):
""" Get all results for resolving input to the specified output representation """
apiurl = API_BASE+'/%s/%s/xml' % (urlquote(input), representation)
if resolvers:
kwargs['resolver'] = ",".join(resolvers)
if kwargs:
apiurl+= '?%... | python | def query(input, representation, resolvers=None, **kwargs):
""" Get all results for resolving input to the specified output representation """
apiurl = API_BASE+'/%s/%s/xml' % (urlquote(input), representation)
if resolvers:
kwargs['resolver'] = ",".join(resolvers)
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