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xray7224/PyPump | pypump/models/note.py | Note.serialize | def serialize(self):
""" Converts the post to something compatible with `json.dumps` """
data = super(Note, self).serialize()
data.update({
"verb": "post",
"object": {
"objectType": self.object_type,
"content": self.content,
}
... | python | def serialize(self):
""" Converts the post to something compatible with `json.dumps` """
data = super(Note, self).serialize()
data.update({
"verb": "post",
"object": {
"objectType": self.object_type,
"content": self.content,
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xray7224/PyPump | pypump/client.py | Client.context | def context(self):
""" Provides request context """
type = "client_associate" if self.key is None else "client_update"
data = {
"type": type,
"application_type": self.type,
}
# is this an update?
if self.key:
data["client_id"] = self.k... | python | def context(self):
""" Provides request context """
type = "client_associate" if self.key is None else "client_update"
data = {
"type": type,
"application_type": self.type,
}
# is this an update?
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xray7224/PyPump | pypump/client.py | Client.request | def request(self, server=None):
""" Sends the request """
request = {
"headers": {"Content-Type": "application/json"},
"timeout": self._pump.timeout,
"data": self.context,
}
url = "{proto}://{server}/{endpoint}".format(
proto=self._pump.pr... | python | def request(self, server=None):
""" Sends the request """
request = {
"headers": {"Content-Type": "application/json"},
"timeout": self._pump.timeout,
"data": self.context,
}
url = "{proto}://{server}/{endpoint}".format(
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xray7224/PyPump | pypump/client.py | Client.register | def register(self, server=None):
""" Registers the client with the Pump API retrieving the id and secret """
if (self.key or self.secret):
return self.update()
server_data = self.request(server)
self.key = server_data["client_id"]
self.secret = server_data["client_s... | python | def register(self, server=None):
""" Registers the client with the Pump API retrieving the id and secret """
if (self.key or self.secret):
return self.update()
server_data = self.request(server)
self.key = server_data["client_id"]
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xray7224/PyPump | pypump/client.py | Client.update | def update(self):
""" Updates the information the Pump server has about the client """
error = ""
if self.key is None:
error = "To update a client you need to provide a key"
if self.secret is None:
error = "To update a client you need to provide the secret"
... | python | def update(self):
""" Updates the information the Pump server has about the client """
error = ""
if self.key is None:
error = "To update a client you need to provide a key"
if self.secret is None:
error = "To update a client you need to provide the secret"
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commx/python-rrdtool | setup.py | compile_extensions | def compile_extensions(macros, compat=False):
"""
Compiler subroutine to test whether some functions are available
on the target system. Since the rrdtool headers shipped with most
packages do not disclose any versioning information, we cannot test
whether a given function is available that way. Ins... | python | def compile_extensions(macros, compat=False):
"""
Compiler subroutine to test whether some functions are available
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xray7224/PyPump | pypump/models/collection.py | Collection.add | def add(self, obj):
""" Adds a member to the collection.
:param obj: Object to add.
Example:
>>> mycollection.add(pump.Person('bob@example.org'))
"""
activity = {
"verb": "add",
"object": {
"objectType": obj.object_type,
... | python | def add(self, obj):
""" Adds a member to the collection.
:param obj: Object to add.
Example:
>>> mycollection.add(pump.Person('bob@example.org'))
"""
activity = {
"verb": "add",
"object": {
"objectType": obj.object_type,
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xray7224/PyPump | pypump/models/collection.py | Collection.remove | def remove(self, obj):
""" Removes a member from the collection.
:param obj: Object to remove.
Example:
>>> mycollection.remove(pump.Person('bob@example.org'))
"""
activity = {
"verb": "remove",
"object": {
"objectType": obj.o... | python | def remove(self, obj):
""" Removes a member from the collection.
:param obj: Object to remove.
Example:
>>> mycollection.remove(pump.Person('bob@example.org'))
"""
activity = {
"verb": "remove",
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xray7224/PyPump | pypump/models/__init__.py | PumpObject._post_activity | def _post_activity(self, activity, unserialize=True):
""" Posts a activity to feed """
# I think we always want to post to feed
feed_url = "{proto}://{server}/api/user/{username}/feed".format(
proto=self._pump.protocol,
server=self._pump.client.server,
usernam... | python | def _post_activity(self, activity, unserialize=True):
""" Posts a activity to feed """
# I think we always want to post to feed
feed_url = "{proto}://{server}/api/user/{username}/feed".format(
proto=self._pump.protocol,
server=self._pump.client.server,
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xray7224/PyPump | pypump/models/__init__.py | PumpObject._add_links | def _add_links(self, links, key="href", proxy_key="proxyURL", endpoints=None):
""" Parses and adds block of links """
if endpoints is None:
endpoints = ["likes", "replies", "shares", "self", "followers",
"following", "lists", "favorites", "members"]
if links... | python | def _add_links(self, links, key="href", proxy_key="proxyURL", endpoints=None):
""" Parses and adds block of links """
if endpoints is None:
endpoints = ["likes", "replies", "shares", "self", "followers",
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xray7224/PyPump | pypump/models/__init__.py | Addressable._set_people | def _set_people(self, people):
""" Sets who the object is sent to """
if hasattr(people, "object_type"):
people = [people]
elif hasattr(people, "__iter__"):
people = list(people)
return people | python | def _set_people(self, people):
""" Sets who the object is sent to """
if hasattr(people, "object_type"):
people = [people]
elif hasattr(people, "__iter__"):
people = list(people)
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xray7224/PyPump | pypump/models/__init__.py | Uploadable.from_file | def from_file(self, filename):
""" Uploads a file from a filename on your system.
:param filename: Path to file on your system.
Example:
>>> myimage.from_file('/path/to/dinner.png')
"""
mimetype = mimetypes.guess_type(filename)[0] or "application/octal-stream"
... | python | def from_file(self, filename):
""" Uploads a file from a filename on your system.
:param filename: Path to file on your system.
Example:
>>> myimage.from_file('/path/to/dinner.png')
"""
mimetype = mimetypes.guess_type(filename)[0] or "application/octal-stream"
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xray7224/PyPump | pypump/models/activity.py | Activity.unserialize | def unserialize(self, data):
""" From JSON -> Activity object """
# copy activity attributes into object
if "author" not in data["object"]:
data["object"]["author"] = data["actor"]
for key in ["to", "cc", "bto", "bcc"]:
if key not in data["object"] and key in dat... | python | def unserialize(self, data):
""" From JSON -> Activity object """
# copy activity attributes into object
if "author" not in data["object"]:
data["object"]["author"] = data["actor"]
for key in ["to", "cc", "bto", "bcc"]:
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xray7224/PyPump | pypump/pypump.py | PyPump.create_store | def create_store(self):
""" Creates store object """
if self.store_class is not None:
return self.store_class.load(self.client.webfinger, self)
raise NotImplementedError("You need to specify PyPump.store_class or override PyPump.create_store method.") | python | def create_store(self):
""" Creates store object """
if self.store_class is not None:
return self.store_class.load(self.client.webfinger, self)
raise NotImplementedError("You need to specify PyPump.store_class or override PyPump.create_store method.") | [
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xray7224/PyPump | pypump/pypump.py | PyPump._build_url | def _build_url(self, endpoint):
""" Returns a fully qualified URL """
server = None
if "://" in endpoint:
# looks like an url, let's break it down
server, endpoint = self._deconstruct_url(endpoint)
endpoint = endpoint.lstrip("/")
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""" Returns a fully qualified URL """
server = None
if "://" in endpoint:
# looks like an url, let's break it down
server, endpoint = self._deconstruct_url(endpoint)
endpoint = endpoint.lstrip("/")
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xray7224/PyPump | pypump/pypump.py | PyPump._deconstruct_url | def _deconstruct_url(self, url):
""" Breaks down URL and returns server and endpoint """
url = url.split("://", 1)[-1]
server, endpoint = url.split("/", 1)
return (server, endpoint) | python | def _deconstruct_url(self, url):
""" Breaks down URL and returns server and endpoint """
url = url.split("://", 1)[-1]
server, endpoint = url.split("/", 1)
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xray7224/PyPump | pypump/pypump.py | PyPump._add_client | def _add_client(self, url, key=None, secret=None):
""" Creates Client object with key and secret for server
and adds it to _server_cache if it doesnt already exist """
if "://" in url:
server, endpoint = self._deconstruct_url(url)
else:
server = url
if s... | python | def _add_client(self, url, key=None, secret=None):
""" Creates Client object with key and secret for server
and adds it to _server_cache if it doesnt already exist """
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server, endpoint = self._deconstruct_url(url)
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xray7224/PyPump | pypump/pypump.py | PyPump.request | def request(self, endpoint, method="GET", data="",
raw=False, params=None, retries=None, client=None,
headers=None, timeout=None, **kwargs):
""" Make request to endpoint with OAuth.
Returns dictionary with response data.
:param endpoint: endpoint path, or a fully... | python | def request(self, endpoint, method="GET", data="",
raw=False, params=None, retries=None, client=None,
headers=None, timeout=None, **kwargs):
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xray7224/PyPump | pypump/pypump.py | PyPump.oauth_request | def oauth_request(self):
""" Makes a oauth connection """
# get tokens from server and make a dict of them.
self._server_tokens = self.request_token()
self.store["oauth-request-token"] = self._server_tokens["token"]
self.store["oauth-request-secret"] = self._server_tokens["token... | python | def oauth_request(self):
""" Makes a oauth connection """
# get tokens from server and make a dict of them.
self._server_tokens = self.request_token()
self.store["oauth-request-token"] = self._server_tokens["token"]
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xray7224/PyPump | pypump/pypump.py | PyPump.construct_oauth_url | def construct_oauth_url(self):
""" Constructs verifier OAuth URL """
response = self._requester(requests.head,
"{0}://{1}/".format(self.protocol, self.client.server),
allow_redirects=False
)
... | python | def construct_oauth_url(self):
""" Constructs verifier OAuth URL """
response = self._requester(requests.head,
"{0}://{1}/".format(self.protocol, self.client.server),
allow_redirects=False
)
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xray7224/PyPump | pypump/pypump.py | PyPump.setup_oauth_client | def setup_oauth_client(self, url=None):
""" Sets up client for requests to pump """
if url and "://" in url:
server, endpoint = self._deconstruct_url(url)
else:
server = self.client.server
if server not in self._server_cache:
self._add_client(server)
... | python | def setup_oauth_client(self, url=None):
""" Sets up client for requests to pump """
if url and "://" in url:
server, endpoint = self._deconstruct_url(url)
else:
server = self.client.server
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xray7224/PyPump | pypump/pypump.py | PyPump.request_token | def request_token(self):
""" Gets OAuth request token """
client = OAuth1(
client_key=self._server_cache[self.client.server].key,
client_secret=self._server_cache[self.client.server].secret,
callback_uri=self.callback,
)
request = {"auth": client}
... | python | def request_token(self):
""" Gets OAuth request token """
client = OAuth1(
client_key=self._server_cache[self.client.server].key,
client_secret=self._server_cache[self.client.server].secret,
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xray7224/PyPump | pypump/pypump.py | PyPump.request_access | def request_access(self, verifier):
""" Get OAuth access token so we can make requests """
client = OAuth1(
client_key=self._server_cache[self.client.server].key,
client_secret=self._server_cache[self.client.server].secret,
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""" Get OAuth access token so we can make requests """
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xray7224/PyPump | pypump/pypump.py | WebPump.logged_in | def logged_in(self):
""" Return boolean if is logged in """
if "oauth-access-token" not in self.store:
return False
response = self.request("/api/whoami", allow_redirects=False)
# It should response with a redirect to our profile if it's logged in
if response.status... | python | def logged_in(self):
""" Return boolean if is logged in """
if "oauth-access-token" not in self.store:
return False
response = self.request("/api/whoami", allow_redirects=False)
# It should response with a redirect to our profile if it's logged in
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreate | def cudnnCreate():
"""
Initialize cuDNN.
Initializes cuDNN and returns a handle to the cuDNN context.
Returns
-------
handle : cudnnHandle
cuDNN context
"""
handle = ctypes.c_void_p()
status = _libcudnn.cudnnCreate(ctypes.byref(handle))
cudnnCheckStatus(status)
re... | python | def cudnnCreate():
"""
Initialize cuDNN.
Initializes cuDNN and returns a handle to the cuDNN context.
Returns
-------
handle : cudnnHandle
cuDNN context
"""
handle = ctypes.c_void_p()
status = _libcudnn.cudnnCreate(ctypes.byref(handle))
cudnnCheckStatus(status)
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnDestroy | def cudnnDestroy(handle):
"""
Release cuDNN resources.
Release hardware resources used by cuDNN.
Parameters
----------
handle : cudnnHandle
cuDNN context.
"""
status = _libcudnn.cudnnDestroy(ctypes.c_void_p(handle))
cudnnCheckStatus(status) | python | def cudnnDestroy(handle):
"""
Release cuDNN resources.
Release hardware resources used by cuDNN.
Parameters
----------
handle : cudnnHandle
cuDNN context.
"""
status = _libcudnn.cudnnDestroy(ctypes.c_void_p(handle))
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetStream | def cudnnSetStream(handle, id):
"""
Set current cuDNN library stream.
Parameters
----------
handle : cudnnHandle
cuDNN context.
id : cudaStream
Stream Id.
"""
status = _libcudnn.cudnnSetStream(handle, id)
cudnnCheckStatus(status) | python | def cudnnSetStream(handle, id):
"""
Set current cuDNN library stream.
Parameters
----------
handle : cudnnHandle
cuDNN context.
id : cudaStream
Stream Id.
"""
status = _libcudnn.cudnnSetStream(handle, id)
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetStream | def cudnnGetStream(handle):
"""
Get current cuDNN library stream.
Parameters
----------
handle : int
cuDNN context.
Returns
-------
id : int
Stream ID.
"""
id = ctypes.c_void_p()
status = _libcudnn.cudnnGetStream(handle, ctypes.byref(id))
cudnnCheckStat... | python | def cudnnGetStream(handle):
"""
Get current cuDNN library stream.
Parameters
----------
handle : int
cuDNN context.
Returns
-------
id : int
Stream ID.
"""
id = ctypes.c_void_p()
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreateTensorDescriptor | def cudnnCreateTensorDescriptor():
"""
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-------
tensor_descriptor : int
Tensor descriptor.
"""
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"""
Create a Tensor descriptor object.
Allocates a cudnnTensorDescriptor_t structure and returns a pointer to it.
Returns
-------
tensor_descriptor : int
Tensor descriptor.
"""
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetTensor4dDescriptor | def cudnnSetTensor4dDescriptor(tensorDesc, format, dataType, n, c, h, w):
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetTensor4dDescriptorEx | def cudnnSetTensor4dDescriptorEx(tensorDesc, dataType, n, c, h, w, nStride, cStride, hStride, wStride):
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetTensor4dDescriptor | def cudnnGetTensor4dDescriptor(tensorDesc):
""""
Get parameters of a Tensor descriptor object.
This function queries the parameters of the previouly initialized Tensor4D descriptor
object.
Parameters
----------
tensorDesc : cudnnTensorDescriptor
Handle to a previously initialized t... | python | def cudnnGetTensor4dDescriptor(tensorDesc):
""""
Get parameters of a Tensor descriptor object.
This function queries the parameters of the previouly initialized Tensor4D descriptor
object.
Parameters
----------
tensorDesc : cudnnTensorDescriptor
Handle to a previously initialized t... | [
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreateFilterDescriptor | def cudnnCreateFilterDescriptor():
""""
Create a filter descriptor.
This function creates a filter descriptor object by allocating the memory needed
to hold its opaque structure.
Parameters
----------
Returns
-------
wDesc : cudnnFilterDescriptor
Handle to a newly allocate... | python | def cudnnCreateFilterDescriptor():
""""
Create a filter descriptor.
This function creates a filter descriptor object by allocating the memory needed
to hold its opaque structure.
Parameters
----------
Returns
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wDesc : cudnnFilterDescriptor
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetFilter4dDescriptor | def cudnnSetFilter4dDescriptor(wDesc, dataType, format, k, c, h, w):
""""
Initialize a filter descriptor.
This function initializes a previously created filter descriptor object into a 4D filter.
Filters layout must be contiguous in memory.
Parameters
----------
wDesc : cudnnFilterDescript... | python | def cudnnSetFilter4dDescriptor(wDesc, dataType, format, k, c, h, w):
""""
Initialize a filter descriptor.
This function initializes a previously created filter descriptor object into a 4D filter.
Filters layout must be contiguous in memory.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetFilter4dDescriptor | def cudnnGetFilter4dDescriptor(wDesc):
""""
Get parameters of filter descriptor.
This function queries the parameters of the previouly initialized filter descriptor object.
Parameters
----------
wDesc : cudnnFilterDescriptor
Handle to a previously created filter descriptor.
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Get parameters of filter descriptor.
This function queries the parameters of the previouly initialized filter descriptor object.
Parameters
----------
wDesc : cudnnFilterDescriptor
Handle to a previously created filter descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreateConvolutionDescriptor | def cudnnCreateConvolutionDescriptor():
""""
Create a convolution descriptor.
This function creates a convolution descriptor object by allocating the memory needed to
hold its opaque structure.
Returns
-------
convDesc : cudnnConvolutionDescriptor
Handle to newly allocated convolut... | python | def cudnnCreateConvolutionDescriptor():
""""
Create a convolution descriptor.
This function creates a convolution descriptor object by allocating the memory needed to
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Returns
-------
convDesc : cudnnConvolutionDescriptor
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetConvolution2dDescriptor | def cudnnSetConvolution2dDescriptor(convDesc, pad_h, pad_w, u, v, dilation_h, dilation_w, mode,
computeType):
""""
Initialize a convolution descriptor.
This function initializes a previously created convolution descriptor object into a 2D
correlation. This function a... | python | def cudnnSetConvolution2dDescriptor(convDesc, pad_h, pad_w, u, v, dilation_h, dilation_w, mode,
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Initialize a convolution descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolution2dDescriptor | def cudnnGetConvolution2dDescriptor(convDesc):
""""
Get a convolution descriptor.
This function queries a previously initialized 2D convolution descriptor object.
Parameters
----------
convDesc : cudnnConvolutionDescriptor
Handle to a previously created convolution descriptor.
Ret... | python | def cudnnGetConvolution2dDescriptor(convDesc):
""""
Get a convolution descriptor.
This function queries a previously initialized 2D convolution descriptor object.
Parameters
----------
convDesc : cudnnConvolutionDescriptor
Handle to a previously created convolution descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolution2dForwardOutputDim | def cudnnGetConvolution2dForwardOutputDim(convDesc, inputTensorDesc, wDesc):
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Return the dimensions of the output tensor given a convolution descriptor.
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Return the dimensions of the output tensor given a convolution descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolutionForwardAlgorithm | def cudnnGetConvolutionForwardAlgorithm(handle, srcDesc, wDesc,
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolutionForwardWorkspaceSize | def cudnnGetConvolutionForwardWorkspaceSize(handle, srcDesc, wDesc,
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This function returns the amount of GPU memory workspace the user needs
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Pa... | python | def cudnnGetConvolutionForwardWorkspaceSize(handle, srcDesc, wDesc,
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSoftmaxForward | def cudnnSoftmaxForward(handle, algorithm, mode, alpha, srcDesc, srcData, beta, destDesc, destData):
""""
This routing computes the softmax function
Parameters
----------
handle : cudnnHandle
Handle to a previously created cuDNN context.
algorithm : cudnnSoftmaxAlgorithm
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This routing computes the softmax function
Parameters
----------
handle : cudnnHandle
Handle to a previously created cuDNN context.
algorithm : cudnnSoftmaxAlgorithm
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreatePoolingDescriptor | def cudnnCreatePoolingDescriptor():
""""
Create pooling descriptor.
This function creates a pooling descriptor object by allocating the memory needed to
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Returns
-------
poolingDesc : cudnnPoolingDescriptor
Newly allocated pooling descriptor.
"""
... | python | def cudnnCreatePoolingDescriptor():
""""
Create pooling descriptor.
This function creates a pooling descriptor object by allocating the memory needed to
hold its opaque structure,
Returns
-------
poolingDesc : cudnnPoolingDescriptor
Newly allocated pooling descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetPooling2dDescriptor | def cudnnSetPooling2dDescriptor(poolingDesc, mode, windowHeight, windowWidth,
verticalPadding, horizontalPadding, verticalStride, horizontalStride):
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Initialize a 2D pooling descriptor.
This function initializes a previously created pooling descriptor object.
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Initialize a 2D pooling descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetPooling2dDescriptor | def cudnnGetPooling2dDescriptor(poolingDesc):
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poolingDesc : cudnnPoolingDescriptor
Handle to a previously created 2D pooling descriptor.
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poolingDesc : cudnnPoolingDescriptor
Handle to a previously created 2D pooling descriptor.
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hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnActivationBackward | def cudnnActivationBackward(handle, mode, alpha, srcDesc, srcData, srcDiffDesc, srcDiffData,
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""""
Gradient of activation function.
This routine computes the gradient of a neuron activation function.
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""""
Gradient of activation function.
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xray7224/PyPump | pypump/store.py | AbstractStore.__prefix_key | def __prefix_key(self, key):
""" This will add the prefix to the key if one exists on the store """
# If there isn't a prefix don't bother
if self.prefix is None:
return key
# Don't prefix key if it already has it
if key.startswith(self.prefix + "-"):
ret... | python | def __prefix_key(self, key):
""" This will add the prefix to the key if one exists on the store """
# If there isn't a prefix don't bother
if self.prefix is None:
return key
# Don't prefix key if it already has it
if key.startswith(self.prefix + "-"):
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xray7224/PyPump | pypump/store.py | AbstractStore.export | def export(self):
""" Exports as dictionary """
data = {}
for key, value in self.items():
data[key] = value
return data | python | def export(self):
""" Exports as dictionary """
data = {}
for key, value in self.items():
data[key] = value
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xray7224/PyPump | pypump/store.py | JSONStore.save | def save(self):
""" Saves dictionary to disk in JSON format. """
if self.filename is None:
raise StoreException("Filename must be set to write store to disk")
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""" Saves dictionary to disk in JSON format. """
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xray7224/PyPump | pypump/store.py | JSONStore.get_filename | def get_filename(cls):
""" Gets filename of store on disk """
config_home = os.environ.get("XDG_CONFIG_HOME", "~/.config")
config_home = os.path.expanduser(config_home)
base_path = os.path.join(config_home, "PyPump")
if not os.path.isdir(base_path):
os.makedirs(base_... | python | def get_filename(cls):
""" Gets filename of store on disk """
config_home = os.environ.get("XDG_CONFIG_HOME", "~/.config")
config_home = os.path.expanduser(config_home)
base_path = os.path.join(config_home, "PyPump")
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xray7224/PyPump | pypump/store.py | JSONStore.load | def load(cls, webfinger, pypump):
""" Load JSON from disk into store object """
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data = json.loads(data)
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""" Load JSON from disk into store object """
filename = cls.get_filename()
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data = json.loads(data)
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joeyespo/py-getch | getch/pause.py | pause | def pause(message='Press any key to continue . . . '):
"""
Prints the specified message if it's not None and waits for a keypress.
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if message is not None:
print(message, end='')
sys.stdout.flush()
getch()
print() | python | def pause(message='Press any key to continue . . . '):
"""
Prints the specified message if it's not None and waits for a keypress.
"""
if message is not None:
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woolfson-group/isambard | isambard/ampal/interactions.py | covalent_bonds | def covalent_bonds(atoms, threshold=1.1):
"""Returns all the covalent bonds in a list of `Atom` pairs.
Notes
-----
Uses information `element_data`, which can be accessed directly
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Parameters
----------
atoms : [(`Atom`... | python | def covalent_bonds(atoms, threshold=1.1):
"""Returns all the covalent bonds in a list of `Atom` pairs.
Notes
-----
Uses information `element_data`, which can be accessed directly
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woolfson-group/isambard | isambard/ampal/interactions.py | find_covalent_bonds | def find_covalent_bonds(ampal, max_range=2.2, threshold=1.1, tag=True):
"""Finds all covalent bonds in the AMPAL object.
Parameters
----------
ampal : AMPAL Object
Any AMPAL object with a `get_atoms` method.
max_range : float, optional
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"""Finds all covalent bonds in the AMPAL object.
Parameters
----------
ampal : AMPAL Object
Any AMPAL object with a `get_atoms` method.
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woolfson-group/isambard | isambard/ampal/interactions.py | generate_covalent_bond_graph | def generate_covalent_bond_graph(covalent_bonds):
"""Generates a graph of the covalent bond network described by the interactions.
Parameters
----------
covalent_bonds: [CovalentBond]
List of `CovalentBond`.
Returns
-------
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A graph of the covalent... | python | def generate_covalent_bond_graph(covalent_bonds):
"""Generates a graph of the covalent bond network described by the interactions.
Parameters
----------
covalent_bonds: [CovalentBond]
List of `CovalentBond`.
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woolfson-group/isambard | isambard/ampal/interactions.py | generate_bond_subgraphs_from_break | def generate_bond_subgraphs_from_break(bond_graph, atom1, atom2):
"""Splits the bond graph between two atoms to producing subgraphs.
Notes
-----
This will not work if there are cycles in the bond graph.
Parameters
----------
bond_graph: networkx.Graph
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woolfson-group/isambard | isambard/ampal/base_ampal.py | cap | def cap(v, l):
"""Shortens string is above certain length."""
s = str(v)
return s if len(s) <= l else s[-l:] | python | def cap(v, l):
"""Shortens string is above certain length."""
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woolfson-group/isambard | isambard/ampal/base_ampal.py | find_atoms_within_distance | def find_atoms_within_distance(atoms, cutoff_distance, point):
"""Returns atoms within the distance from the point.
Parameters
----------
atoms : [ampal.atom]
A list of `ampal.atoms`.
cutoff_distance : float
Maximum distance from point.
point : (float, float, float)
Refe... | python | def find_atoms_within_distance(atoms, cutoff_distance, point):
"""Returns atoms within the distance from the point.
Parameters
----------
atoms : [ampal.atom]
A list of `ampal.atoms`.
cutoff_distance : float
Maximum distance from point.
point : (float, float, float)
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woolfson-group/isambard | isambard/ampal/base_ampal.py | centre_of_atoms | def centre_of_atoms(atoms, mass_weighted=True):
""" Returns centre point of any list of atoms.
Parameters
----------
atoms : list
List of AMPAL atom objects.
mass_weighted : bool, optional
If True returns centre of mass, otherwise just geometric centre of points.
Returns
--... | python | def centre_of_atoms(atoms, mass_weighted=True):
""" Returns centre point of any list of atoms.
Parameters
----------
atoms : list
List of AMPAL atom objects.
mass_weighted : bool, optional
If True returns centre of mass, otherwise just geometric centre of points.
Returns
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.assign_force_field | def assign_force_field(self, ff, mol2=False):
"""Assigns force field parameters to Atoms in the AMPAL object.
Parameters
----------
ff: BuffForceField
The force field to be used for scoring.
mol2: bool, optional
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"""Assigns force field parameters to Atoms in the AMPAL object.
Parameters
----------
ff: BuffForceField
The force field to be used for scoring.
mol2: bool, optional
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.update_ff | def update_ff(self, ff, mol2=False, force_ff_assign=False):
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----------
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.get_internal_energy | def get_internal_energy(self, assign_ff=True, ff=None, mol2=False,
force_ff_assign=False):
"""Calculates the internal energy of the AMPAL object.
This method is assigned to the buff_internal_energy property,
using the default arguments.
Parameters
--... | python | def get_internal_energy(self, assign_ff=True, ff=None, mol2=False,
force_ff_assign=False):
"""Calculates the internal energy of the AMPAL object.
This method is assigned to the buff_internal_energy property,
using the default arguments.
Parameters
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.rotate | def rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True):
"""Rotates every atom in the AMPAL object.
Parameters
----------
angle : float
Angle that AMPAL object will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about w... | python | def rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True):
"""Rotates every atom in the AMPAL object.
Parameters
----------
angle : float
Angle that AMPAL object will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about w... | [
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Angle that AMPAL object will be rotated.
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Axis about which the AMPAL object will be rotated.
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.translate | def translate(self, vector, inc_alt_states=True):
"""Translates every atom in the AMPAL object.
Parameters
----------
vector : 3D Vector (tuple, list, numpy.array)
Vector used for translation.
inc_alt_states : bool, optional
If true, will rotate atoms in ... | python | def translate(self, vector, inc_alt_states=True):
"""Translates every atom in the AMPAL object.
Parameters
----------
vector : 3D Vector (tuple, list, numpy.array)
Vector used for translation.
inc_alt_states : bool, optional
If true, will rotate atoms in ... | [
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Vector used for translation.
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woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.rmsd | def rmsd(self, other, backbone=False):
"""Calculates the RMSD between two AMPAL objects.
Notes
-----
No fitting operation is performs and both AMPAL objects must
have the same number of atoms.
Parameters
----------
other : AMPAL Object
Any AM... | python | def rmsd(self, other, backbone=False):
"""Calculates the RMSD between two AMPAL objects.
Notes
-----
No fitting operation is performs and both AMPAL objects must
have the same number of atoms.
Parameters
----------
other : AMPAL Object
Any AM... | [
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other : AMPAL Object
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.append | def append(self, item):
"""Appends a `Monomer to the `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(item, Monomer):
self._monomers.append(item)
else:
raise TypeError(
'Only Monomer objects can be append... | python | def append(self, item):
"""Appends a `Monomer to the `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(item, Monomer):
self._monomers.append(item)
else:
raise TypeError(
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.extend | def extend(self, polymer):
"""Extends the `Polymer` with the contents of another `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(polymer, Polymer):
self._monomers.extend(polymer)
else:
raise TypeError(
'... | python | def extend(self, polymer):
"""Extends the `Polymer` with the contents of another `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(polymer, Polymer):
self._monomers.extend(polymer)
else:
raise TypeError(
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.get_monomers | def get_monomers(self, ligands=True):
"""Retrieves all the `Monomers` from the AMPAL object.
Parameters
----------
ligands : bool, optional
If true, will include ligand `Monomers`.
"""
if ligands and self.ligands:
monomers = self._monomers + self.... | python | def get_monomers(self, ligands=True):
"""Retrieves all the `Monomers` from the AMPAL object.
Parameters
----------
ligands : bool, optional
If true, will include ligand `Monomers`.
"""
if ligands and self.ligands:
monomers = self._monomers + self.... | [
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.get_atoms | def get_atoms(self, ligands=True, inc_alt_states=False):
"""Flat list of all the Atoms in the Polymer.
Parameters
----------
inc_alt_states : bool
If true atoms from alternate conformations are included rather
than only the "active" states.
Returns
... | python | def get_atoms(self, ligands=True, inc_alt_states=False):
"""Flat list of all the Atoms in the Polymer.
Parameters
----------
inc_alt_states : bool
If true atoms from alternate conformations are included rather
than only the "active" states.
Returns
... | [
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.relabel_monomers | def relabel_monomers(self, labels=None):
"""Relabels the either in numerically or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
Raised if the number of labels does not... | python | def relabel_monomers(self, labels=None):
"""Relabels the either in numerically or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.relabel_atoms | def relabel_atoms(self, start=1):
"""Relabels all `Atoms` in numerical order.
Parameters
----------
start : int, optional
Offset the labelling by `start` residues.
"""
counter = start
for atom in self.get_atoms():
atom.id = counter
... | python | def relabel_atoms(self, start=1):
"""Relabels all `Atoms` in numerical order.
Parameters
----------
start : int, optional
Offset the labelling by `start` residues.
"""
counter = start
for atom in self.get_atoms():
atom.id = counter
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.make_pdb | def make_pdb(self, alt_states=False, inc_ligands=True):
"""Generates a PDB string for the `Polymer`.
Parameters
----------
alt_states : bool, optional
Include alternate conformations for `Monomers` in PDB.
inc_ligands : bool, optional
Includes `Ligands` i... | python | def make_pdb(self, alt_states=False, inc_ligands=True):
"""Generates a PDB string for the `Polymer`.
Parameters
----------
alt_states : bool, optional
Include alternate conformations for `Monomers` in PDB.
inc_ligands : bool, optional
Includes `Ligands` i... | [
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woolfson-group/isambard | isambard/ampal/base_ampal.py | Atom.rotate | def rotate(self, angle, axis, point=None, radians=False):
"""Rotates `Atom` by `angle`.
Parameters
----------
angle : float
Angle that `Atom` will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about which the `Atom` will be rotated.
... | python | def rotate(self, angle, axis, point=None, radians=False):
"""Rotates `Atom` by `angle`.
Parameters
----------
angle : float
Angle that `Atom` will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about which the `Atom` will be rotated.
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woolfson-group/isambard | isambard/tools/file_parsing.py | dict_from_mmcif | def dict_from_mmcif(mmcif, path=True):
"""Parse mmcif file into a dictionary.
Notes
-----
Full list of keys/value types, and further information on them can be viewed here:
http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
All values in the returned dict are str or list(str).... | python | def dict_from_mmcif(mmcif, path=True):
"""Parse mmcif file into a dictionary.
Notes
-----
Full list of keys/value types, and further information on them can be viewed here:
http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
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woolfson-group/isambard | isambard/tools/file_parsing.py | get_protein_dict | def get_protein_dict(cif_data):
""" Parse cif_data dict for a subset of its data.
Notes
-----
cif_data dict contains all the data from the .cif file, with values as strings.
This function returns a more 'human readable' dictionary of key-value pairs.
The keys have simpler (and still often more ... | python | def get_protein_dict(cif_data):
""" Parse cif_data dict for a subset of its data.
Notes
-----
cif_data dict contains all the data from the .cif file, with values as strings.
This function returns a more 'human readable' dictionary of key-value pairs.
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cif_data dict contains all the data from the .cif file, with values as strings.
This function returns a more 'human readable' dictionary of key-value pairs.
The keys have simpler (and still often more descriptive!) names, and the values are ... | [
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woolfson-group/isambard | isambard/tools/file_parsing.py | parse_PISCES_output | def parse_PISCES_output(pisces_output, path=False):
""" Takes the output list of a PISCES cull and returns in a usable dictionary.
Notes
-----
Designed for outputs of protein sequence redundancy culls conducted using the PISCES server.
http://dunbrack.fccc.edu/PISCES.php
G. Wang and R. L. Dunbr... | python | def parse_PISCES_output(pisces_output, path=False):
""" Takes the output list of a PISCES cull and returns in a usable dictionary.
Notes
-----
Designed for outputs of protein sequence redundancy culls conducted using the PISCES server.
http://dunbrack.fccc.edu/PISCES.php
G. Wang and R. L. Dunbr... | [
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http://dunbrack.fccc.edu/PISCES.php
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woolfson-group/isambard | isambard/tools/file_parsing.py | download_decode | def download_decode(URL, encoding='utf-8', verbose=True):
""" Downloads data from URL and returns decoded contents."""
if verbose:
print("Downloading data from " + URL)
req = Request(URL)
try:
with urlopen(req) as u:
decoded_file = u.read().decode(encoding)
except URLErro... | python | def download_decode(URL, encoding='utf-8', verbose=True):
""" Downloads data from URL and returns decoded contents."""
if verbose:
print("Downloading data from " + URL)
req = Request(URL)
try:
with urlopen(req) as u:
decoded_file = u.read().decode(encoding)
except URLErro... | [
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woolfson-group/isambard | isambard/tools/file_parsing.py | olderado_best_model | def olderado_best_model(pdb_id):
""" Checks the Olderado web server and returns the most representative conformation for PDB NMR structures.
Notes
-----
Uses OLDERADO from the EBI.
See http://www.ebi.ac.uk/pdbe/nmr/olderado/ and citations therein.
Parameters
----------
pdb_id : str
... | python | def olderado_best_model(pdb_id):
""" Checks the Olderado web server and returns the most representative conformation for PDB NMR structures.
Notes
-----
Uses OLDERADO from the EBI.
See http://www.ebi.ac.uk/pdbe/nmr/olderado/ and citations therein.
Parameters
----------
pdb_id : str
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pdb_id : str
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woolfson-group/isambard | isambard/optimisation/optimizer.py | buff_eval | def buff_eval(params):
"""Builds and evaluates BUFF energy of model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence,
and the parameters for model building.
Returns
-------
model.bude_score: float
BUF... | python | def buff_eval(params):
"""Builds and evaluates BUFF energy of model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence,
and the parameters for model building.
Returns
-------
model.bude_score: float
BUF... | [
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woolfson-group/isambard | isambard/optimisation/optimizer.py | buff_internal_eval | def buff_internal_eval(params):
"""Builds and evaluates BUFF internal energy of a model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence
and the parameters for model building.
Returns
-------
model.bude_score... | python | def buff_internal_eval(params):
"""Builds and evaluates BUFF internal energy of a model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence
and the parameters for model building.
Returns
-------
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woolfson-group/isambard | isambard/optimisation/optimizer.py | rmsd_eval | def rmsd_eval(rmsd_params):
"""Builds a model and runs profit against a reference model.
Parameters
----------
rmsd_params
Returns
-------
rmsd: float
rmsd against reference model as calculated by profit.
"""
specification, sequence, parsed_ind, reference_pdb = rmsd_params
... | python | def rmsd_eval(rmsd_params):
"""Builds a model and runs profit against a reference model.
Parameters
----------
rmsd_params
Returns
-------
rmsd: float
rmsd against reference model as calculated by profit.
"""
specification, sequence, parsed_ind, reference_pdb = rmsd_params
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woolfson-group/isambard | isambard/optimisation/optimizer.py | comparator_eval | def comparator_eval(comparator_params):
"""Gets BUFF score for interaction between two AMPAL objects
"""
top1, top2, params1, params2, seq1, seq2, movements = comparator_params
xrot, yrot, zrot, xtrans, ytrans, ztrans = movements
obj1 = top1(*params1)
obj2 = top2(*params2)
obj2.rotate(xrot, ... | python | def comparator_eval(comparator_params):
"""Gets BUFF score for interaction between two AMPAL objects
"""
top1, top2, params1, params2, seq1, seq2, movements = comparator_params
xrot, yrot, zrot, xtrans, ytrans, ztrans = movements
obj1 = top1(*params1)
obj2 = top2(*params2)
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woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseOptimizer.parameters | def parameters(self, sequence, value_means, value_ranges, arrangement):
"""Relates the individual to be evolved to the full parameter string.
Parameters
----------
sequence: str
Full amino acid sequence for specification object to be
optimized. Must be equal to t... | python | def parameters(self, sequence, value_means, value_ranges, arrangement):
"""Relates the individual to be evolved to the full parameter string.
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----------
sequence: str
Full amino acid sequence for specification object to be
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woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseScore.make_energy_funnel_data | def make_energy_funnel_data(self, cores=1):
"""Compares models created during the minimisation to the best model.
Returns
-------
energy_rmsd_gen: [(float, float, int)]
A list of triples containing the BUFF score, RMSD to the
top model and generation of a model g... | python | def make_energy_funnel_data(self, cores=1):
"""Compares models created during the minimisation to the best model.
Returns
-------
energy_rmsd_gen: [(float, float, int)]
A list of triples containing the BUFF score, RMSD to the
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woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseScore.funnel_rebuild | def funnel_rebuild(psg_trm_spec):
"""Rebuilds a model and compares it to a reference model.
Parameters
----------
psg_trm: (([float], float, int), AMPAL, specification)
A tuple containing the parameters, score and generation for a
model as well as a model of the ... | python | def funnel_rebuild(psg_trm_spec):
"""Rebuilds a model and compares it to a reference model.
Parameters
----------
psg_trm: (([float], float, int), AMPAL, specification)
A tuple containing the parameters, score and generation for a
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woolfson-group/isambard | isambard/optimisation/optimizer.py | OptDE.update_pop | def update_pop(self):
"""Updates the population according to crossover and fitness criteria.
"""
candidates = []
for ind in self.population:
candidates.append(self.crossover(ind))
self._params['model_count'] += len(candidates)
self.assign_fitnesses(candidates)... | python | def update_pop(self):
"""Updates the population according to crossover and fitness criteria.
"""
candidates = []
for ind in self.population:
candidates.append(self.crossover(ind))
self._params['model_count'] += len(candidates)
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woolfson-group/isambard | isambard/optimisation/optimizer.py | OptPSO.initialize_pop | def initialize_pop(self):
"""Generates initial population with random positions and speeds."""
self.population = self.toolbox.swarm(n=self._params['popsize'])
if self._params['neighbours']:
for i in range(len(self.population)):
self.population[i].ident = i
... | python | def initialize_pop(self):
"""Generates initial population with random positions and speeds."""
self.population = self.toolbox.swarm(n=self._params['popsize'])
if self._params['neighbours']:
for i in range(len(self.population)):
self.population[i].ident = i
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woolfson-group/isambard | isambard/optimisation/optimizer.py | OptGA.initialize_pop | def initialize_pop(self):
"""Assigns initial fitnesses."""
self.toolbox.register("individual", self.generate)
self.toolbox.register("population", tools.initRepeat,
list, self.toolbox.individual)
self.population = self.toolbox.population(n=self._params['popsi... | python | def initialize_pop(self):
"""Assigns initial fitnesses."""
self.toolbox.register("individual", self.generate)
self.toolbox.register("population", tools.initRepeat,
list, self.toolbox.individual)
self.population = self.toolbox.population(n=self._params['popsi... | [
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woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameter.randomise_proposed_value | def randomise_proposed_value(self):
"""Creates a randomly the proposed value.
Raises
------
TypeError
Raised if this method is called on a static value.
TypeError
Raised if the parameter type is unknown.
"""
if self.parameter_type is MMCPa... | python | def randomise_proposed_value(self):
"""Creates a randomly the proposed value.
Raises
------
TypeError
Raised if this method is called on a static value.
TypeError
Raised if the parameter type is unknown.
"""
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woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameter.accept_proposed_value | def accept_proposed_value(self):
"""Changes the current value to the proposed value."""
if self.proposed_value is not None:
self.current_value = self.proposed_value
self.proposed_value = None
return | python | def accept_proposed_value(self):
"""Changes the current value to the proposed value."""
if self.proposed_value is not None:
self.current_value = self.proposed_value
self.proposed_value = None
return | [
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woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation.start_optimisation | def start_optimisation(self, rounds, temp=298.15):
"""Begin the optimisation run.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
"""
... | python | def start_optimisation(self, rounds, temp=298.15):
"""Begin the optimisation run.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
"""
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The number of rounds of optimisation to perform.
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The temperature (in K) used during the optimisation. | [
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woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation._generate_initial_model | def _generate_initial_model(self):
"""Creates the initial model for the optimistation.
Raises
------
TypeError
Raised if the model failed to build. This could be due to
parameters being passed to the specification in the wrong
format.
"""
... | python | def _generate_initial_model(self):
"""Creates the initial model for the optimistation.
Raises
------
TypeError
Raised if the model failed to build. This could be due to
parameters being passed to the specification in the wrong
format.
"""
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woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation._mmc_loop | def _mmc_loop(self, rounds, temp=298.15, verbose=True):
"""The main MMC loop.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
verbose :... | python | def _mmc_loop(self, rounds, temp=298.15, verbose=True):
"""The main MMC loop.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
verbose :... | [
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The number of rounds of optimisation to perform.
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The temperature (in K) used during the optimisation.
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woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | DE._crossover | def _crossover(self, ind):
"""Used by the evolution process to generate a new individual.
Notes
-----
This is a tweaked version of the classical DE crossover
algorithm, the main difference that candidate parameters are
generated using a lognormal distribution. Bound hand... | python | def _crossover(self, ind):
"""Used by the evolution process to generate a new individual.
Notes
-----
This is a tweaked version of the classical DE crossover
algorithm, the main difference that candidate parameters are
generated using a lognormal distribution. Bound hand... | [
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woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | PSO._generate | def _generate(self):
"""Generates a particle using the creator function.
Notes
-----
Position and speed are uniformly randomly seeded within
allowed bounds. The particle also has speed limit settings
taken from global values.
Returns
-------
part... | python | def _generate(self):
"""Generates a particle using the creator function.
Notes
-----
Position and speed are uniformly randomly seeded within
allowed bounds. The particle also has speed limit settings
taken from global values.
Returns
-------
part... | [
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Returns
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woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | PSO.update_particle | def update_particle(self, part, chi=0.729843788, c=2.05):
"""Constriction factor update particle method.
Notes
-----
Looks for a list of neighbours attached to a particle and
uses the particle's best position and that of the best
neighbour.
"""
neighbour_... | python | def update_particle(self, part, chi=0.729843788, c=2.05):
"""Constriction factor update particle method.
Notes
-----
Looks for a list of neighbours attached to a particle and
uses the particle's best position and that of the best
neighbour.
"""
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Looks for a list of neighbours attached to a particle and
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woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | CMAES._make_individual | def _make_individual(self, paramlist):
"""Makes an individual particle."""
part = creator.Individual(paramlist)
part.ident = None
return part | python | def _make_individual(self, paramlist):
"""Makes an individual particle."""
part = creator.Individual(paramlist)
part.ident = None
return part | [
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woolfson-group/isambard | isambard/add_ons/filesystem.py | number_of_mmols | def number_of_mmols(code):
""" Number of .mmol files associated with code in the PDBE.
Notes
-----
This function makes a series of calls to the PDBE website using the requests module. This can make it slow!
Parameters
----------
code : str
PDB code.
Returns
-------
num... | python | def number_of_mmols(code):
""" Number of .mmol files associated with code in the PDBE.
Notes
-----
This function makes a series of calls to the PDBE website using the requests module. This can make it slow!
Parameters
----------
code : str
PDB code.
Returns
-------
num... | [
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Notes
-----
This function makes a series of calls to the PDBE website using the requests module. This can make it slow!
Parameters
----------
code : str
PDB code.
Returns
-------
num_mmols : int
Raises
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woolfson-group/isambard | isambard/add_ons/filesystem.py | get_mmol | def get_mmol(code, mmol_number=None, outfile=None):
""" Get mmol file from PDBe and return its content as a string. Write to file if outfile given.
Parameters
----------
code : str
PDB code.
mmol_number : int
mmol number (biological assembly number) of file to download. Numbers from... | python | def get_mmol(code, mmol_number=None, outfile=None):
""" Get mmol file from PDBe and return its content as a string. Write to file if outfile given.
Parameters
----------
code : str
PDB code.
mmol_number : int
mmol number (biological assembly number) of file to download. Numbers from... | [
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PDB code.
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mmol number (biological assembly number) of file to download. Numbers from PDBe.
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woolfson-group/isambard | isambard/add_ons/filesystem.py | get_mmcif | def get_mmcif(code, outfile=None):
""" Get mmcif file associated with code from PDBE.
Parameters
----------
code : str
PDB code.
outfile : str
Filepath. Writes returned value to this file.
Returns
-------
mmcif_file : str
Filepath to the mmcif file.
"""
... | python | def get_mmcif(code, outfile=None):
""" Get mmcif file associated with code from PDBE.
Parameters
----------
code : str
PDB code.
outfile : str
Filepath. Writes returned value to this file.
Returns
-------
mmcif_file : str
Filepath to the mmcif file.
"""
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PDB code.
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Filepath. Writes returned value to this file.
Returns
-------
mmcif_file : str
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