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Kortemme-Lab/klab | klab/biblio/doi.py | DOI.get_info | def get_info(self):
'Retrieve the data from CrossRef.'
escaped_doi = urllib2.quote(self.doi, '')
html = get_resource("www.crossref.org", '/guestquery?queryType=doi&restype=unixref&doi=%s&doi_search=Search' % escaped_doi)
xml_matches = []
for m in re.finditer('(<doi_records>.*?</... | python | def get_info(self):
'Retrieve the data from CrossRef.'
escaped_doi = urllib2.quote(self.doi, '')
html = get_resource("www.crossref.org", '/guestquery?queryType=doi&restype=unixref&doi=%s&doi_search=Search' % escaped_doi)
xml_matches = []
for m in re.finditer('(<doi_records>.*?</... | [
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Kortemme-Lab/klab | klab/bio/spackle.py | Spackler.add_backbone_atoms_linearly_from_loop_filepaths | def add_backbone_atoms_linearly_from_loop_filepaths(self, loop_json_filepath, fasta_filepath, residue_ids):
'''A utility wrapper around add_backbone_atoms_linearly. Adds backbone atoms in a straight line from the first to
the last residue of residue_ids.
loop_json_filepath is a path to a ... | python | def add_backbone_atoms_linearly_from_loop_filepaths(self, loop_json_filepath, fasta_filepath, residue_ids):
'''A utility wrapper around add_backbone_atoms_linearly. Adds backbone atoms in a straight line from the first to
the last residue of residue_ids.
loop_json_filepath is a path to a ... | [
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Kortemme-Lab/klab | klab/bio/spackle.py | Spackler.add_atoms_linearly | def add_atoms_linearly(self, start_atom, end_atom, new_atoms, jitterbug = 0.2):
'''A low-level function which adds new_atoms between start_atom and end_atom. This function does not validate the
input i.e. the calling functions are responsible for ensuring that the insertion makes sense.
R... | python | def add_atoms_linearly(self, start_atom, end_atom, new_atoms, jitterbug = 0.2):
'''A low-level function which adds new_atoms between start_atom and end_atom. This function does not validate the
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PBR/MQ2 | MQ2/qtl.py | QTL.to_string | def to_string(self):
""" Return the string as it should be presented in a MapChart
input file.
"""
return '%s %s %s %s %s' % (
self.trait, self.start_position, self.peak_start_position,
self.peak_stop_position, self.stop_position) | python | def to_string(self):
""" Return the string as it should be presented in a MapChart
input file.
"""
return '%s %s %s %s %s' % (
self.trait, self.start_position, self.peak_start_position,
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aacanakin/glim | glim/cli.py | main | def main():
"""
The single entry point to glim command line interface.Main method is called
from pypi console_scripts key or by glim.py on root.This function
initializes a new app given the glim commands and app commands if app
exists.
Usage
-----
$ python glim/cli.py start
$ py... | python | def main():
"""
The single entry point to glim command line interface.Main method is called
from pypi console_scripts key or by glim.py on root.This function
initializes a new app given the glim commands and app commands if app
exists.
Usage
-----
$ python glim/cli.py start
$ py... | [
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$ python glim/cli.py start
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aacanakin/glim | glim/cli.py | make_app | def make_app(env, commandadapter=None):
"""
Function creates an app given environment
"""
mconfig = import_module('app.config.%s' % env, pass_errors=True)
if mconfig is None and paths.app_exists():
print(colored('Configuration for "%s" environment is not found' % env, 'red'))
return ... | python | def make_app(env, commandadapter=None):
"""
Function creates an app given environment
"""
mconfig = import_module('app.config.%s' % env, pass_errors=True)
if mconfig is None and paths.app_exists():
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projectshift/shift-boiler | boiler/user/views_social.py | BaseSocial.callback | def callback(self):
""" Generate callback url for provider """
next = request.args.get('next') or None
endpoint = 'social.{}.handle'.format(self.provider)
return url_for(endpoint, _external=True, next=next) | python | def callback(self):
""" Generate callback url for provider """
next = request.args.get('next') or None
endpoint = 'social.{}.handle'.format(self.provider)
return url_for(endpoint, _external=True, next=next) | [
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projectshift/shift-boiler | boiler/user/views_social.py | BaseSocial.next | def next(self):
""" Where to redirect after authorization """
next = request.args.get('next')
if next is None:
params = self.default_redirect_params
next = url_for(self.default_redirect_endpoint, **params)
return next | python | def next(self):
""" Where to redirect after authorization """
next = request.args.get('next')
if next is None:
params = self.default_redirect_params
next = url_for(self.default_redirect_endpoint, **params)
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projectshift/shift-boiler | boiler/user/views_social.py | BaseHandle.dispatch_request | def dispatch_request(self):
""" Handle redirect back from provider """
if current_user.is_authenticated:
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# clear previous!
if 'social_data' in session:
del session['social_data']
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tech-pi/doufo | src/python/doufo/tensor/binary.py | project | def project(v, n):
"""
Project Vector v onto plane with normal vector n.
"""
return v - matmul(v, n) * n / (norm(n) ** 2.0) | python | def project(v, n):
"""
Project Vector v onto plane with normal vector n.
"""
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46elks/elkme | elkme/main.py | main | def main():
"""Executed on run"""
args = parse_args()
if args.version:
from .__init__ import __version__, __release_date__
print('elkme %s (release date %s)' % (__version__, __release_date__))
print('(c) 2015-2017 46elks AB <hello@46elks.com>')
print(small_elk)
exit(... | python | def main():
"""Executed on run"""
args = parse_args()
if args.version:
from .__init__ import __version__, __release_date__
print('elkme %s (release date %s)' % (__version__, __release_date__))
print('(c) 2015-2017 46elks AB <hello@46elks.com>')
print(small_elk)
exit(... | [
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clement-alexandre/TotemBionet | totembionet/src/ggea/ggea.py | Graph._build_graph | def _build_graph(self) -> nx.DiGraph:
""" Private method to build the graph from the model. """
digraph = nx.DiGraph()
for state in self.model.all_states():
self._number_of_states += 1
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""" Private method to build the graph from the model. """
digraph = nx.DiGraph()
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clement-alexandre/TotemBionet | totembionet/src/ggea/ggea.py | Graph._transform_state_to_string | def _transform_state_to_string(self, state: State) -> str:
"""
Private method which transform a state to a string.
Examples
--------
The model contains 2 genes: operon = {0, 1, 2}
mucuB = {0, 1}
>>> graph._transform_state_to_string({... | python | def _transform_state_to_string(self, state: State) -> str:
"""
Private method which transform a state to a string.
Examples
--------
The model contains 2 genes: operon = {0, 1, 2}
mucuB = {0, 1}
>>> graph._transform_state_to_string({... | [
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clement-alexandre/TotemBionet | totembionet/src/ggea/ggea.py | Graph.as_dot | def as_dot(self) -> str:
""" Return as a string the dot version of the graph. """
return nx.drawing.nx_pydot.to_pydot(self._graph).to_string() | python | def as_dot(self) -> str:
""" Return as a string the dot version of the graph. """
return nx.drawing.nx_pydot.to_pydot(self._graph).to_string() | [
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clement-alexandre/TotemBionet | totembionet/src/ggea/ggea.py | Graph.export_to_dot | def export_to_dot(self, filename: str = 'output') -> None:
""" Export the graph to the dot file "filename.dot". """
with open(filename + '.dot', 'w') as output:
output.write(self.as_dot()) | python | def export_to_dot(self, filename: str = 'output') -> None:
""" Export the graph to the dot file "filename.dot". """
with open(filename + '.dot', 'w') as output:
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speechinformaticslab/vfclust | vfclust/vfclust.py | get_duration_measures | def get_duration_measures(source_file_path,
output_path=None,
phonemic=False,
semantic=False,
quiet=False,
similarity_file = None,
threshold = None):
"""Parses ... | python | def get_duration_measures(source_file_path,
output_path=None,
phonemic=False,
semantic=False,
quiet=False,
similarity_file = None,
threshold = None):
"""Parses ... | [
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.create_from_textgrid | def create_from_textgrid(self,word_list):
""" Fills the ParsedResponse object with a list of TextGrid.Word objects originally from a .TextGrid file.
:param list word_list: List of TextGrid.Word objects corresponding to words/tokens in the subject response.
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""" Fills the ParsedResponse object with a list of TextGrid.Word objects originally from a .TextGrid file.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.lemmatize | def lemmatize(self):
"""Lemmatize all Units in self.unit_list.
Modifies:
- self.unit_list: converts the .text property into its lemmatized form.
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those words' respective canonical forms. This is done to en... | python | def lemmatize(self):
"""Lemmatize all Units in self.unit_list.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.tokenize | def tokenize(self):
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Modifies:
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This is done because many names may be composed of multiple words, e.g.,
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"""Tokenizes all multiword names in the list of Units.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.make_compound_word | def make_compound_word(self, start_index, how_many):
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:param int start_index: Index of first Unit in self.unit_list to be combined
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"""Combines two Units in self.unit_list to make a compound word token.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.remove_unit | def remove_unit(self, index):
'''Removes the unit at the given index in self.unit_list. Does not modify any other units.'''
if not self.quiet:
print "Removing", self.unit_list[index].text
self.unit_list.pop(index) | python | def remove_unit(self, index):
'''Removes the unit at the given index in self.unit_list. Does not modify any other units.'''
if not self.quiet:
print "Removing", self.unit_list[index].text
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.combine_same_stem_units | def combine_same_stem_units(self, index):
"""Combines adjacent words with the same stem into a single unit.
:param int index: Index of Unit in self.unit_list to be combined with the
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Modifies:
- self.unit_list: Modifies the .original_text property of... | python | def combine_same_stem_units(self, index):
"""Combines adjacent words with the same stem into a single unit.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.display | def display(self):
"""Pretty-prints the ParsedResponse to the screen."""
table_list = []
table_list.append(("Text","Orig. Text","Start time","End time", "Phonetic"))
for unit in self.unit_list:
table_list.append((unit.text,
"/".join(unit.origin... | python | def display(self):
"""Pretty-prints the ParsedResponse to the screen."""
table_list = []
table_list.append(("Text","Orig. Text","Start time","End time", "Phonetic"))
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.generate_phonetic_representation | def generate_phonetic_representation(self, word):
"""
Returns a generated phonetic representation for a word.
:param str word: a word to be phoneticized.
:return: A list of phonemes representing the phoneticized word.
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Returns a generated phonetic representation for a word.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.modify_phonetic_representation | def modify_phonetic_representation(self, phonetic_representation):
""" Returns a compact phonetic representation given a CMUdict-formatted representation.
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speechinformaticslab/vfclust | vfclust/vfclust.py | ParsedResponse.clean | def clean(self):
""" Removes any Units that are not applicable given the current semantic or phonetic category.
Modifies:
- self.unit_list: Removes Units from this list that do not fit into the clustering category.
it does by by either combining units to make compound words,... | python | def clean(self):
""" Removes any Units that are not applicable given the current semantic or phonetic category.
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.load_lsa_information | def load_lsa_information(self):
"""Loads a dictionary from disk that maps permissible words to their LSA term vectors."""
if not (49 < int(self.clustering_parameter) < 101):
raise Exception('Only LSA dimensionalities in the range 50-100' +
' are supported.')
... | python | def load_lsa_information(self):
"""Loads a dictionary from disk that maps permissible words to their LSA term vectors."""
if not (49 < int(self.clustering_parameter) < 101):
raise Exception('Only LSA dimensionalities in the range 50-100' +
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.get_similarity_measures | def get_similarity_measures(self):
"""Helper function for computing similarity measures."""
if not self.quiet:
print
print "Computing", self.current_similarity_measure, "similarity..."
self.compute_similarity_scores() | python | def get_similarity_measures(self):
"""Helper function for computing similarity measures."""
if not self.quiet:
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.get_raw_counts | def get_raw_counts(self):
"""Determines counts for unique words, repetitions, etc using the raw text response.
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- COUNT_total_words: count of words (i.e. utterances with semantic content) spoken
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"""Determines counts for unique words, repetitions, etc using the raw text response.
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_similarity_score | def compute_similarity_score(self, unit1, unit2):
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""" Returns the similarity score between two words.
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_collection_measures | def compute_collection_measures(self, no_singletons=False):
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_duration_measures | def compute_duration_measures(self):
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_response_vowel_duration | def compute_response_vowel_duration(self, prefix):
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_between_collection_interval_duration | def compute_between_collection_interval_duration(self, prefix):
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.compute_within_collection_interval_duration | def compute_within_collection_interval_duration(self, prefix):
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speechinformaticslab/vfclust | vfclust/vfclust.py | VFClustEngine.print_output | def print_output(self):
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inveniosoftware/invenio-pidrelations | invenio_pidrelations/contrib/versioning.py | PIDNodeVersioning.insert_child | def insert_child(self, child_pid, index=-1):
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if child_pid.status != PIDStatus.REGISTERED:
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"""Insert a Version child PID."""
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inveniosoftware/invenio-pidrelations | invenio_pidrelations/contrib/versioning.py | PIDNodeVersioning.remove_child | def remove_child(self, child_pid):
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Extends the base method call by redirecting from the parent to the
last child.
"""
if child_pid.status == PIDStatus.RESERVED:
raise PIDRelationConsistencyError(
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adaptive-learning/proso-apps | proso_feedback/views.py | feedback | def feedback(request):
"""
Send feedback to the authors of the system.
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html
turn on the HTML version of the API
POST parameters (JSON):
text:
the main feedback content
email (optional):
user's e-mail
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"""
Send feedback to the authors of the system.
GET parameters:
html
turn on the HTML version of the API
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the main feedback content
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html
turn on the HTML version of the API
POST parameters (JSON):
text:
the main feedback content
email (optional):
user's e-mail
username (optional):
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adaptive-learning/proso-apps | proso_feedback/views.py | rating | def rating(request):
"""
Rate the current practice.
GET parameters:
html
turn on the HTML version of the API
POST parameters (JSON):
value:
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(2) appropriate... | python | def rating(request):
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Rate the current practice.
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html
turn on the HTML version of the API
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projectshift/shift-boiler | boiler/cli/colors.py | colour | def colour(colour, message, bold=False):
""" Color a message """
return style(fg=colour, text=message, bold=bold) | python | def colour(colour, message, bold=False):
""" Color a message """
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kata198/QueryableList | QueryableList/Base.py | QueryableListBase.customFilter | def customFilter(self, filterFunc):
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MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/credential.py | Credential.uri | def uri(self):
"""
Return sqlalchemy connect string URI.
"""
return self.uri_template.format(
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port="" if self.port is None else self.port,
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password="" if self.passw... | python | def uri(self):
"""
Return sqlalchemy connect string URI.
"""
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MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/credential.py | Credential.from_json | def from_json(cls, json_file, json_path=None, key_mapping=None):
"""
Load connection credential from json file.
:param json_file: str, path to json file
:param json_path: str, dot notation of the path to the credential dict.
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"""
Load connection credential from json file.
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MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/credential.py | Credential.from_s3_json | def from_s3_json(cls, bucket_name, key,
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aws_profile=None,
aws_access_key_id=None,
aws_secret_access_key=None,
region_name=None): # pragma: no cover
"""
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aws_secret_access_key=None,
region_name=None): # pragma: no cover
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"""
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MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/credential.py | Credential.to_dict | def to_dict(self):
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password=self.password,
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Convert credentials into a dict.
"""
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gregoil/ipdbugger | ipdbugger/__init__.py | start_debugging | def start_debugging():
"""Start a debugging session after catching an exception.
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"""
exc_type, exc_value, exc_tb = sys.exc_info()
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"""Start a debugging session after catching an exception.
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gregoil/ipdbugger | ipdbugger/__init__.py | get_last_lineno | def get_last_lineno(node):
"""Recursively find the last line number of the ast node."""
max_lineno = 0
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max_lineno = node.lineno
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max_lineno = 0
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gregoil/ipdbugger | ipdbugger/__init__.py | IPDBugger.do_raise | def do_raise(self, arg):
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# Annotating the exception for a continual re-raise
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gregoil/ipdbugger | ipdbugger/__init__.py | IPDBugger.do_retry | def do_retry(self, arg):
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gregoil/ipdbugger | ipdbugger/__init__.py | IPDBugger.dispatch_line | def dispatch_line(self, frame):
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gregoil/ipdbugger | ipdbugger/__init__.py | ErrorsCatchTransformer.wrap_with_try | def wrap_with_try(self, node):
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gregoil/ipdbugger | ipdbugger/__init__.py | ErrorsCatchTransformer.try_except_handler | def try_except_handler(self, node):
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projectshift/shift-boiler | boiler/user/session_interface.py | BoilerSessionInterface.save_session | def save_session(self, *args, **kwargs):
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Skip setting session cookie if requested via g.stateless_sessions
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# do not send session cookie
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mardix/Mocha | mocha/utils.py | _InspectMethodsDecorators.parse | def parse(self):
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trendels/rhino | rhino/response.py | filter_304_headers | def filter_304_headers(headers):
"""Filter a list of headers to include in a "304 Not Modified" response."""
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trendels/rhino | rhino/response.py | Response.set_cookie | def set_cookie(self, key, value='', max_age=None, path='/', domain=None,
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"""
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return self
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assamite/creamas | creamas/examples/grid/ukko.py | _get_ukko_report | def _get_ukko_report():
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'''Get Ukko's report from the fixed URL.
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assamite/creamas | creamas/examples/grid/ukko.py | get_nodes | def get_nodes(n=8, exclude=[], loop=None):
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brunato/lograptor | lograptor/tui.py | get_unix_ioctl_terminal_size | def get_unix_ioctl_terminal_size():
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def ioctl_gwinsz(fd):
try:
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import termios
import struct
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... | python | def get_unix_ioctl_terminal_size():
"""Get the terminal size of a UNIX terminal using the ioctl UNIX command."""
def ioctl_gwinsz(fd):
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import fcntl
import termios
import struct
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PBR/MQ2 | MQ2/add_marker_to_qtls.py | add_marker_to_qtl | def add_marker_to_qtl(qtl, map_list):
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:arg map_list: the genetic map containing the list of markers.
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:arg qtl: a row of the QTL list.
:arg map_list: the genetic map containing the list of markers.
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kata198/QueryableList | QueryableList/Builder.py | QueryBuilder.addFilter | def addFilter(self, filterMethod=FILTER_METHOD_AND, **kwargs):
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@param additional args - Filter arguments. @see QueryableListBase.filter
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'''
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kata198/QueryableList | QueryableList/Builder.py | QueryBuilder.copy | def copy(self):
'''
copy - Create a copy of this query.
@return <QueryBuilder> - a copy of this query
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ret = QueryBuilder()
ret.filters = copy.copy(self.filters)
return ret | python | def copy(self):
'''
copy - Create a copy of this query.
@return <QueryBuilder> - a copy of this query
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ret = QueryBuilder()
ret.filters = copy.copy(self.filters)
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kata198/QueryableList | QueryableList/Builder.py | QueryBuilder._applyFilter | def _applyFilter(lst, filterMethod, filterArgs):
'''
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@return QueryableList - a QueryableList containing the elements of the resulting filter
'''
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Fire-Proof/cuepy | cuepy/cuepy.py | CorsairSDK._raise_corsair_error | def _raise_corsair_error(self, error=None, message=""):
"""
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:param error: specify error type
:type error: int
:param message: specify error message
:type message: str
"""
if error is None:
... | python | def _raise_corsair_error(self, error=None, message=""):
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:param message: specify error message
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Fire-Proof/cuepy | cuepy/cuepy.py | CorsairSDK.device_count | def device_count(self):
"""
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:returns: amount of CUE devices
:rtype: int
"""
device_count = get_device_count(self.corsair_sdk)
if device_count == -1:
self._raise_corsair_error()
return device_count | python | def device_count(self):
"""
Find amount of CUE devices
:returns: amount of CUE devices
:rtype: int
"""
device_count = get_device_count(self.corsair_sdk)
if device_count == -1:
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Fire-Proof/cuepy | cuepy/cuepy.py | CorsairSDK.led_id_from_char | def led_id_from_char(self, char):
"""
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:param char: Character to find led_id from
:type char: str
:returns: id for led
:rtype: int
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led_id = get_led_id_for_key_name(self.corsair_sdk, bytes(char))
... | python | def led_id_from_char(self, char):
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Get id of a led by the letter
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:param char: Character to find led_id from
:type char: str
:returns: id for led
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Fire-Proof/cuepy | cuepy/cuepy.py | CorsairSDK.set_led | def set_led(self, led_id, color):
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:type led_id: int
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Set color of an led
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Fire-Proof/cuepy | cuepy/cuepy.py | CorsairSDK.request_control | def request_control(self, device_id, access_mode=True):
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Request exclusive control of device
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:type device_id: int
:param args: extra parameters
:param kwargs: extra parameters
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Fire-Proof/cuepy | cuepy/cuepy.py | Device.device_info | def device_info(self, device_id=None):
"""
Return device information, if device_id is not specified, return for this device
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:type device_id: int
:returns: dict containing information about device
:rtype: dict
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Kortemme-Lab/klab | klab/bio/uniprot.py | get_obsolete_acc_to_uniparc | def get_obsolete_acc_to_uniparc(acc):
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:param acc: The UniProt accession number.
:return: The corresponding UniParc ID.
Warning: This is a fragile function as the underlying website generation ... | python | def get_obsolete_acc_to_uniparc(acc):
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Kortemme-Lab/klab | klab/bio/uniprot.py | get_common_PDB_IDs | def get_common_PDB_IDs(pdb_id, cache_dir = None, exception_on_failure = True):
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Kortemme-Lab/klab | klab/bio/uniprot.py | UniProtACEntry._parse_sequence_tag | def _parse_sequence_tag(self):
'''Parses the sequence and atomic mass.'''
#main_tags = self._dom.getElementsByTagName("uniprot")
#assert(len(main_tags) == 1)
#entry_tags = main_tags[0].getElementsByTagName("entry")
#assert(len(entry_tags) == 1)
#entry_tags[0]
ent... | python | def _parse_sequence_tag(self):
'''Parses the sequence and atomic mass.'''
#main_tags = self._dom.getElementsByTagName("uniprot")
#assert(len(main_tags) == 1)
#entry_tags = main_tags[0].getElementsByTagName("entry")
#assert(len(entry_tags) == 1)
#entry_tags[0]
ent... | [
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joe513/django-cool-pagination | django_cool_paginator/templatetags/cool_paginate.py | cool_paginate | def cool_paginate(context, **kwargs) -> dict:
"""Main function for pagination process."""
names = (
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'previous_name',
'elastic',
'page_obj',
)
return_dict = {name: value for name, value in zip(names, map(kwargs.get, names))}
if context.g... | python | def cool_paginate(context, **kwargs) -> dict:
"""Main function for pagination process."""
names = (
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'elastic',
'page_obj',
)
return_dict = {name: value for name, value in zip(names, map(kwargs.get, names))}
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projectshift/shift-boiler | boiler/timer/restart_timer.py | time_restarts | def time_restarts(data_path):
""" When called will create a file and measure its mtime on restarts """
path = os.path.join(data_path, 'last_restarted')
if not os.path.isfile(path):
with open(path, 'a'):
os.utime(path, None)
last_modified = os.stat(path).st_mtime
with open(path,... | python | def time_restarts(data_path):
""" When called will create a file and measure its mtime on restarts """
path = os.path.join(data_path, 'last_restarted')
if not os.path.isfile(path):
with open(path, 'a'):
os.utime(path, None)
last_modified = os.stat(path).st_mtime
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MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/pt.py | from_stmt | def from_stmt(stmt, engine, **kwargs):
"""
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:param stmt:
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result_proxy = engine.execute(stmt, **kwarg... | python | def from_stmt(stmt, engine, **kwargs):
"""
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:param stmt:
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.compute_stability_classification | def compute_stability_classification(self, predicted_data, record, dataframe_record):
'''Calculate the stability classification for this case.'''
stability_classification, stability_classication_x_cutoff, stability_classication_y_cutoff = None, self.stability_classication_x_cutoff, self.stability_classi... | python | def compute_stability_classification(self, predicted_data, record, dataframe_record):
'''Calculate the stability classification for this case.'''
stability_classification, stability_classication_x_cutoff, stability_classication_y_cutoff = None, self.stability_classication_x_cutoff, self.stability_classi... | [
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.compute_absolute_error | def compute_absolute_error(self, predicted_data, record, dataframe_record):
'''Calculate the absolute error for this case.'''
absolute_error = abs(record['DDG'] - predicted_data[self.ddg_analysis_type])
dataframe_record['AbsoluteError'] = absolute_error | python | def compute_absolute_error(self, predicted_data, record, dataframe_record):
'''Calculate the absolute error for this case.'''
absolute_error = abs(record['DDG'] - predicted_data[self.ddg_analysis_type])
dataframe_record['AbsoluteError'] = absolute_error | [
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.count_residues | def count_residues(self, record, pdb_record):
'''Count the number of residues in the chains for the case.'''
mutations = self.get_record_mutations(record)
pdb_chains = set([m['Chain'] for m in mutations])
assert(len(pdb_chains) == 1) # we expect monomeric cases
pdb_chain = pdb_ch... | python | def count_residues(self, record, pdb_record):
'''Count the number of residues in the chains for the case.'''
mutations = self.get_record_mutations(record)
pdb_chains = set([m['Chain'] for m in mutations])
assert(len(pdb_chains) == 1) # we expect monomeric cases
pdb_chain = pdb_ch... | [
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.full_analysis | def full_analysis(self, analysis_set, output_directory, verbose = True, compile_pdf = True, quick_plots = False):
'''Combines calculate_metrics, write_dataframe_to_csv, and plot'''
if not os.path.isdir(output_directory):
os.makedirs(output_directory)
self.analysis_directory = output_... | python | def full_analysis(self, analysis_set, output_directory, verbose = True, compile_pdf = True, quick_plots = False):
'''Combines calculate_metrics, write_dataframe_to_csv, and plot'''
if not os.path.isdir(output_directory):
os.makedirs(output_directory)
self.analysis_directory = output_... | [
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.get_unique_ajps | def get_unique_ajps( benchmark_runs ):
"""
Determines which join parameters are unique
"""
br_ajps = {}
for br in benchmark_runs:
for ajp in br.additional_join_parameters:
if ajp not in br_ajps:
br_ajps[ajp] = set()
... | python | def get_unique_ajps( benchmark_runs ):
"""
Determines which join parameters are unique
"""
br_ajps = {}
for br in benchmark_runs:
for ajp in br.additional_join_parameters:
if ajp not in br_ajps:
br_ajps[ajp] = set()
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | BenchmarkRun.plot_optimum_prediction_fraction_correct_cutoffs_over_range | def plot_optimum_prediction_fraction_correct_cutoffs_over_range(self, analysis_set, min_stability_classication_x_cutoff, max_stability_classication_x_cutoff, suppress_plot = False, analysis_file_prefix = None, verbose = True):
'''Plots the optimum cutoff for the predictions to maximize the fraction correct metr... | python | def plot_optimum_prediction_fraction_correct_cutoffs_over_range(self, analysis_set, min_stability_classication_x_cutoff, max_stability_classication_x_cutoff, suppress_plot = False, analysis_file_prefix = None, verbose = True):
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