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train | QueueManager.connect | Creates connection to RabbitMQ server | zengine/tornado_server/ws_to_queue.py | def connect(self):
"""
Creates connection to RabbitMQ server
"""
if self.connecting:
log.info('PikaClient: Already connecting to RabbitMQ')
return
log.info('PikaClient: Connecting to RabbitMQ')
self.connecting = True
self.connection = Tor... | def connect(self):
"""
Creates connection to RabbitMQ server
"""
if self.connecting:
log.info('PikaClient: Already connecting to RabbitMQ')
return
log.info('PikaClient: Connecting to RabbitMQ')
self.connecting = True
self.connection = Tor... | [
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train | QueueManager.on_connected | AMQP connection callback.
Creates input channel.
Args:
connection: AMQP connection | zengine/tornado_server/ws_to_queue.py | def on_connected(self, connection):
"""
AMQP connection callback.
Creates input channel.
Args:
connection: AMQP connection
"""
log.info('PikaClient: connected to RabbitMQ')
self.connected = True
self.in_channel = self.connection.channel(self.o... | def on_connected(self, connection):
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AMQP connection callback.
Creates input channel.
Args:
connection: AMQP connection
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train | QueueManager.on_channel_open | Input channel creation callback
Queue declaration done here
Args:
channel: input channel | zengine/tornado_server/ws_to_queue.py | def on_channel_open(self, channel):
"""
Input channel creation callback
Queue declaration done here
Args:
channel: input channel
"""
self.in_channel.exchange_declare(exchange='input_exc', type='topic', durable=True)
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"""
Input channel creation callback
Queue declaration done here
Args:
channel: input channel
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train | QueueManager.on_input_queue_declare | Input queue declaration callback.
Input Queue/Exchange binding done here
Args:
queue: input queue | zengine/tornado_server/ws_to_queue.py | def on_input_queue_declare(self, queue):
"""
Input queue declaration callback.
Input Queue/Exchange binding done here
Args:
queue: input queue
"""
self.in_channel.queue_bind(callback=None,
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Input queue declaration callback.
Input Queue/Exchange binding done here
Args:
queue: input queue
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self.in_channel.queue_bind(callback=None,
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train | WsgiApp.wsgi_app | Incoming request handler.
:param request: Werkzeug request object | alexandra/wsgi.py | def wsgi_app(self, request):
"""Incoming request handler.
:param request: Werkzeug request object
"""
try:
if request.method != 'POST':
abort(400)
try:
# Python 2.7 compatibility
data = request.data
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"""Incoming request handler.
:param request: Werkzeug request object
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try:
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abort(400)
try:
# Python 2.7 compatibility
data = request.data
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train | WithMixin.close | close opened file
:param force: force closing of externally opened file or buffer | CGRtools/files/_CGRrw.py | def close(self, force=False):
"""
close opened file
:param force: force closing of externally opened file or buffer
"""
if self.__write:
self.write = self.__write_adhoc
self.__write = False
if not self._is_buffer or force:
self._file.... | def close(self, force=False):
"""
close opened file
:param force: force closing of externally opened file or buffer
"""
if self.__write:
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self.__write = False
if not self._is_buffer or force:
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train | CGRread._convert_reaction | map unmapped atoms. | CGRtools/files/_CGRrw.py | def _convert_reaction(self, reaction):
if not (reaction['reactants'] or reaction['products'] or reaction['reagents']):
raise ValueError('empty reaction')
maps = {'reactants': [], 'products': [], 'reagents': []}
for i, tmp in maps.items():
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for i, tmp in maps.items():
for molecule in reaction[i]:
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train | Aromatize.aromatize | convert structure to aromatic form
:return: number of processed rings | CGRtools/algorithms/aromatics.py | def aromatize(self):
"""
convert structure to aromatic form
:return: number of processed rings
"""
rings = [x for x in self.sssr if 4 < len(x) < 7]
if not rings:
return 0
total = 0
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... | def aromatize(self):
"""
convert structure to aromatic form
:return: number of processed rings
"""
rings = [x for x in self.sssr if 4 < len(x) < 7]
if not rings:
return 0
total = 0
while True:
c = self._quinonize(rings, 'order')
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train | Crawler.crawl_cmd | Runs the crawl job for n rounds
:param seed_list: lines of seed URLs
:param n: number of rounds
:return: number of successful rounds | nutch/crawl.py | def crawl_cmd(self, seed_list, n):
'''
Runs the crawl job for n rounds
:param seed_list: lines of seed URLs
:param n: number of rounds
:return: number of successful rounds
'''
print("Num Rounds "+str(n))
cc = self.proxy.Crawl(seed=seed_list, rounds=n)
... | def crawl_cmd(self, seed_list, n):
'''
Runs the crawl job for n rounds
:param seed_list: lines of seed URLs
:param n: number of rounds
:return: number of successful rounds
'''
print("Num Rounds "+str(n))
cc = self.proxy.Crawl(seed=seed_list, rounds=n)
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train | Crawler.load_xml_conf | Creates a new config from xml file.
:param xml_file: path to xml file. Format : nutch-site.xml or nutch-default.xml
:param id:
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:param id:
:return: config object
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import xml.... | def load_xml_conf(self, xml_file, id):
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Creates a new config from xml file.
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train | Crawler.create_cmd | 'create' sub-command
:param args: cli arguments
:return: | nutch/crawl.py | def create_cmd(self, args):
'''
'create' sub-command
:param args: cli arguments
:return:
'''
cmd = args.get('cmd_create')
if cmd == 'conf':
conf_file = args['conf_file']
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'''
'create' sub-command
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cmd = args.get('cmd_create')
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train | MRVwrite.close | write close tag of MRV file and close opened file
:param force: force closing of externally opened file or buffer | CGRtools/files/MRVrw.py | def close(self, *args, **kwargs):
"""
write close tag of MRV file and close opened file
:param force: force closing of externally opened file or buffer
"""
if not self.__finalized:
self._file.write('</cml>')
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write close tag of MRV file and close opened file
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train | MRVwrite.write | write single molecule or reaction into file | CGRtools/files/MRVrw.py | def write(self, data):
"""
write single molecule or reaction into file
"""
self._file.write('<cml>')
self.__write(data)
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write single molecule or reaction into file
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self._file.write('<cml>')
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train | MDLread._load_cache | the method is implemented for the purpose of optimization, byte positions will not be re-read from a file
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the old version of byte offsets will be loaded
:return: list of byte offsets from exi... | CGRtools/files/_MDLrw.py | def _load_cache(self):
"""
the method is implemented for the purpose of optimization, byte positions will not be re-read from a file
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the old version of byte offsets will be loaded
... | def _load_cache(self):
"""
the method is implemented for the purpose of optimization, byte positions will not be re-read from a file
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the old version of byte offsets will be loaded
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train | MDLread._dump_cache | _shifts dumps in /tmp directory after reboot it will drop | CGRtools/files/_MDLrw.py | def _dump_cache(self, _shifts):
"""
_shifts dumps in /tmp directory after reboot it will drop
"""
with open(self.__cache_path, 'wb') as f:
dump(_shifts, f) | def _dump_cache(self, _shifts):
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_shifts dumps in /tmp directory after reboot it will drop
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train | get_task_types | List task types for current user
.. code-block:: python
# request:
{
'view': '_zops_get_task_types',
}
# response:
{
'task_types': [
{'name': string, # wf ... | zengine/views/system.py | def get_task_types(current):
"""
List task types for current user
.. code-block:: python
# request:
{
'view': '_zops_get_task_types',
}
# response:
{
'task_types':... | def get_task_types(current):
"""
List task types for current user
.. code-block:: python
# request:
{
'view': '_zops_get_task_types',
}
# response:
{
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train | get_task_detail | Show task details
.. code-block:: python
# request:
{
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'key': key,
}
# response:
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"""
Show task details
.. code-block:: python
# request:
{
'view': '_zops_get_task_detail',
'key': key,
}
# response:
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Show task details
.. code-block:: python
# request:
{
'view': '_zops_get_task_detail',
'key': key,
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# response:
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train | get_task_actions | List task types for current user
.. code-block:: python
# request:
{
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# response:
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"""
List task types for current user
.. code-block:: python
# request:
{
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List task types for current user
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train | get_tasks | List task invitations of current user
.. code-block:: python
# request:
{
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"""
List task invitations of current user
.. code-block:: python
# request:
{
'view': '_zops_get_tasks',
'state': string, # one of these:
# "active", "future", "finished", "expire... | def get_tasks(current):
"""
List task invitations of current user
.. code-block:: python
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train | reduce_memory_usage | reduce memory usage of the dataframe
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"""reduce memory usage of the dataframe
- convert runIDs to categorical
- downcast ints and floats
"""
usage_pre = df.memory_usage(deep=True).sum()
if "runIDs" in df:
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train | check_existance | Check if the file supplied as input exists. | nanoget/utils.py | def check_existance(f):
"""Check if the file supplied as input exists."""
if not opath.isfile(f):
logging.error("Nanoget: File provided doesn't exist or the path is incorrect: {}".format(f))
sys.exit("File provided doesn't exist or the path is incorrect: {}".format(f)) | def check_existance(f):
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train | RoleSwitching.list_user_roles | Lists user roles as selectable except user's current role. | zengine/views/role_switching.py | def list_user_roles(self):
"""
Lists user roles as selectable except user's current role.
"""
_form = JsonForm(current=self.current, title=_(u"Switch Role"))
_form.help_text = "Your current role: %s %s" % (self.current.role.unit.name,
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"""
Lists user roles as selectable except user's current role.
"""
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train | RoleSwitching.change_user_role | Changes user's role from current role to chosen role. | zengine/views/role_switching.py | def change_user_role(self):
"""
Changes user's role from current role to chosen role.
"""
# Get chosen role_key from user form.
role_key = self.input['form']['role_options']
# Assign chosen switch role key to user's last_login_role_key field
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"""
Changes user's role from current role to chosen role.
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train | RoleSwitching.get_user_switchable_roles | Returns user's role list except current role as a tuple
(role.key, role.name)
Returns:
(list): list of tuples, user's role list except current role | zengine/views/role_switching.py | def get_user_switchable_roles(self):
"""
Returns user's role list except current role as a tuple
(role.key, role.name)
Returns:
(list): list of tuples, user's role list except current role
"""
roles = []
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... | def get_user_switchable_roles(self):
"""
Returns user's role list except current role as a tuple
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(list): list of tuples, user's role list except current role
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train | KibanaManager.put_object | Wrapper for es.index, determines metadata needed to index from obj.
If you have a raw object json string you can hard code these:
index is .kibana (as of kibana4);
id can be A-Za-z0-9\- and must be unique;
doc_type is either visualization, dashboard, search
or for settings do... | kibana/manager.py | def put_object(self, obj):
# TODO consider putting into a ES class
self.pr_dbg('put_obj: %s' % self.json_dumps(obj))
"""
Wrapper for es.index, determines metadata needed to index from obj.
If you have a raw object json string you can hard code these:
index is .kibana (as ... | def put_object(self, obj):
# TODO consider putting into a ES class
self.pr_dbg('put_obj: %s' % self.json_dumps(obj))
"""
Wrapper for es.index, determines metadata needed to index from obj.
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if obj['_id'] is None or obj['_id'] == "":
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train | KibanaManager.json_dumps | Serializer for consistency | kibana/manager.py | def json_dumps(self, obj):
"""Serializer for consistency"""
return json.dumps(obj, sort_keys=True, indent=4, separators=(',', ': ')) | def json_dumps(self, obj):
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train | KibanaManager.safe_filename | Santize obj name into fname and verify doesn't already exist | kibana/manager.py | def safe_filename(self, otype, oid):
"""Santize obj name into fname and verify doesn't already exist"""
permitted = set(['_', '-', '(', ')'])
oid = ''.join([c for c in oid if c.isalnum() or c in permitted])
while oid.find('--') != -1:
oid = oid.replace('--', '-')
ext ... | def safe_filename(self, otype, oid):
"""Santize obj name into fname and verify doesn't already exist"""
permitted = set(['_', '-', '(', ')'])
oid = ''.join([c for c in oid if c.isalnum() or c in permitted])
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train | KibanaManager.write_object_to_file | Convert obj (dict) to json string and write to file | kibana/manager.py | def write_object_to_file(self, obj, path='.', filename=None):
"""Convert obj (dict) to json string and write to file"""
output = self.json_dumps(obj) + '\n'
if filename is None:
filename = self.safe_filename(obj['_type'], obj['_id'])
filename = os.path.join(path, filename)
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filename = self.safe_filename(obj['_type'], obj['_id'])
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train | KibanaManager.write_pkg_to_file | Write a list of related objs to file | kibana/manager.py | def write_pkg_to_file(self, name, objects, path='.', filename=None):
"""Write a list of related objs to file"""
# Kibana uses an array of docs, do the same
# as opposed to a dict of docs
pkg_objs = []
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pkg_objs = []
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train | KibanaManager.get_objects | Return all objects of type (assumes < MAX_HITS) | kibana/manager.py | def get_objects(self, search_field, search_val):
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train | KibanaManager.get_dashboard_full | Get DB and all objs needed to duplicate it | kibana/manager.py | def get_dashboard_full(self, db_name):
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objects = {}
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train | CamundaProcessParser.parse_node | Overrides ProcessParser.parse_node
Parses and attaches the inputOutput tags that created by Camunda Modeller
Args:
node: xml task node
Returns:
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node: xml task node
Returns:
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train | CamundaProcessParser._get_description | Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns: | zengine/lib/camunda_parser.py | def _get_description(self):
"""
Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
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train | CamundaProcessParser.get_name | Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
Returns:
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"""
Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
Returns:
str. WF name.
"""
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Returns:
str. WF name.
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ns = {'ns': '{%s}' % BPMN_MODEL_NS}
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train | CamundaProcessParser._parse_input_data | Parses inputOutput part camunda modeller extensions.
Args:
node: SpiffWorkflow Node object.
Returns:
Data dict. | zengine/lib/camunda_parser.py | def _parse_input_data(self, node):
"""
Parses inputOutput part camunda modeller extensions.
Args:
node: SpiffWorkflow Node object.
Returns:
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"""
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try:
for nod in self._get_input_nodes(node):
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node: SpiffWorkflow Node object.
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train | CamundaProcessParser._get_lane_properties | Parses the given XML node
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node (xml): XML node.
.. code-block:: xml
<bpmn2:lane id="Lane_8" name="Lane 8">
<bpmn2:extensionElements>
<camunda:properties>
<camunda:property value="foo,bar" name="perms"/>
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Parses the given XML node
Args:
node (xml): XML node.
.. code-block:: xml
<bpmn2:lane id="Lane_8" name="Lane 8">
<bpmn2:extensionElements>
<camunda:properties>
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"""
Parses the given XML node
Args:
node (xml): XML node.
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<bpmn2:lane id="Lane_8" name="Lane 8">
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train | CamundaProcessParser._parse_input_node | :param node: xml node
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train | InMemoryPackager.package_in_memory | Generates wf packages from workflow diagrams.
Args:
workflow_name: Name of wf
workflow_files: Diagram file.
Returns:
Workflow package (file like) object | zengine/lib/camunda_parser.py | def package_in_memory(cls, workflow_name, workflow_files):
"""
Generates wf packages from workflow diagrams.
Args:
workflow_name: Name of wf
workflow_files: Diagram file.
Returns:
Workflow package (file like) object
"""
s = StringIO... | def package_in_memory(cls, workflow_name, workflow_files):
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Generates wf packages from workflow diagrams.
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workflow_name: Name of wf
workflow_files: Diagram file.
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train | CGRpreparer.compose | condense reaction container to CGR. see init for details about cgr_type
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condense reaction container to CGR. see init for details about cgr_type
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train | BaseContainer.add_atom | new atom addition | CGRtools/containers/common.py | def add_atom(self, atom, _map=None):
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new atom addition
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train | BaseContainer.add_bond | implementation of bond addition | CGRtools/containers/common.py | def add_bond(self, atom1, atom2, bond):
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implementation of bond addition
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train | BaseContainer.delete_bond | implementation of bond removing | CGRtools/containers/common.py | def delete_bond(self, n, m):
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implementation of bond removing
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self.remove_edge(n, m)
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implementation of bond removing
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train | BaseContainer.environment | pairs of (bond, atom) connected to atom
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:return: list | CGRtools/containers/common.py | def environment(self, atom):
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pairs of (bond, atom) connected to atom
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:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view provides a read-only view
of the original structure scaffold withou... | CGRtools/containers/common.py | def substructure(self, atoms, meta=False, as_view=True):
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create substructure containing atoms from nbunch list
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:param meta: if True metadata will be copied to substructure
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create substructure containing atoms from nbunch list
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train | BaseContainer.augmented_substructure | create substructure containing atoms and their neighbors
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:param deep: number of bonds between ... | CGRtools/containers/common.py | def augmented_substructure(self, atoms, dante=False, deep=1, meta=False, as_view=True):
"""
create substructure containing atoms and their neighbors
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create substructure containing atoms and their neighbors
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train | BaseContainer.split | split disconnected structure to connected substructures
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"""
split disconnected structure to connected substructures
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train | BaseContainer.bonds | iterate other all bonds | CGRtools/containers/common.py | def bonds(self):
"""
iterate other all bonds
"""
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seen.add(n)
for m, bond in m_bond.items():
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iterate other all bonds
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train | BaseContainer._get_subclass | need for cyclic import solving | CGRtools/containers/common.py | def _get_subclass(name):
"""
need for cyclic import solving
"""
return next(x for x in BaseContainer.__subclasses__() if x.__name__ == name) | def _get_subclass(name):
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need for cyclic import solving
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train | _default_make_pool | Creates a urllib3.PoolManager object that has SSL verification enabled
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"""Creates a urllib3.PoolManager object that has SSL verification enabled
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if not http.ca_certs:
http.ca_certs = _certifi_where_for_ssl_version()
ssl_disabled = http.disable_ssl_certificate_validation
cert_reqs... | def _default_make_pool(http, proxy_info):
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train | run_workers | subprocess handler | zengine/wf_daemon.py | def run_workers(no_subprocess, watch_paths=None, is_background=False):
"""
subprocess handler
"""
import atexit, os, subprocess, signal
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subprocess handler
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train | Worker.exit | Properly close the AMQP connections | zengine/wf_daemon.py | def exit(self, signal=None, frame=None):
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Properly close the AMQP connections
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self.connection.close()
log.info("Worker exiting")
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Properly close the AMQP connections
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train | Worker.connect | make amqp connection and create channels and queue binding | zengine/wf_daemon.py | def connect(self):
"""
make amqp connection and create channels and queue binding
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train | Worker.clear_queue | clear outs all messages from INPUT_QUEUE_NAME | zengine/wf_daemon.py | def clear_queue(self):
"""
clear outs all messages from INPUT_QUEUE_NAME
"""
def remove_message(ch, method, properties, body):
print("Removed message: %s" % body)
self.input_channel.basic_consume(remove_message, queue=self.INPUT_QUEUE_NAME, no_ack=True)
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clear outs all messages from INPUT_QUEUE_NAME
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actual consuming of incoming works starts here
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method: amqp method
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ch: amqp channel
method: amqp method
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train | get_progress | Args:
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Returns: | zengine/models/workflow_manager.py | def get_progress(start, finish):
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Args:
start (DateTime): start date
finish (DateTime): finish date
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train | sync_wf_cache | BG Job for storing wf state to DB | zengine/models/workflow_manager.py | def sync_wf_cache(current):
"""
BG Job for storing wf state to DB
"""
wf_cache = WFCache(current)
wf_state = wf_cache.get() # unicode serialized json to dict, all values are unicode
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BG Job for storing wf state to DB
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train | DiagramXML.get_or_create_by_content | if xml content updated, create a new entry for given wf name
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name: name of wf
content: xml content
Returns (DiagramXML(), bool): A tuple with two members.
(DiagramXML instance and True if it's new or False it's already exists | zengine/models/workflow_manager.py | def get_or_create_by_content(cls, name, content):
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if xml content updated, create a new entry for given wf name
Args:
name: name of wf
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train | BPMNParser.get_description | Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns str: WF description | zengine/models/workflow_manager.py | def get_description(self):
"""
Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns str: WF description
"""
paths = ['bpmn:collaboration/bpmn:participant/bpmn:documentation',
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... | def get_description(self):
"""
Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns str: WF description
"""
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train | BPMNParser.get_name | Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
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str. WF name. | zengine/models/workflow_manager.py | def get_name(self):
"""
Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
Returns:
str. WF name.
"""
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train | BPMNWorkflow.set_xml | updates xml link if there aren't any running instances of this wf
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diagram: XMLDiagram object | zengine/models/workflow_manager.py | def set_xml(self, diagram, force=False):
"""
updates xml link if there aren't any running instances of this wf
Args:
diagram: XMLDiagram object
"""
no_of_running = WFInstance.objects.filter(wf=self, finished=False, started=True).count()
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diagram: XMLDiagram object
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train | Task.create_wf_instances | Creates wf instances.
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roles (list): role list
Returns:
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"""
Creates wf instances.
Args:
roles (list): role list
Returns:
(list): wf instances
"""
# if roles specified then create an instance for each role
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Creates wf instances.
Args:
roles (list): role list
Returns:
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"""
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train | Task.create_tasks | will create a WFInstance per object
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"""
will create a WFInstance per object
and per TaskInvitation for each role and WFInstance
"""
roles = self.get_roles()
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train | Task.get_object_query_dict | returns objects keys according to self.object_query_code
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which can be json encoded queryset filter dict or key=value set
in the following format: ```"key=val, key2 = val2 , key3= value with spaces"```
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train | Task.get_object_keys | returns object keys according to task definition
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train | Task.get_model_objects | Fetches model objects by filtering with kwargs
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"""
Fetches model objects by filtering with kwargs
If wfi_role is specified, then we expect kwargs contains a
filter value starting with role,
e.g. {'user': 'role.program.user'}
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train | Task.get_roles | Returns:
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"""
Returns:
Role instances according to task definition.
"""
if self.role.exist:
# return explicitly selected role
return [self.role]
else:
roles = []
if self.role_query_code:
# use... | def get_roles(self):
"""
Returns:
Role instances according to task definition.
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train | Task.post_save | can be removed when a proper task manager admin interface implemented | zengine/models/workflow_manager.py | def post_save(self):
"""can be removed when a proper task manager admin interface implemented"""
if self.run:
self.run = False
self.create_tasks()
self.save() | def post_save(self):
"""can be removed when a proper task manager admin interface implemented"""
if self.run:
self.run = False
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train | TaskInvitation.delete_other_invitations | When one person use an invitation, we should delete other invitations | zengine/models/workflow_manager.py | def delete_other_invitations(self):
"""
When one person use an invitation, we should delete other invitations
"""
# TODO: Signal logged-in users to remove the task from their task list
self.objects.filter(instance=self.instance).exclude(key=self.key).delete() | def delete_other_invitations(self):
"""
When one person use an invitation, we should delete other invitations
"""
# TODO: Signal logged-in users to remove the task from their task list
self.objects.filter(instance=self.instance).exclude(key=self.key).delete() | [
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train | WFCache.save | write wf state to DB through MQ >> Worker >> _zops_sync_wf_cache
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wf_state dict: wf state
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train | Compose.compose | compose 2 graphs to CGR
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train | CGRCompose.decompose | decompose CGR to pair of Molecules, which represents reactants and products state of reaction
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train | CycleTimeQueries.cycle_data | Get data from JIRA for cycle/flow times and story points size change.
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train | NSQSender._is_ready | Is NSQ running and have space to receive messages? | logagg/nsqsender.py | def _is_ready(self, topic_name):
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Is NSQ running and have space to receive messages?
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train | QueryContainer._matcher | QueryContainer < MoleculeContainer
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] | cimm-kzn/CGRtools | python | https://github.com/cimm-kzn/CGRtools/blob/15a19b04f6e4e1d0dab8e0d32a0877c7f7d70f34/CGRtools/containers/query.py#L48-L57 | [
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train | Calculate2D.calculate2d | recalculate 2d coordinates. currently rings can be calculated badly.
:param scale: rescale calculated positions.
:param force: ignore existing coordinates of atoms | CGRtools/algorithms/calculate2d.py | def calculate2d(self, force=False, scale=1):
"""
recalculate 2d coordinates. currently rings can be calculated badly.
:param scale: rescale calculated positions.
:param force: ignore existing coordinates of atoms
"""
dist = {}
# length forces
for n, m_bon... | def calculate2d(self, force=False, scale=1):
"""
recalculate 2d coordinates. currently rings can be calculated badly.
:param scale: rescale calculated positions.
:param force: ignore existing coordinates of atoms
"""
dist = {}
# length forces
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train | Knight.possible_moves | Finds all possible knight moves
:type: position Board
:rtype: list | chess_py/pieces/knight.py | def possible_moves(self, position):
"""
Finds all possible knight moves
:type: position Board
:rtype: list
"""
for direction in [0, 1, 2, 3]:
angles = self._rotate_direction_ninety_degrees(direction)
for angle in angles:
try:
... | def possible_moves(self, position):
"""
Finds all possible knight moves
:type: position Board
:rtype: list
"""
for direction in [0, 1, 2, 3]:
angles = self._rotate_direction_ninety_degrees(direction)
for angle in angles:
try:
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train | CGRContainer.centers_list | get a list of lists of atoms of reaction centers | CGRtools/containers/cgr.py | def centers_list(self):
""" get a list of lists of atoms of reaction centers
"""
center = set()
adj = defaultdict(set)
for n, atom in self.atoms():
if atom._reactant != atom._product:
center.add(n)
for n, m, bond in self.bonds():
i... | def centers_list(self):
""" get a list of lists of atoms of reaction centers
"""
center = set()
adj = defaultdict(set)
for n, atom in self.atoms():
if atom._reactant != atom._product:
center.add(n)
for n, m, bond in self.bonds():
i... | [
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train | CGRContainer.center_atoms | get list of atoms of reaction center (atoms with dynamic: bonds, charges, radicals). | CGRtools/containers/cgr.py | def center_atoms(self):
""" get list of atoms of reaction center (atoms with dynamic: bonds, charges, radicals).
"""
nodes = set()
for n, atom in self.atoms():
if atom._reactant != atom._product:
nodes.add(n)
for n, m, bond in self.bonds():
... | def center_atoms(self):
""" get list of atoms of reaction center (atoms with dynamic: bonds, charges, radicals).
"""
nodes = set()
for n, atom in self.atoms():
if atom._reactant != atom._product:
nodes.add(n)
for n, m, bond in self.bonds():
... | [
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train | CGRContainer.center_bonds | get list of bonds of reaction center (bonds with dynamic orders). | CGRtools/containers/cgr.py | def center_bonds(self):
""" get list of bonds of reaction center (bonds with dynamic orders).
"""
return [(n, m) for n, m, bond in self.bonds() if bond._reactant != bond._product] | def center_bonds(self):
""" get list of bonds of reaction center (bonds with dynamic orders).
"""
return [(n, m) for n, m, bond in self.bonds() if bond._reactant != bond._product] | [
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train | CGRContainer.reset_query_marks | set or reset hyb and neighbors marks to atoms. | CGRtools/containers/cgr.py | def reset_query_marks(self):
"""
set or reset hyb and neighbors marks to atoms.
"""
for i, atom in self.atoms():
neighbors = 0
hybridization = 1
p_neighbors = 0
p_hybridization = 1
# hyb 1- sp3; 2- sp2; 3- sp1; 4- aromatic
... | def reset_query_marks(self):
"""
set or reset hyb and neighbors marks to atoms.
"""
for i, atom in self.atoms():
neighbors = 0
hybridization = 1
p_neighbors = 0
p_hybridization = 1
# hyb 1- sp3; 2- sp2; 3- sp1; 4- aromatic
... | [
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train | CGRContainer.substructure | create substructure containing atoms from nbunch list
:param atoms: list of atoms numbers of substructure
:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view provides a read-only view
of the original structure scaffold withou... | CGRtools/containers/cgr.py | def substructure(self, atoms, meta=False, as_view=True):
"""
create substructure containing atoms from nbunch list
:param atoms: list of atoms numbers of substructure
:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view pr... | def substructure(self, atoms, meta=False, as_view=True):
"""
create substructure containing atoms from nbunch list
:param atoms: list of atoms numbers of substructure
:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view pr... | [
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train | CGRContainer._matcher | CGRContainer < CGRContainer | CGRtools/containers/cgr.py | def _matcher(self, other):
"""
CGRContainer < CGRContainer
"""
if isinstance(other, CGRContainer):
return GraphMatcher(other, self, lambda x, y: x == y, lambda x, y: x == y)
raise TypeError('only cgr-cgr possible') | def _matcher(self, other):
"""
CGRContainer < CGRContainer
"""
if isinstance(other, CGRContainer):
return GraphMatcher(other, self, lambda x, y: x == y, lambda x, y: x == y)
raise TypeError('only cgr-cgr possible') | [
"CGRContainer",
"<",
"CGRContainer"
] | cimm-kzn/CGRtools | python | https://github.com/cimm-kzn/CGRtools/blob/15a19b04f6e4e1d0dab8e0d32a0877c7f7d70f34/CGRtools/containers/cgr.py#L150-L156 | [
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train | CGRContainer.__plain_bfs | modified NX fast BFS node generator | CGRtools/containers/cgr.py | def __plain_bfs(adj, source):
"""modified NX fast BFS node generator"""
seen = set()
nextlevel = {source}
while nextlevel:
thislevel = nextlevel
nextlevel = set()
for v in thislevel:
if v not in seen:
yield v
... | def __plain_bfs(adj, source):
"""modified NX fast BFS node generator"""
seen = set()
nextlevel = {source}
while nextlevel:
thislevel = nextlevel
nextlevel = set()
for v in thislevel:
if v not in seen:
yield v
... | [
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] | cimm-kzn/CGRtools | python | https://github.com/cimm-kzn/CGRtools/blob/15a19b04f6e4e1d0dab8e0d32a0877c7f7d70f34/CGRtools/containers/cgr.py#L159-L170 | [
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train | DefaultOptions.token | Returns authorization token provided by Cocaine.
The real meaning of the token is determined by its type. For example OAUTH2 token will
have "bearer" type.
:return: A tuple of token type and body. | cocaine/detail/defaults.py | def token(self):
"""
Returns authorization token provided by Cocaine.
The real meaning of the token is determined by its type. For example OAUTH2 token will
have "bearer" type.
:return: A tuple of token type and body.
"""
if self._token is None:
toke... | def token(self):
"""
Returns authorization token provided by Cocaine.
The real meaning of the token is determined by its type. For example OAUTH2 token will
have "bearer" type.
:return: A tuple of token type and body.
"""
if self._token is None:
toke... | [
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] | cocaine/cocaine-framework-python | python | https://github.com/cocaine/cocaine-framework-python/blob/d8a30074b6338bac4389eb996e00d404338115e4/cocaine/detail/defaults.py#L116-L129 | [
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train | Logger._send | Send a message lazy formatted with args.
External log attributes can be passed via named attribute `extra`,
like in logging from the standart library.
Note:
* Attrs must be dict, otherwise the whole message would be skipped.
* The key field in an attr is converted to str... | cocaine/detail/logger.py | def _send(self):
""" Send a message lazy formatted with args.
External log attributes can be passed via named attribute `extra`,
like in logging from the standart library.
Note:
* Attrs must be dict, otherwise the whole message would be skipped.
* The key field i... | def _send(self):
""" Send a message lazy formatted with args.
External log attributes can be passed via named attribute `extra`,
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Note:
* Attrs must be dict, otherwise the whole message would be skipped.
* The key field i... | [
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