repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | read_yaml_config | def read_yaml_config(filename, check=True, osreplace=True, exit=True):
"""
reads in a yaml file from the specified filename. If check is set to true
the code will fail if the file does not exist. However if it is set to
false and the file does not exist, None is returned.
:param exit: if true is ex... | python | def read_yaml_config(filename, check=True, osreplace=True, exit=True):
"""
reads in a yaml file from the specified filename. If check is set to true
the code will fail if the file does not exist. However if it is set to
false and the file does not exist, None is returned.
:param exit: if true is ex... | reads in a yaml file from the specified filename. If check is set to true
the code will fail if the file does not exist. However if it is set to
false and the file does not exist, None is returned.
:param exit: if true is exist with sys exit
:param osreplace: if true replaces environment variables from... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L129-L185 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | custom_print | def custom_print(data_structure, indent):
"""
prints a given data structure such as a dict or ordered dict at a given indentation level
:param data_structure:
:param indent:
:return:
"""
for key, value in data_structure.items():
print("\n%s%s:" % (' ' * attribute_indent * indent, ... | python | def custom_print(data_structure, indent):
"""
prints a given data structure such as a dict or ordered dict at a given indentation level
:param data_structure:
:param indent:
:return:
"""
for key, value in data_structure.items():
print("\n%s%s:" % (' ' * attribute_indent * indent, ... | prints a given data structure such as a dict or ordered dict at a given indentation level
:param data_structure:
:param indent:
:return: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L209-L223 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | OrderedJsonEncoder.encode | def encode(self, o, depth=0):
"""
encode the json object at given depth
:param o: the object
:param depth: the depth
:return: the json encoding
"""
if isinstance(o, OrderedDict):
return "{" + ",\n ".join([self.encode(k) + ":" +
... | python | def encode(self, o, depth=0):
"""
encode the json object at given depth
:param o: the object
:param depth: the depth
:return: the json encoding
"""
if isinstance(o, OrderedDict):
return "{" + ",\n ".join([self.encode(k) + ":" +
... | encode the json object at given depth
:param o: the object
:param depth: the depth
:return: the json encoding | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L194-L206 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict._update_meta | def _update_meta(self):
"""
internal function to define the metadata regarding filename, location,
and prefix.
"""
for v in ["filename", "location", "prefix"]:
if "meta" not in self:
self["meta"] = {}
self["meta"][v] = self[v]
d... | python | def _update_meta(self):
"""
internal function to define the metadata regarding filename, location,
and prefix.
"""
for v in ["filename", "location", "prefix"]:
if "meta" not in self:
self["meta"] = {}
self["meta"][v] = self[v]
d... | internal function to define the metadata regarding filename, location,
and prefix. | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L264-L273 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.load | def load(self, filename):
"""
Loads the yaml file with the given filename.
:param filename: the name of the yaml file
"""
self._set_filename(filename)
if os.path.isfile(self['location']):
# d = OrderedDict(read_yaml_config(self['location'], check=True))
... | python | def load(self, filename):
"""
Loads the yaml file with the given filename.
:param filename: the name of the yaml file
"""
self._set_filename(filename)
if os.path.isfile(self['location']):
# d = OrderedDict(read_yaml_config(self['location'], check=True))
... | Loads the yaml file with the given filename.
:param filename: the name of the yaml file | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L284-L307 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.error_keys_not_found | def error_keys_not_found(self, keys):
"""
Check if the requested keys are found in the dict.
:param keys: keys to be looked for
"""
try:
log.error("Filename: {0}".format(self['meta']['location']))
except:
log.error("Filename: {0}".format(self['loc... | python | def error_keys_not_found(self, keys):
"""
Check if the requested keys are found in the dict.
:param keys: keys to be looked for
"""
try:
log.error("Filename: {0}".format(self['meta']['location']))
except:
log.error("Filename: {0}".format(self['loc... | Check if the requested keys are found in the dict.
:param keys: keys to be looked for | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L361-L379 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.yaml | def yaml(self):
"""
returns the yaml output of the dict.
"""
return ordered_dump(OrderedDict(self),
Dumper=yaml.SafeDumper,
default_flow_style=False) | python | def yaml(self):
"""
returns the yaml output of the dict.
"""
return ordered_dump(OrderedDict(self),
Dumper=yaml.SafeDumper,
default_flow_style=False) | returns the yaml output of the dict. | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L393-L399 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.get | def get(self, *keys):
"""
returns the dict of the information as read from the yaml file. To
access the file safely, you can use the keys in the order of the
access.
Example: get("provisioner","policy") will return the value of
config["provisioner"]["policy"] from the yam... | python | def get(self, *keys):
"""
returns the dict of the information as read from the yaml file. To
access the file safely, you can use the keys in the order of the
access.
Example: get("provisioner","policy") will return the value of
config["provisioner"]["policy"] from the yam... | returns the dict of the information as read from the yaml file. To
access the file safely, you can use the keys in the order of the
access.
Example: get("provisioner","policy") will return the value of
config["provisioner"]["policy"] from the yaml file if it does not exists
an er... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L425-L447 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.set | def set(self, value, *keys):
"""
Sets the dict of the information as read from the yaml file. To access
the file safely, you can use the keys in the order of the access.
Example: set("{'project':{'fg82':[i0-i10]}}", "provisioner","policy")
will set the value of config["provisione... | python | def set(self, value, *keys):
"""
Sets the dict of the information as read from the yaml file. To access
the file safely, you can use the keys in the order of the access.
Example: set("{'project':{'fg82':[i0-i10]}}", "provisioner","policy")
will set the value of config["provisione... | Sets the dict of the information as read from the yaml file. To access
the file safely, you can use the keys in the order of the access.
Example: set("{'project':{'fg82':[i0-i10]}}", "provisioner","policy")
will set the value of config["provisioner"]["policy"] in the yaml file if
it does... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L449-L477 |
cloudmesh/cloudmesh-common | cloudmesh/common/BaseConfigDict.py | BaseConfigDict.attribute | def attribute(self, keys):
"""
TODO: document this method
:param keys:
"""
if self['meta']['prefix'] is None:
k = keys
else:
k = self['meta']['prefix'] + "." + keys
return self.get(k) | python | def attribute(self, keys):
"""
TODO: document this method
:param keys:
"""
if self['meta']['prefix'] is None:
k = keys
else:
k = self['meta']['prefix'] + "." + keys
return self.get(k) | TODO: document this method
:param keys: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/BaseConfigDict.py#L488-L498 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.flatwrite | def flatwrite(cls, table,
order=None,
header=None,
output="table",
sort_keys=True,
show_none="",
sep="."
):
"""
writes the information given in the table
:param table: th... | python | def flatwrite(cls, table,
order=None,
header=None,
output="table",
sort_keys=True,
show_none="",
sep="."
):
"""
writes the information given in the table
:param table: th... | writes the information given in the table
:param table: the table of values
:param order: the order of the columns
:param header: the header for the columns
:param output: the format (default is table, values are raw, csv, json, yaml, dict
:param sort_keys: if true the table is s... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L24-L50 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.write | def write(cls, table,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""
):
"""
writes the information given in the table
:param table: the table of values
:param order: the order of th... | python | def write(cls, table,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""
):
"""
writes the information given in the table
:param table: the table of values
:param order: the order of th... | writes the information given in the table
:param table: the table of values
:param order: the order of the columns
:param header: the header for the columns
:param output: the format (default is table, values are raw, csv, json, yaml, dict
:param sort_keys: if true the table is s... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L53-L88 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.list | def list(cls,
l,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""
):
"""
:param l: l is a list not a dict
:param order:
:param header:
:param output:
:param sor... | python | def list(cls,
l,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""
):
"""
:param l: l is a list not a dict
:param order:
:param header:
:param output:
:param sor... | :param l: l is a list not a dict
:param order:
:param header:
:param output:
:param sort_keys:
:param show_none:
:return: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L91-L119 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.dict | def dict(cls,
d,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""):
"""
TODO
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the column... | python | def dict(cls,
d,
order=None,
header=None,
output="table",
sort_keys=True,
show_none=""):
"""
TODO
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the column... | TODO
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the columns are printed.
The order is specified by the key names of the dict.
:type order:
:param header: The Header of each of the columns
:type header:... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L122-L166 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.csv | def csv(cls,
d,
order=None,
header=None,
sort_keys=True):
"""
prints a table in csv format
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the columns are printed.
T... | python | def csv(cls,
d,
order=None,
header=None,
sort_keys=True):
"""
prints a table in csv format
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the columns are printed.
T... | prints a table in csv format
:param d: A a dict with dicts of the same type.
:type d: dict
:param order:The order in which the columns are printed.
The order is specified by the key names of the dict.
:type order:
:param header: The Header of each of the colu... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L169-L226 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.dict_table | def dict_table(cls,
d,
order=None,
header=None,
sort_keys=True,
show_none="",
max_width=40):
"""prints a pretty table from an dict of dicts
:param d: A a dict with dicts of the same type.
... | python | def dict_table(cls,
d,
order=None,
header=None,
sort_keys=True,
show_none="",
max_width=40):
"""prints a pretty table from an dict of dicts
:param d: A a dict with dicts of the same type.
... | prints a pretty table from an dict of dicts
:param d: A a dict with dicts of the same type.
Each key will be a column
:param order: The order in which the columns are printed.
The order is specified by the key names of the dict.
:param header: The Hea... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L229-L300 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.attribute | def attribute(cls,
d,
header=None,
order=None,
sort_keys=True,
output="table"):
"""prints a attribute/key value table
:param d: A a dict with dicts of the same type.
Each key will be a colu... | python | def attribute(cls,
d,
header=None,
order=None,
sort_keys=True,
output="table"):
"""prints a attribute/key value table
:param d: A a dict with dicts of the same type.
Each key will be a colu... | prints a attribute/key value table
:param d: A a dict with dicts of the same type.
Each key will be a column
:param order: The order in which the columns are printed.
The order is specified by the key names of the dict.
:param header: The Header... | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L303-L350 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.print_list | def print_list(cls, l, output='table'):
"""
prints a list
:param l: the list
:param output: the output, default is a table
:return:
"""
def dict_from_list(l):
"""
returns a dict from a list for printing
:param l: the list
... | python | def print_list(cls, l, output='table'):
"""
prints a list
:param l: the list
:param output: the output, default is a table
:return:
"""
def dict_from_list(l):
"""
returns a dict from a list for printing
:param l: the list
... | prints a list
:param l: the list
:param output: the output, default is a table
:return: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L353-L391 |
cloudmesh/cloudmesh-common | cloudmesh/common/Printer.py | Printer.row_table | def row_table(cls, d, order=None, labels=None):
"""prints a pretty table from data in the dict.
:param d: A dict to be printed
:param order: The order in which the columns are printed.
The order is specified by the key names of the dict.
:param labels: The array of ... | python | def row_table(cls, d, order=None, labels=None):
"""prints a pretty table from data in the dict.
:param d: A dict to be printed
:param order: The order in which the columns are printed.
The order is specified by the key names of the dict.
:param labels: The array of ... | prints a pretty table from data in the dict.
:param d: A dict to be printed
:param order: The order in which the columns are printed.
The order is specified by the key names of the dict.
:param labels: The array of labels for the column | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/Printer.py#L394-L424 |
cloudmesh/cloudmesh-common | cloudmesh/common/ssh/authorized_keys.py | get_fingerprint_from_public_key | def get_fingerprint_from_public_key(pubkey):
"""Generate the fingerprint of a public key
:param str pubkey: the value of the public key
:returns: fingerprint
:rtype: str
"""
# TODO: why is there a tmpdir?
with tempdir() as workdir:
key = os.path.join(workdir, 'key.pub')
wit... | python | def get_fingerprint_from_public_key(pubkey):
"""Generate the fingerprint of a public key
:param str pubkey: the value of the public key
:returns: fingerprint
:rtype: str
"""
# TODO: why is there a tmpdir?
with tempdir() as workdir:
key = os.path.join(workdir, 'key.pub')
wit... | Generate the fingerprint of a public key
:param str pubkey: the value of the public key
:returns: fingerprint
:rtype: str | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/ssh/authorized_keys.py#L17-L40 |
cloudmesh/cloudmesh-common | cloudmesh/common/ssh/authorized_keys.py | AuthorizedKeys.load | def load(cls, path):
"""
load the keys from a path
:param path: the filename (path) in which we find the keys
:return:
"""
auth = cls()
with open(path) as fd:
for pubkey in itertools.imap(str.strip, fd):
# skip empty lines
... | python | def load(cls, path):
"""
load the keys from a path
:param path: the filename (path) in which we find the keys
:return:
"""
auth = cls()
with open(path) as fd:
for pubkey in itertools.imap(str.strip, fd):
# skip empty lines
... | load the keys from a path
:param path: the filename (path) in which we find the keys
:return: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/ssh/authorized_keys.py#L52-L66 |
cloudmesh/cloudmesh-common | cloudmesh/common/ssh/authorized_keys.py | AuthorizedKeys.add | def add(self, pubkey):
"""
add a public key.
:param pubkey: the filename to the public key
:return:
"""
f = get_fingerprint_from_public_key(pubkey)
if f not in self._keys:
self._order[len(self._keys)] = f
self._keys[f] = pubkey | python | def add(self, pubkey):
"""
add a public key.
:param pubkey: the filename to the public key
:return:
"""
f = get_fingerprint_from_public_key(pubkey)
if f not in self._keys:
self._order[len(self._keys)] = f
self._keys[f] = pubkey | add a public key.
:param pubkey: the filename to the public key
:return: | https://github.com/cloudmesh/cloudmesh-common/blob/ae4fae09cd78205d179ea692dc58f0b0c8fea2b8/cloudmesh/common/ssh/authorized_keys.py#L68-L77 |
ella/ella | ella/photos/newman_admin.py | PhotoAdmin.thumb | def thumb(self, obj):
"""
Generates html and thumbnails for admin site.
"""
format, created = Format.objects.get_or_create(name='newman_thumb',
defaults={
'max_width': 100,
'max_height': 100,
'flex... | python | def thumb(self, obj):
"""
Generates html and thumbnails for admin site.
"""
format, created = Format.objects.get_or_create(name='newman_thumb',
defaults={
'max_width': 100,
'max_height': 100,
'flex... | Generates html and thumbnails for admin site. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/newman_admin.py#L125-L146 |
ssalentin/plip | plip/plipcmd.py | process_pdb | def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
if not as_string:
startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
else:
startmessa... | python | def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
if not as_string:
startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
else:
startmessa... | Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/plipcmd.py#L53-L97 |
ssalentin/plip | plip/plipcmd.py | download_structure | def download_structure(inputpdbid):
"""Given a PDB ID, downloads the corresponding PDB structure.
Checks for validity of ID and handles error while downloading.
Returns the path of the downloaded file."""
try:
if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein':
... | python | def download_structure(inputpdbid):
"""Given a PDB ID, downloads the corresponding PDB structure.
Checks for validity of ID and handles error while downloading.
Returns the path of the downloaded file."""
try:
if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein':
... | Given a PDB ID, downloads the corresponding PDB structure.
Checks for validity of ID and handles error while downloading.
Returns the path of the downloaded file. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/plipcmd.py#L100-L116 |
ssalentin/plip | plip/plipcmd.py | remove_duplicates | def remove_duplicates(slist):
"""Checks input lists for duplicates and returns
a list with unique entries"""
unique = list(set(slist))
difference = len(slist) - len(unique)
if difference == 1:
write_message("Removed one duplicate entry from input list.\n")
if difference > 1:
writ... | python | def remove_duplicates(slist):
"""Checks input lists for duplicates and returns
a list with unique entries"""
unique = list(set(slist))
difference = len(slist) - len(unique)
if difference == 1:
write_message("Removed one duplicate entry from input list.\n")
if difference > 1:
writ... | Checks input lists for duplicates and returns
a list with unique entries | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/plipcmd.py#L119-L128 |
ssalentin/plip | plip/plipcmd.py | main | def main(inputstructs, inputpdbids):
"""Main function. Calls functions for processing, report generation and visualization."""
pdbid, pdbpath = None, None
# #@todo For multiprocessing, implement better stacktracing for errors
# Print title and version
title = "* Protein-Ligand Interaction Profiler v... | python | def main(inputstructs, inputpdbids):
"""Main function. Calls functions for processing, report generation and visualization."""
pdbid, pdbpath = None, None
# #@todo For multiprocessing, implement better stacktracing for errors
# Print title and version
title = "* Protein-Ligand Interaction Profiler v... | Main function. Calls functions for processing, report generation and visualization. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/plipcmd.py#L131-L177 |
ssalentin/plip | plip/plipcmd.py | main_init | def main_init():
"""Parse command line arguments and start main script for analysis."""
parser = ArgumentParser(prog="PLIP", description=descript)
pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file
# '-' as file name reads from stdin
pdbstructure.add_arg... | python | def main_init():
"""Parse command line arguments and start main script for analysis."""
parser = ArgumentParser(prog="PLIP", description=descript)
pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file
# '-' as file name reads from stdin
pdbstructure.add_arg... | Parse command line arguments and start main script for analysis. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/plipcmd.py#L184-L307 |
ella/ella | ella/photos/admin.py | FormatedPhotoForm.clean | def clean(self):
"""
Validation function that checks the dimensions of the crop whether it fits into the original and the format.
"""
data = self.cleaned_data
photo = data['photo']
if (
(data['crop_left'] > photo.width) or
(data['crop_top'] > photo... | python | def clean(self):
"""
Validation function that checks the dimensions of the crop whether it fits into the original and the format.
"""
data = self.cleaned_data
photo = data['photo']
if (
(data['crop_left'] > photo.width) or
(data['crop_top'] > photo... | Validation function that checks the dimensions of the crop whether it fits into the original and the format. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/admin.py#L16-L30 |
ella/ella | ella/photos/admin.py | FormatForm.clean | def clean(self):
"""
Check format name uniqueness for sites
:return: cleaned_data
"""
data = self.cleaned_data
formats = Format.objects.filter(name=data['name'])
if self.instance:
formats = formats.exclude(pk=self.instance.pk)
exists_sites =... | python | def clean(self):
"""
Check format name uniqueness for sites
:return: cleaned_data
"""
data = self.cleaned_data
formats = Format.objects.filter(name=data['name'])
if self.instance:
formats = formats.exclude(pk=self.instance.pk)
exists_sites =... | Check format name uniqueness for sites
:return: cleaned_data | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/admin.py#L37-L58 |
ella/ella | ella/photos/admin.py | PhotoOptions.format_photo_json | def format_photo_json(self, request, photo, format):
"Used in admin image 'crop tool'."
try:
photo = get_cached_object(Photo, pk=photo)
format = get_cached_object(Format, pk=format)
content = {
'error': False,
'image':settings.MEDIA_URL... | python | def format_photo_json(self, request, photo, format):
"Used in admin image 'crop tool'."
try:
photo = get_cached_object(Photo, pk=photo)
format = get_cached_object(Format, pk=format)
content = {
'error': False,
'image':settings.MEDIA_URL... | Used in admin image 'crop tool'. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/admin.py#L114-L129 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.set_initial_representations | def set_initial_representations(self):
"""Set the initial representations"""
self.update_model_dict()
self.rc("background solid white")
self.rc("setattr g display 0") # Hide all pseudobonds
self.rc("~display #%i & :/isHet & ~:%s" % (self.model_dict[self.plipname], self.hetid)) | python | def set_initial_representations(self):
"""Set the initial representations"""
self.update_model_dict()
self.rc("background solid white")
self.rc("setattr g display 0") # Hide all pseudobonds
self.rc("~display #%i & :/isHet & ~:%s" % (self.model_dict[self.plipname], self.hetid)) | Set the initial representations | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L36-L41 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.update_model_dict | def update_model_dict(self):
"""Updates the model dictionary"""
dct = {}
models = self.chimera.openModels
for md in models.list():
dct[md.name] = md.id
self.model_dict = dct | python | def update_model_dict(self):
"""Updates the model dictionary"""
dct = {}
models = self.chimera.openModels
for md in models.list():
dct[md.name] = md.id
self.model_dict = dct | Updates the model dictionary | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L43-L49 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.atom_by_serialnumber | def atom_by_serialnumber(self):
"""Provides a dictionary mapping serial numbers to their atom objects."""
atm_by_snum = {}
for atom in self.model.atoms:
atm_by_snum[atom.serialNumber] = atom
return atm_by_snum | python | def atom_by_serialnumber(self):
"""Provides a dictionary mapping serial numbers to their atom objects."""
atm_by_snum = {}
for atom in self.model.atoms:
atm_by_snum[atom.serialNumber] = atom
return atm_by_snum | Provides a dictionary mapping serial numbers to their atom objects. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L51-L56 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_hydrophobic | def show_hydrophobic(self):
"""Visualizes hydrophobic contacts."""
grp = self.getPseudoBondGroup("Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model])
grp.lineType = self.chimera.Dash
grp.lineWidth = 3
grp.color = self.colorbyname('gray')
for i in self.plc... | python | def show_hydrophobic(self):
"""Visualizes hydrophobic contacts."""
grp = self.getPseudoBondGroup("Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model])
grp.lineType = self.chimera.Dash
grp.lineWidth = 3
grp.color = self.colorbyname('gray')
for i in self.plc... | Visualizes hydrophobic contacts. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L58-L65 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_hbonds | def show_hbonds(self):
"""Visualizes hydrogen bonds."""
grp = self.getPseudoBondGroup("Hydrogen Bonds-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i in self.plcomplex.hbonds.ldon_id:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.... | python | def show_hbonds(self):
"""Visualizes hydrogen bonds."""
grp = self.getPseudoBondGroup("Hydrogen Bonds-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i in self.plcomplex.hbonds.ldon_id:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.... | Visualizes hydrogen bonds. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L67-L78 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_halogen | def show_halogen(self):
"""Visualizes halogen bonds."""
grp = self.getPseudoBondGroup("HalogenBonds-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i in self.plcomplex.halogen_bonds:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.col... | python | def show_halogen(self):
"""Visualizes halogen bonds."""
grp = self.getPseudoBondGroup("HalogenBonds-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i in self.plcomplex.halogen_bonds:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.col... | Visualizes halogen bonds. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L80-L88 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_stacking | def show_stacking(self):
"""Visualizes pi-stacking interactions."""
grp = self.getPseudoBondGroup("pi-Stacking-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, stack in enumerate(self.plcomplex.pistacking):
m = sel... | python | def show_stacking(self):
"""Visualizes pi-stacking interactions."""
grp = self.getPseudoBondGroup("pi-Stacking-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, stack in enumerate(self.plcomplex.pistacking):
m = sel... | Visualizes pi-stacking interactions. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L90-L112 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_cationpi | def show_cationpi(self):
"""Visualizes cation-pi interactions"""
grp = self.getPseudoBondGroup("Cation-Pi-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, cat in enumerate(self.plcomplex.pication):
m = self.model
... | python | def show_cationpi(self):
"""Visualizes cation-pi interactions"""
grp = self.getPseudoBondGroup("Cation-Pi-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, cat in enumerate(self.plcomplex.pication):
m = self.model
... | Visualizes cation-pi interactions | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L114-L139 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_sbridges | def show_sbridges(self):
"""Visualizes salt bridges."""
# Salt Bridges
grp = self.getPseudoBondGroup("Salt Bridges-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, sbridge in enumerate(self.plcomplex.saltbridges):
... | python | def show_sbridges(self):
"""Visualizes salt bridges."""
# Salt Bridges
grp = self.getPseudoBondGroup("Salt Bridges-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, sbridge in enumerate(self.plcomplex.saltbridges):
... | Visualizes salt bridges. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L141-L167 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_wbridges | def show_wbridges(self):
"""Visualizes water bridges"""
grp = self.getPseudoBondGroup("Water Bridges-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i, wbridge in enumerate(self.plcomplex.waterbridges):
c = grp.newPseudoBond(self.atoms[wbridge.water_id], sel... | python | def show_wbridges(self):
"""Visualizes water bridges"""
grp = self.getPseudoBondGroup("Water Bridges-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i, wbridge in enumerate(self.plcomplex.waterbridges):
c = grp.newPseudoBond(self.atoms[wbridge.water_id], sel... | Visualizes water bridges | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L169-L183 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.show_metal | def show_metal(self):
"""Visualizes metal coordination."""
grp = self.getPseudoBondGroup("Metal Coordination-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i, metal in enumerate(self.plcomplex.metal_complexes):
c = grp.newPseudoBond(self.atoms[metal.metal_i... | python | def show_metal(self):
"""Visualizes metal coordination."""
grp = self.getPseudoBondGroup("Metal Coordination-%i" % self.tid, associateWith=[self.model])
grp.lineWidth = 3
for i, metal in enumerate(self.plcomplex.metal_complexes):
c = grp.newPseudoBond(self.atoms[metal.metal_i... | Visualizes metal coordination. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L185-L197 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.cleanup | def cleanup(self):
"""Clean up the visualization."""
if not len(self.water_ids) == 0:
# Hide all non-interacting water molecules
water_selection = []
for wid in self.water_ids:
water_selection.append('serialNumber=%i' % wid)
self.rc("~disp... | python | def cleanup(self):
"""Clean up the visualization."""
if not len(self.water_ids) == 0:
# Hide all non-interacting water molecules
water_selection = []
for wid in self.water_ids:
water_selection.append('serialNumber=%i' % wid)
self.rc("~disp... | Clean up the visualization. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L199-L213 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.zoom_to_ligand | def zoom_to_ligand(self):
"""Centers the view on the ligand and its binding site residues."""
self.rc("center #%i & :%s" % (self.model_dict[self.plipname], self.hetid)) | python | def zoom_to_ligand(self):
"""Centers the view on the ligand and its binding site residues."""
self.rc("center #%i & :%s" % (self.model_dict[self.plipname], self.hetid)) | Centers the view on the ligand and its binding site residues. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L215-L217 |
ssalentin/plip | plip/modules/chimeraplip.py | ChimeraVisualizer.refinements | def refinements(self):
"""Details for the visualization."""
self.rc("setattr a color gray @CENTROID")
self.rc("setattr a radius 0.3 @CENTROID")
self.rc("represent sphere @CENTROID")
self.rc("setattr a color orange @CHARGE")
self.rc("setattr a radius 0.4 @CHARGE")
... | python | def refinements(self):
"""Details for the visualization."""
self.rc("setattr a color gray @CENTROID")
self.rc("setattr a radius 0.3 @CENTROID")
self.rc("represent sphere @CENTROID")
self.rc("setattr a color orange @CHARGE")
self.rc("setattr a radius 0.4 @CHARGE")
... | Details for the visualization. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/chimeraplip.py#L219-L227 |
ella/ella | ella/core/migrations/0002_remove_shit_data.py | Migration.forwards | def forwards(self, orm):
"Write your forwards methods here."
if not db.dry_run:
for pl in orm['core.Placement'].objects.all():
pl.listing_set.update(publishable=pl.publishable)
publishable = pl.publishable
publishable.publish_from = pl.publish_... | python | def forwards(self, orm):
"Write your forwards methods here."
if not db.dry_run:
for pl in orm['core.Placement'].objects.all():
pl.listing_set.update(publishable=pl.publishable)
publishable = pl.publishable
publishable.publish_from = pl.publish_... | Write your forwards methods here. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/migrations/0002_remove_shit_data.py#L11-L20 |
ella/ella | ella/photos/formatter.py | Formatter.format | def format(self):
"""
Crop and resize the supplied image. Return the image and the crop_box used.
If the input format is JPEG and in EXIF there is information about rotation, use it and rotate resulting image.
"""
if hasattr(self.image, '_getexif'):
self.rotate_exif()... | python | def format(self):
"""
Crop and resize the supplied image. Return the image and the crop_box used.
If the input format is JPEG and in EXIF there is information about rotation, use it and rotate resulting image.
"""
if hasattr(self.image, '_getexif'):
self.rotate_exif()... | Crop and resize the supplied image. Return the image and the crop_box used.
If the input format is JPEG and in EXIF there is information about rotation, use it and rotate resulting image. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L22-L31 |
ella/ella | ella/photos/formatter.py | Formatter.set_format | def set_format(self):
"""
Check if the format has a flexible height, if so check if the ratio
of the flexible format is closer to the actual ratio of the image. If
so use that instead of the default values (f.max_width, f.max_height).
"""
f = self.fmt
if f.flexib... | python | def set_format(self):
"""
Check if the format has a flexible height, if so check if the ratio
of the flexible format is closer to the actual ratio of the image. If
so use that instead of the default values (f.max_width, f.max_height).
"""
f = self.fmt
if f.flexib... | Check if the format has a flexible height, if so check if the ratio
of the flexible format is closer to the actual ratio of the image. If
so use that instead of the default values (f.max_width, f.max_height). | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L33-L47 |
ella/ella | ella/photos/formatter.py | Formatter.get_crop_box | def get_crop_box(self):
"""
Get coordinates of the rectangle defining the new image boundaries. It
takes into acount any specific wishes from the model (explicitely
passed in crop_box), the desired format and it's options
(flexible_height, nocrop) and mainly it's ratio. After dim... | python | def get_crop_box(self):
"""
Get coordinates of the rectangle defining the new image boundaries. It
takes into acount any specific wishes from the model (explicitely
passed in crop_box), the desired format and it's options
(flexible_height, nocrop) and mainly it's ratio. After dim... | Get coordinates of the rectangle defining the new image boundaries. It
takes into acount any specific wishes from the model (explicitely
passed in crop_box), the desired format and it's options
(flexible_height, nocrop) and mainly it's ratio. After dimensions of
the format were specified... | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L49-L89 |
ella/ella | ella/photos/formatter.py | Formatter.center_important_part | def center_important_part(self, crop_box):
"""
If important_box was specified, make sure it lies inside the crop box.
"""
if not self.important_box:
return crop_box
# shortcuts
ib = self.important_box
cl, ct, cr, cb = crop_box
iw, ih = self.im... | python | def center_important_part(self, crop_box):
"""
If important_box was specified, make sure it lies inside the crop box.
"""
if not self.important_box:
return crop_box
# shortcuts
ib = self.important_box
cl, ct, cr, cb = crop_box
iw, ih = self.im... | If important_box was specified, make sure it lies inside the crop box. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L91-L121 |
ella/ella | ella/photos/formatter.py | Formatter.crop_to_ratio | def crop_to_ratio(self):
" Get crop coordinates and perform the crop if we get any. "
crop_box = self.get_crop_box()
if not crop_box:
return
crop_box = self.center_important_part(crop_box)
iw, ih = self.image.size
# see if we want to crop something from out... | python | def crop_to_ratio(self):
" Get crop coordinates and perform the crop if we get any. "
crop_box = self.get_crop_box()
if not crop_box:
return
crop_box = self.center_important_part(crop_box)
iw, ih = self.image.size
# see if we want to crop something from out... | Get crop coordinates and perform the crop if we get any. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L124-L153 |
ella/ella | ella/photos/formatter.py | Formatter.get_resized_size | def get_resized_size(self):
"""
Get target size for the stretched or shirnked image to fit within the
target dimensions. Do not stretch images if not format.stretch.
Note that this method is designed to operate on already cropped image.
"""
f = self.fmt
iw, ih = ... | python | def get_resized_size(self):
"""
Get target size for the stretched or shirnked image to fit within the
target dimensions. Do not stretch images if not format.stretch.
Note that this method is designed to operate on already cropped image.
"""
f = self.fmt
iw, ih = ... | Get target size for the stretched or shirnked image to fit within the
target dimensions. Do not stretch images if not format.stretch.
Note that this method is designed to operate on already cropped image. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L155-L178 |
ella/ella | ella/photos/formatter.py | Formatter.resize | def resize(self):
"""
Get target size for a cropped image and do the resizing if we got
anything usable.
"""
resized_size = self.get_resized_size()
if not resized_size:
return
self.image = self.image.resize(resized_size, Image.ANTIALIAS) | python | def resize(self):
"""
Get target size for a cropped image and do the resizing if we got
anything usable.
"""
resized_size = self.get_resized_size()
if not resized_size:
return
self.image = self.image.resize(resized_size, Image.ANTIALIAS) | Get target size for a cropped image and do the resizing if we got
anything usable. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L180-L189 |
ella/ella | ella/photos/formatter.py | Formatter.rotate_exif | def rotate_exif(self):
"""
Rotate image via exif information.
Only 90, 180 and 270 rotations are supported.
"""
exif = self.image._getexif() or {}
rotation = exif.get(TAGS['Orientation'], 1)
rotations = {
6: -90,
3: -180,
8: -2... | python | def rotate_exif(self):
"""
Rotate image via exif information.
Only 90, 180 and 270 rotations are supported.
"""
exif = self.image._getexif() or {}
rotation = exif.get(TAGS['Orientation'], 1)
rotations = {
6: -90,
3: -180,
8: -2... | Rotate image via exif information.
Only 90, 180 and 270 rotations are supported. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/formatter.py#L191-L207 |
ssalentin/plip | plip/modules/visualize.py | select_by_ids | def select_by_ids(selname, idlist, selection_exists=False, chunksize=20, restrict=None):
"""Selection with a large number of ids concatenated into a selection
list can cause buffer overflow in PyMOL. This function takes a selection
name and and list of IDs (list of integers) as input and makes a careful
... | python | def select_by_ids(selname, idlist, selection_exists=False, chunksize=20, restrict=None):
"""Selection with a large number of ids concatenated into a selection
list can cause buffer overflow in PyMOL. This function takes a selection
name and and list of IDs (list of integers) as input and makes a careful
... | Selection with a large number of ids concatenated into a selection
list can cause buffer overflow in PyMOL. This function takes a selection
name and and list of IDs (list of integers) as input and makes a careful
step-by-step selection (packages of 20 by default) | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/visualize.py#L18-L30 |
ssalentin/plip | plip/modules/visualize.py | visualize_in_pymol | def visualize_in_pymol(plcomplex):
"""Visualizes the protein-ligand pliprofiler at one site in PyMOL."""
vis = PyMOLVisualizer(plcomplex)
#####################
# Set everything up #
#####################
pdbid = plcomplex.pdbid
lig_members = plcomplex.lig_members
chain = plcomplex.cha... | python | def visualize_in_pymol(plcomplex):
"""Visualizes the protein-ligand pliprofiler at one site in PyMOL."""
vis = PyMOLVisualizer(plcomplex)
#####################
# Set everything up #
#####################
pdbid = plcomplex.pdbid
lig_members = plcomplex.lig_members
chain = plcomplex.cha... | Visualizes the protein-ligand pliprofiler at one site in PyMOL. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/visualize.py#L33-L134 |
ella/ella | ella/core/views.py | get_content_type | def get_content_type(ct_name):
"""
A helper function that returns ContentType object based on its slugified verbose_name_plural.
Results of this function is cached to improve performance.
:Parameters:
- `ct_name`: Slugified verbose_name_plural of the target model.
:Exceptions:
- ... | python | def get_content_type(ct_name):
"""
A helper function that returns ContentType object based on its slugified verbose_name_plural.
Results of this function is cached to improve performance.
:Parameters:
- `ct_name`: Slugified verbose_name_plural of the target model.
:Exceptions:
- ... | A helper function that returns ContentType object based on its slugified verbose_name_plural.
Results of this function is cached to improve performance.
:Parameters:
- `ct_name`: Slugified verbose_name_plural of the target model.
:Exceptions:
- `Http404`: if no matching ContentType is fo... | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L423-L445 |
ella/ella | ella/core/views.py | get_templates | def get_templates(name, slug=None, category=None, app_label=None, model_label=None):
"""
Returns templates in following format and order:
* ``'page/category/%s/content_type/%s.%s/%s/%s' % (<CATEGORY_PART>, app_label, model_label, slug, name)``
* ``'page/category/%s/content_type/%s.%s/%s' % (<CATEGORY_P... | python | def get_templates(name, slug=None, category=None, app_label=None, model_label=None):
"""
Returns templates in following format and order:
* ``'page/category/%s/content_type/%s.%s/%s/%s' % (<CATEGORY_PART>, app_label, model_label, slug, name)``
* ``'page/category/%s/content_type/%s.%s/%s' % (<CATEGORY_P... | Returns templates in following format and order:
* ``'page/category/%s/content_type/%s.%s/%s/%s' % (<CATEGORY_PART>, app_label, model_label, slug, name)``
* ``'page/category/%s/content_type/%s.%s/%s' % (<CATEGORY_PART>, app_label, model_label, name)``
* ``'page/category/%s/%s' % (<CATEGORY_PART>, name)``
... | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L449-L518 |
ella/ella | ella/core/views.py | get_templates_from_publishable | def get_templates_from_publishable(name, publishable):
"""
Returns the same template list as `get_templates` but gets values from `Publishable` instance.
"""
slug = publishable.slug
category = publishable.category
app_label = publishable.content_type.app_label
model_label = publishable.conte... | python | def get_templates_from_publishable(name, publishable):
"""
Returns the same template list as `get_templates` but gets values from `Publishable` instance.
"""
slug = publishable.slug
category = publishable.category
app_label = publishable.content_type.app_label
model_label = publishable.conte... | Returns the same template list as `get_templates` but gets values from `Publishable` instance. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L521-L529 |
ella/ella | ella/core/views.py | export | def export(request, count, name='', content_type=None):
"""
Export banners.
:Parameters:
- `count`: number of objects to pass into the template
- `name`: name of the template ( page/export/banner.html is default )
- `models`: list of Model classes to include
"""
t_list = []
... | python | def export(request, count, name='', content_type=None):
"""
Export banners.
:Parameters:
- `count`: number of objects to pass into the template
- `name`: name of the template ( page/export/banner.html is default )
- `models`: list of Model classes to include
"""
t_list = []
... | Export banners.
:Parameters:
- `count`: number of objects to pass into the template
- `name`: name of the template ( page/export/banner.html is default )
- `models`: list of Model classes to include | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L538-L562 |
ella/ella | ella/core/views.py | EllaCoreView.get_templates | def get_templates(self, context, template_name=None):
" Extract parameters for `get_templates` from the context. "
if not template_name:
template_name = self.template_name
kw = {}
if 'object' in context:
o = context['object']
kw['slug'] = o.slug
... | python | def get_templates(self, context, template_name=None):
" Extract parameters for `get_templates` from the context. "
if not template_name:
template_name = self.template_name
kw = {}
if 'object' in context:
o = context['object']
kw['slug'] = o.slug
... | Extract parameters for `get_templates` from the context. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L82-L97 |
ella/ella | ella/core/views.py | ListContentType._archive_entry_year | def _archive_entry_year(self, category):
" Return ARCHIVE_ENTRY_YEAR from settings (if exists) or year of the newest object in category "
year = getattr(settings, 'ARCHIVE_ENTRY_YEAR', None)
if not year:
n = now()
try:
year = Listing.objects.filter(
... | python | def _archive_entry_year(self, category):
" Return ARCHIVE_ENTRY_YEAR from settings (if exists) or year of the newest object in category "
year = getattr(settings, 'ARCHIVE_ENTRY_YEAR', None)
if not year:
n = now()
try:
year = Listing.objects.filter(
... | Return ARCHIVE_ENTRY_YEAR from settings (if exists) or year of the newest object in category | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/core/views.py#L321-L334 |
ella/ella | ella/photos/models.py | Photo.save | def save(self, **kwargs):
"""Overrides models.Model.save.
- Generates slug.
- Saves image file.
"""
if not self.width or not self.height:
self.width, self.height = self.image.width, self.image.height
# prefill the slug with the ID, it requires double save
... | python | def save(self, **kwargs):
"""Overrides models.Model.save.
- Generates slug.
- Saves image file.
"""
if not self.width or not self.height:
self.width, self.height = self.image.width, self.image.height
# prefill the slug with the ID, it requires double save
... | Overrides models.Model.save.
- Generates slug.
- Saves image file. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L110-L152 |
ella/ella | ella/photos/models.py | Format.get_blank_img | def get_blank_img(self):
"""
Return fake ``FormatedPhoto`` object to be used in templates when an error
occurs in image generation.
"""
if photos_settings.DEBUG:
return self.get_placeholder_img()
out = {
'blank': True,
'width': self.ma... | python | def get_blank_img(self):
"""
Return fake ``FormatedPhoto`` object to be used in templates when an error
occurs in image generation.
"""
if photos_settings.DEBUG:
return self.get_placeholder_img()
out = {
'blank': True,
'width': self.ma... | Return fake ``FormatedPhoto`` object to be used in templates when an error
occurs in image generation. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L216-L230 |
ella/ella | ella/photos/models.py | Format.get_placeholder_img | def get_placeholder_img(self):
"""
Returns fake ``FormatedPhoto`` object grabbed from image placeholder
generator service for the purpose of debugging when images
are not available but we still want to see something.
"""
pars = {
'width': self.max_width,
... | python | def get_placeholder_img(self):
"""
Returns fake ``FormatedPhoto`` object grabbed from image placeholder
generator service for the purpose of debugging when images
are not available but we still want to see something.
"""
pars = {
'width': self.max_width,
... | Returns fake ``FormatedPhoto`` object grabbed from image placeholder
generator service for the purpose of debugging when images
are not available but we still want to see something. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L232-L248 |
ella/ella | ella/photos/models.py | Format.save | def save(self, **kwargs):
"""Overrides models.Model.save.
- Delete formatted photos if format save and not now created
(because of possible changes)
"""
if self.id:
for f_photo in self.formatedphoto_set.all():
f_photo.delete()
super(Format... | python | def save(self, **kwargs):
"""Overrides models.Model.save.
- Delete formatted photos if format save and not now created
(because of possible changes)
"""
if self.id:
for f_photo in self.formatedphoto_set.all():
f_photo.delete()
super(Format... | Overrides models.Model.save.
- Delete formatted photos if format save and not now created
(because of possible changes) | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L254-L265 |
ella/ella | ella/photos/models.py | FormatedPhoto.generate | def generate(self, save=True):
"""
Generates photo file in current format.
If ``save`` is ``True``, file is saved too.
"""
stretched_photo, crop_box = self._generate_img()
# set crop_box to (0,0,0,0) if photo not cropped
if not crop_box:
crop_box = 0... | python | def generate(self, save=True):
"""
Generates photo file in current format.
If ``save`` is ``True``, file is saved too.
"""
stretched_photo, crop_box = self._generate_img()
# set crop_box to (0,0,0,0) if photo not cropped
if not crop_box:
crop_box = 0... | Generates photo file in current format.
If ``save`` is ``True``, file is saved too. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L375-L400 |
ella/ella | ella/photos/models.py | FormatedPhoto.save | def save(self, **kwargs):
"""Overrides models.Model.save
- Removes old file from the FS
- Generates new file.
"""
self.remove_file()
if not self.image:
self.generate(save=False)
else:
self.image.name = self.file()
super(FormatedPho... | python | def save(self, **kwargs):
"""Overrides models.Model.save
- Removes old file from the FS
- Generates new file.
"""
self.remove_file()
if not self.image:
self.generate(save=False)
else:
self.image.name = self.file()
super(FormatedPho... | Overrides models.Model.save
- Removes old file from the FS
- Generates new file. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L402-L413 |
ella/ella | ella/photos/models.py | FormatedPhoto.file | def file(self):
""" Method returns formated photo path - derived from format.id and source Photo filename """
if photos_settings.FORMATED_PHOTO_FILENAME is not None:
return photos_settings.FORMATED_PHOTO_FILENAME(self)
source_file = path.split(self.photo.image.name)
return pa... | python | def file(self):
""" Method returns formated photo path - derived from format.id and source Photo filename """
if photos_settings.FORMATED_PHOTO_FILENAME is not None:
return photos_settings.FORMATED_PHOTO_FILENAME(self)
source_file = path.split(self.photo.image.name)
return pa... | Method returns formated photo path - derived from format.id and source Photo filename | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/photos/models.py#L427-L432 |
ella/ella | ella/positions/templatetags/positions.py | _get_category_from_pars_var | def _get_category_from_pars_var(template_var, context):
'''
get category from template variable or from tree_path
'''
cat = template_var.resolve(context)
if isinstance(cat, basestring):
cat = Category.objects.get_by_tree_path(cat)
return cat | python | def _get_category_from_pars_var(template_var, context):
'''
get category from template variable or from tree_path
'''
cat = template_var.resolve(context)
if isinstance(cat, basestring):
cat = Category.objects.get_by_tree_path(cat)
return cat | get category from template variable or from tree_path | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/templatetags/positions.py#L11-L18 |
ella/ella | ella/positions/templatetags/positions.py | position | def position(parser, token):
"""
Render a given position for category.
If some position is not defined for first category, position from its parent
category is used unless nofallback is specified.
Syntax::
{% position POSITION_NAME for CATEGORY [nofallback] %}{% endposition %}
{% p... | python | def position(parser, token):
"""
Render a given position for category.
If some position is not defined for first category, position from its parent
category is used unless nofallback is specified.
Syntax::
{% position POSITION_NAME for CATEGORY [nofallback] %}{% endposition %}
{% p... | Render a given position for category.
If some position is not defined for first category, position from its parent
category is used unless nofallback is specified.
Syntax::
{% position POSITION_NAME for CATEGORY [nofallback] %}{% endposition %}
{% position POSITION_NAME for CATEGORY using ... | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/templatetags/positions.py#L22-L40 |
ella/ella | ella/positions/templatetags/positions.py | ifposition | def ifposition(parser, token):
"""
Syntax::
{% ifposition POSITION_NAME ... for CATEGORY [nofallback] %}
{% else %}
{% endifposition %}
"""
bits = list(token.split_contents())
end_tag = 'end' + bits[0]
nofallback = False
if bits[-1] == 'nofallback':
nofallb... | python | def ifposition(parser, token):
"""
Syntax::
{% ifposition POSITION_NAME ... for CATEGORY [nofallback] %}
{% else %}
{% endifposition %}
"""
bits = list(token.split_contents())
end_tag = 'end' + bits[0]
nofallback = False
if bits[-1] == 'nofallback':
nofallb... | Syntax::
{% ifposition POSITION_NAME ... for CATEGORY [nofallback] %}
{% else %}
{% endifposition %} | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/templatetags/positions.py#L77-L109 |
ssalentin/plip | plip/modules/detection.py | filter_contacts | def filter_contacts(pairings):
"""Filter interactions by two criteria:
1. No interactions between the same residue (important for intra mode).
2. No duplicate interactions (A with B and B with A, also important for intra mode)."""
if not config.INTRA:
return pairings
filtered1_pairings = [p ... | python | def filter_contacts(pairings):
"""Filter interactions by two criteria:
1. No interactions between the same residue (important for intra mode).
2. No duplicate interactions (A with B and B with A, also important for intra mode)."""
if not config.INTRA:
return pairings
filtered1_pairings = [p ... | Filter interactions by two criteria:
1. No interactions between the same residue (important for intra mode).
2. No duplicate interactions (A with B and B with A, also important for intra mode). | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L22-L45 |
ssalentin/plip | plip/modules/detection.py | hydrophobic_interactions | def hydrophobic_interactions(atom_set_a, atom_set_b):
"""Detection of hydrophobic pliprofiler between atom_set_a (binding site) and atom_set_b (ligand).
Definition: All pairs of qualified carbon atoms within a distance of HYDROPH_DIST_MAX
"""
data = namedtuple('hydroph_interaction', 'bsatom bsatom_orig_... | python | def hydrophobic_interactions(atom_set_a, atom_set_b):
"""Detection of hydrophobic pliprofiler between atom_set_a (binding site) and atom_set_b (ligand).
Definition: All pairs of qualified carbon atoms within a distance of HYDROPH_DIST_MAX
"""
data = namedtuple('hydroph_interaction', 'bsatom bsatom_orig_... | Detection of hydrophobic pliprofiler between atom_set_a (binding site) and atom_set_b (ligand).
Definition: All pairs of qualified carbon atoms within a distance of HYDROPH_DIST_MAX | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L52-L72 |
ssalentin/plip | plip/modules/detection.py | hbonds | def hbonds(acceptors, donor_pairs, protisdon, typ):
"""Detection of hydrogen bonds between sets of acceptors and donor pairs.
Definition: All pairs of hydrogen bond acceptor and donors with
donor hydrogens and acceptor showing a distance within HBOND DIST MIN and HBOND DIST MAX
and donor angles above HB... | python | def hbonds(acceptors, donor_pairs, protisdon, typ):
"""Detection of hydrogen bonds between sets of acceptors and donor pairs.
Definition: All pairs of hydrogen bond acceptor and donors with
donor hydrogens and acceptor showing a distance within HBOND DIST MIN and HBOND DIST MAX
and donor angles above HB... | Detection of hydrogen bonds between sets of acceptors and donor pairs.
Definition: All pairs of hydrogen bond acceptor and donors with
donor hydrogens and acceptor showing a distance within HBOND DIST MIN and HBOND DIST MAX
and donor angles above HBOND_DON_ANGLE_MIN | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L75-L117 |
ssalentin/plip | plip/modules/detection.py | pistacking | def pistacking(rings_bs, rings_lig):
"""Return all pi-stackings between the given aromatic ring systems in receptor and ligand."""
data = namedtuple(
'pistack', 'proteinring ligandring distance angle offset type restype resnr reschain restype_l resnr_l reschain_l')
pairings = []
for r, l in iter... | python | def pistacking(rings_bs, rings_lig):
"""Return all pi-stackings between the given aromatic ring systems in receptor and ligand."""
data = namedtuple(
'pistack', 'proteinring ligandring distance angle offset type restype resnr reschain restype_l resnr_l reschain_l')
pairings = []
for r, l in iter... | Return all pi-stackings between the given aromatic ring systems in receptor and ligand. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L120-L156 |
ssalentin/plip | plip/modules/detection.py | pication | def pication(rings, pos_charged, protcharged):
"""Return all pi-Cation interaction between aromatic rings and positively charged groups.
For tertiary and quaternary amines, check also the angle between the ring and the nitrogen.
"""
data = namedtuple(
'pication', 'ring charge distance offset typ... | python | def pication(rings, pos_charged, protcharged):
"""Return all pi-Cation interaction between aromatic rings and positively charged groups.
For tertiary and quaternary amines, check also the angle between the ring and the nitrogen.
"""
data = namedtuple(
'pication', 'ring charge distance offset typ... | Return all pi-Cation interaction between aromatic rings and positively charged groups.
For tertiary and quaternary amines, check also the angle between the ring and the nitrogen. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L159-L208 |
ssalentin/plip | plip/modules/detection.py | saltbridge | def saltbridge(poscenter, negcenter, protispos):
"""Detect all salt bridges (pliprofiler between centers of positive and negative charge)"""
data = namedtuple(
'saltbridge', 'positive negative distance protispos resnr restype reschain resnr_l restype_l reschain_l')
pairings = []
for pc, nc in it... | python | def saltbridge(poscenter, negcenter, protispos):
"""Detect all salt bridges (pliprofiler between centers of positive and negative charge)"""
data = namedtuple(
'saltbridge', 'positive negative distance protispos resnr restype reschain resnr_l restype_l reschain_l')
pairings = []
for pc, nc in it... | Detect all salt bridges (pliprofiler between centers of positive and negative charge) | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L211-L229 |
ssalentin/plip | plip/modules/detection.py | halogen | def halogen(acceptor, donor):
"""Detect all halogen bonds of the type Y-O...X-C"""
data = namedtuple('halogenbond', 'acc acc_orig_idx don don_orig_idx distance don_angle acc_angle restype '
'resnr reschain restype_l resnr_l reschain_l donortype acctype sidechain')
pairin... | python | def halogen(acceptor, donor):
"""Detect all halogen bonds of the type Y-O...X-C"""
data = namedtuple('halogenbond', 'acc acc_orig_idx don don_orig_idx distance don_angle acc_angle restype '
'resnr reschain restype_l resnr_l reschain_l donortype acctype sidechain')
pairin... | Detect all halogen bonds of the type Y-O...X-C | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L232-L260 |
ssalentin/plip | plip/modules/detection.py | water_bridges | def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
"""Find water-bridged hydrogen bonds between ligand and protein. For now only considers bridged of first degree."""
data = namedtuple('waterbridge', 'a a_orig_idx atype d d_orig_idx dtype h water water_orig_idx distance_aw '
... | python | def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
"""Find water-bridged hydrogen bonds between ligand and protein. For now only considers bridged of first degree."""
data = namedtuple('waterbridge', 'a a_orig_idx atype d d_orig_idx dtype h water water_orig_idx distance_aw '
... | Find water-bridged hydrogen bonds between ligand and protein. For now only considers bridged of first degree. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L263-L330 |
ssalentin/plip | plip/modules/detection.py | metal_complexation | def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
"""Find all metal complexes between metals and appropriate groups in both protein and ligand, as well as water"""
data = namedtuple('metal_complex', 'metal metal_orig_idx metal_type target target_orig_idx target_type '
... | python | def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
"""Find all metal complexes between metals and appropriate groups in both protein and ligand, as well as water"""
data = namedtuple('metal_complex', 'metal metal_orig_idx metal_type target target_orig_idx target_type '
... | Find all metal complexes between metals and appropriate groups in both protein and ligand, as well as water | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/detection.py#L333-L485 |
ssalentin/plip | plip/modules/plipxml.py | XMLStorage.getdata | def getdata(self, tree, location, force_string=False):
"""Gets XML data from a specific element and handles types."""
found = tree.xpath('%s/text()' % location)
if not found:
return None
else:
data = found[0]
if force_string:
return data
... | python | def getdata(self, tree, location, force_string=False):
"""Gets XML data from a specific element and handles types."""
found = tree.xpath('%s/text()' % location)
if not found:
return None
else:
data = found[0]
if force_string:
return data
... | Gets XML data from a specific element and handles types. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/plipxml.py#L18-L39 |
ssalentin/plip | plip/modules/plipxml.py | XMLStorage.getcoordinates | def getcoordinates(self, tree, location):
"""Gets coordinates from a specific element in PLIP XML"""
return tuple(float(x) for x in tree.xpath('.//%s/*/text()' % location)) | python | def getcoordinates(self, tree, location):
"""Gets coordinates from a specific element in PLIP XML"""
return tuple(float(x) for x in tree.xpath('.//%s/*/text()' % location)) | Gets coordinates from a specific element in PLIP XML | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/plipxml.py#L41-L43 |
ssalentin/plip | plip/modules/plipxml.py | BSite.get_atom_mapping | def get_atom_mapping(self):
"""Parses the ligand atom mapping."""
# Atom mappings
smiles_to_pdb_mapping = self.bindingsite.xpath('mappings/smiles_to_pdb/text()')
if smiles_to_pdb_mapping == []:
self.mappings = {'smiles_to_pdb': None, 'pdb_to_smiles': None}
else:
... | python | def get_atom_mapping(self):
"""Parses the ligand atom mapping."""
# Atom mappings
smiles_to_pdb_mapping = self.bindingsite.xpath('mappings/smiles_to_pdb/text()')
if smiles_to_pdb_mapping == []:
self.mappings = {'smiles_to_pdb': None, 'pdb_to_smiles': None}
else:
... | Parses the ligand atom mapping. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/plipxml.py#L249-L259 |
ssalentin/plip | plip/modules/plipxml.py | BSite.get_counts | def get_counts(self):
"""counts the interaction types and backbone hydrogen bonding in a binding site"""
hbondsback = len([hb for hb in self.hbonds if not hb.sidechain])
counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds),
'wbridges': len(self.wbridges... | python | def get_counts(self):
"""counts the interaction types and backbone hydrogen bonding in a binding site"""
hbondsback = len([hb for hb in self.hbonds if not hb.sidechain])
counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds),
'wbridges': len(self.wbridges... | counts the interaction types and backbone hydrogen bonding in a binding site | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/plipxml.py#L261-L271 |
ssalentin/plip | plip/modules/plipxml.py | PLIPXMLREST.load_data | def load_data(self, pdbid):
"""Loads and parses an XML resource and saves it as a tree if successful"""
f = urlopen("http://projects.biotec.tu-dresden.de/plip-rest/pdb/%s?format=xml" % pdbid.lower())
self.doc = etree.parse(f) | python | def load_data(self, pdbid):
"""Loads and parses an XML resource and saves it as a tree if successful"""
f = urlopen("http://projects.biotec.tu-dresden.de/plip-rest/pdb/%s?format=xml" % pdbid.lower())
self.doc = etree.parse(f) | Loads and parses an XML resource and saves it as a tree if successful | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/plipxml.py#L303-L306 |
ella/ella | ella/articles/migrations/0005_move_updated_to_publishable.py | Migration.forwards | def forwards(self, orm):
"Write your forwards methods here."
for a in orm.Article.objects.all():
if a.updated:
a.last_updated = a.updated
a.save(force_update=True) | python | def forwards(self, orm):
"Write your forwards methods here."
for a in orm.Article.objects.all():
if a.updated:
a.last_updated = a.updated
a.save(force_update=True) | Write your forwards methods here. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/articles/migrations/0005_move_updated_to_publishable.py#L16-L21 |
ssalentin/plip | plip/modules/webservices.py | check_pdb_status | def check_pdb_status(pdbid):
"""Returns the status and up-to-date entry in the PDB for a given PDB ID"""
url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid
xmlf = urlopen(url)
xml = et.parse(xmlf)
xmlf.close()
status = None
current_pdbid = pdbid
for df in xml.xpath('//r... | python | def check_pdb_status(pdbid):
"""Returns the status and up-to-date entry in the PDB for a given PDB ID"""
url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid
xmlf = urlopen(url)
xml = et.parse(xmlf)
xmlf.close()
status = None
current_pdbid = pdbid
for df in xml.xpath('//r... | Returns the status and up-to-date entry in the PDB for a given PDB ID | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/webservices.py#L22-L34 |
ssalentin/plip | plip/modules/webservices.py | fetch_pdb | def fetch_pdb(pdbid):
"""Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
pdbid = pdbid.lower()
write_message('\nChecking status of PDB ID %s ... ' % pdbid)
state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID
if state... | python | def fetch_pdb(pdbid):
"""Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
pdbid = pdbid.lower()
write_message('\nChecking status of PDB ID %s ... ' % pdbid)
state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID
if state... | Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/webservices.py#L37-L59 |
ella/ella | ella/positions/models.py | PositionBox | def PositionBox(position, *args, **kwargs):
" Delegate the boxing. "
obj = position.target
return getattr(position.target, 'box_class', Box)(obj, *args, **kwargs) | python | def PositionBox(position, *args, **kwargs):
" Delegate the boxing. "
obj = position.target
return getattr(position.target, 'box_class', Box)(obj, *args, **kwargs) | Delegate the boxing. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/models.py#L57-L60 |
ella/ella | ella/positions/models.py | PositionManager.get_active_position | def get_active_position(self, category, name, nofallback=False):
"""
Get active position for given position name.
params:
category - Category model to look for
name - name of the position
nofallback - if True than do not fall back to parent
... | python | def get_active_position(self, category, name, nofallback=False):
"""
Get active position for given position name.
params:
category - Category model to look for
name - name of the position
nofallback - if True than do not fall back to parent
... | Get active position for given position name.
params:
category - Category model to look for
name - name of the position
nofallback - if True than do not fall back to parent
category if active position is not found for category | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/models.py#L26-L54 |
ella/ella | ella/positions/models.py | Position.render | def render(self, context, nodelist, box_type):
" Render the position. "
if not self.target:
if self.target_ct:
# broken Generic FK:
log.warning('Broken target for position with pk %r', self.pk)
return ''
try:
return ... | python | def render(self, context, nodelist, box_type):
" Render the position. "
if not self.target:
if self.target_ct:
# broken Generic FK:
log.warning('Broken target for position with pk %r', self.pk)
return ''
try:
return ... | Render the position. | https://github.com/ella/ella/blob/4a1414991f649dc21c4b777dc6b41a922a13faa7/ella/positions/models.py#L119-L139 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.set_initial_representations | def set_initial_representations(self):
"""General settings for PyMOL"""
self.standard_settings()
cmd.set('dash_gap', 0) # Show not dashes, but lines for the pliprofiler
cmd.set('ray_shadow', 0) # Turn on ray shadows for clearer ray-traced images
cmd.set('cartoon_color', 'myligh... | python | def set_initial_representations(self):
"""General settings for PyMOL"""
self.standard_settings()
cmd.set('dash_gap', 0) # Show not dashes, but lines for the pliprofiler
cmd.set('ray_shadow', 0) # Turn on ray shadows for clearer ray-traced images
cmd.set('cartoon_color', 'myligh... | General settings for PyMOL | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L24-L33 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.standard_settings | def standard_settings(self):
"""Sets up standard settings for a nice visualization."""
cmd.set('bg_rgb', [1.0, 1.0, 1.0]) # White background
cmd.set('depth_cue', 0) # Turn off depth cueing (no fog)
cmd.set('cartoon_side_chain_helper', 1) # Improve combined visualization of sticks and ... | python | def standard_settings(self):
"""Sets up standard settings for a nice visualization."""
cmd.set('bg_rgb', [1.0, 1.0, 1.0]) # White background
cmd.set('depth_cue', 0) # Turn off depth cueing (no fog)
cmd.set('cartoon_side_chain_helper', 1) # Improve combined visualization of sticks and ... | Sets up standard settings for a nice visualization. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L46-L54 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.set_custom_colorset | def set_custom_colorset(self):
"""Defines a colorset with matching colors. Provided by Joachim."""
cmd.set_color('myorange', '[253, 174, 97]')
cmd.set_color('mygreen', '[171, 221, 164]')
cmd.set_color('myred', '[215, 25, 28]')
cmd.set_color('myblue', '[43, 131, 186]')
cmd... | python | def set_custom_colorset(self):
"""Defines a colorset with matching colors. Provided by Joachim."""
cmd.set_color('myorange', '[253, 174, 97]')
cmd.set_color('mygreen', '[171, 221, 164]')
cmd.set_color('myred', '[215, 25, 28]')
cmd.set_color('myblue', '[43, 131, 186]')
cmd... | Defines a colorset with matching colors. Provided by Joachim. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L56-L63 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.show_hydrophobic | def show_hydrophobic(self):
"""Visualizes hydrophobic contacts."""
hydroph = self.plcomplex.hydrophobic_contacts
if not len(hydroph.bs_ids) == 0:
self.select_by_ids('Hydrophobic-P', hydroph.bs_ids, restrict=self.protname)
self.select_by_ids('Hydrophobic-L', hydroph.lig_id... | python | def show_hydrophobic(self):
"""Visualizes hydrophobic contacts."""
hydroph = self.plcomplex.hydrophobic_contacts
if not len(hydroph.bs_ids) == 0:
self.select_by_ids('Hydrophobic-P', hydroph.bs_ids, restrict=self.protname)
self.select_by_ids('Hydrophobic-L', hydroph.lig_id... | Visualizes hydrophobic contacts. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L83-L98 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.show_hbonds | def show_hbonds(self):
"""Visualizes hydrogen bonds."""
hbonds = self.plcomplex.hbonds
for group in [['HBondDonor-P', hbonds.prot_don_id],
['HBondAccept-P', hbonds.prot_acc_id]]:
if not len(group[1]) == 0:
self.select_by_ids(group[0], group[1], r... | python | def show_hbonds(self):
"""Visualizes hydrogen bonds."""
hbonds = self.plcomplex.hbonds
for group in [['HBondDonor-P', hbonds.prot_don_id],
['HBondAccept-P', hbonds.prot_acc_id]]:
if not len(group[1]) == 0:
self.select_by_ids(group[0], group[1], r... | Visualizes hydrogen bonds. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L100-L120 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.show_halogen | def show_halogen(self):
"""Visualize halogen bonds."""
halogen = self.plcomplex.halogen_bonds
all_don_x, all_acc_o = [], []
for h in halogen:
all_don_x.append(h.don_id)
all_acc_o.append(h.acc_id)
cmd.select('tmp_bs', 'id %i & %s' % (h.acc_id, self.prot... | python | def show_halogen(self):
"""Visualize halogen bonds."""
halogen = self.plcomplex.halogen_bonds
all_don_x, all_acc_o = [], []
for h in halogen:
all_don_x.append(h.don_id)
all_acc_o.append(h.acc_id)
cmd.select('tmp_bs', 'id %i & %s' % (h.acc_id, self.prot... | Visualize halogen bonds. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L122-L137 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.show_stacking | def show_stacking(self):
"""Visualize pi-stacking interactions."""
stacks = self.plcomplex.pistacking
for i, stack in enumerate(stacks):
pires_ids = '+'.join(map(str, stack.proteinring_atoms))
pilig_ids = '+'.join(map(str, stack.ligandring_atoms))
cmd.select('... | python | def show_stacking(self):
"""Visualize pi-stacking interactions."""
stacks = self.plcomplex.pistacking
for i, stack in enumerate(stacks):
pires_ids = '+'.join(map(str, stack.proteinring_atoms))
pilig_ids = '+'.join(map(str, stack.ligandring_atoms))
cmd.select('... | Visualize pi-stacking interactions. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L139-L166 |
ssalentin/plip | plip/modules/pymolplip.py | PyMOLVisualizer.show_cationpi | def show_cationpi(self):
"""Visualize cation-pi interactions."""
for i, p in enumerate(self.plcomplex.pication):
cmd.pseudoatom('ps-picat-1-%i' % i, pos=p.ring_center)
cmd.pseudoatom('ps-picat-2-%i' % i, pos=p.charge_center)
if p.protcharged:
cmd.pseud... | python | def show_cationpi(self):
"""Visualize cation-pi interactions."""
for i, p in enumerate(self.plcomplex.pication):
cmd.pseudoatom('ps-picat-1-%i' % i, pos=p.ring_center)
cmd.pseudoatom('ps-picat-2-%i' % i, pos=p.charge_center)
if p.protcharged:
cmd.pseud... | Visualize cation-pi interactions. | https://github.com/ssalentin/plip/blob/906c8d36463689779b403f6c2c9ed06174acaf9a/plip/modules/pymolplip.py#L168-L191 |
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