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2b3d666a531dec98fbcb07dc31247dfc0ac5a8f35ab6df078510177b79b013cb | def extract_eventualities_from_parsed_result(self, parsed_result, output_format='Eventuality', in_order=True, **kw):
' This method extracts eventualities from parsed_result of one sentence.\n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_parsed_result only supports Eventuality or json.')
return self.eventuality_extractor.extract_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw) | This method extracts eventualities from parsed_result of one sentence. | aser/extract/aser_extractor.py | extract_eventualities_from_parsed_result | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_eventualities_from_parsed_result(self, parsed_result, output_format='Eventuality', in_order=True, **kw):
' \n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_parsed_result only supports Eventuality or json.')
return self.eventuality_extractor.extract_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw) | def extract_eventualities_from_parsed_result(self, parsed_result, output_format='Eventuality', in_order=True, **kw):
' \n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_parsed_result only supports Eventuality or json.')
return self.eventuality_extractor.extract_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw)<|docstring|>This method extracts eventualities from parsed_result of one sentence.<|endoftext|> |
7728e3e72bb066392e894cba6fe0c2678ab0a471fb4a02f6a4e282b1520d7f55 | def extract_eventualities_from_text(self, text, output_format='Eventuality', in_order=True, annotators=None, **kw):
' This method extracts all eventualities for each sentence.\n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_text only supports Eventuality or json.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_eventualities_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw) | This method extracts all eventualities for each sentence. | aser/extract/aser_extractor.py | extract_eventualities_from_text | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_eventualities_from_text(self, text, output_format='Eventuality', in_order=True, annotators=None, **kw):
' \n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_text only supports Eventuality or json.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_eventualities_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw) | def extract_eventualities_from_text(self, text, output_format='Eventuality', in_order=True, annotators=None, **kw):
' \n '
if (output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities_from_text only supports Eventuality or json.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_eventualities_from_parsed_result(parsed_result, output_format=output_format, in_order=in_order, **kw)<|docstring|>This method extracts all eventualities for each sentence.<|endoftext|> |
85e40e853c738a85b8452bff4b002f12fa0c905a6eb93865deeea8af8eeb4dd0 | def extract_relations_from_parsed_result(self, parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw):
' This method extracts relations among extracted eventualities.\n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_parsed_result only supports Relation or triple.')
return self.relation_extractor.extract_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw) | This method extracts relations among extracted eventualities. | aser/extract/aser_extractor.py | extract_relations_from_parsed_result | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_relations_from_parsed_result(self, parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw):
' \n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_parsed_result only supports Relation or triple.')
return self.relation_extractor.extract_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw) | def extract_relations_from_parsed_result(self, parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw):
' \n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_parsed_result only supports Relation or triple.')
return self.relation_extractor.extract_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw)<|docstring|>This method extracts relations among extracted eventualities.<|endoftext|> |
e5572d2ae80ab3d9ed1de37382902612520e35865bcc100592de67f1a1232b17 | def extract_relations_from_text(self, text, output_format='Relation', in_order=True, annotators=None, **kw):
' This method extracts relations from parsed_result of one paragraph.\n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_text only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result)
return self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw) | This method extracts relations from parsed_result of one paragraph. | aser/extract/aser_extractor.py | extract_relations_from_text | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_relations_from_text(self, text, output_format='Relation', in_order=True, annotators=None, **kw):
' \n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_text only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result)
return self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw) | def extract_relations_from_text(self, text, output_format='Relation', in_order=True, annotators=None, **kw):
' \n '
if (output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations_from_text only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result)
return self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format=output_format, in_order=in_order, **kw)<|docstring|>This method extracts relations from parsed_result of one paragraph.<|endoftext|> |
73d87adbd2c89f9d76d4c152f8abbb0d46b5b33bb9666b254604932b816d7fb4 | def extract_from_parsed_result(self, parsed_result, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, **kw):
' This method extracts eventualities and relations from parsed_result of one paragraph.\n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
if (not isinstance(parsed_result, (list, tuple, dict))):
raise NotImplementedError
if isinstance(parsed_result, dict):
is_single_sent = True
parsed_result = [parsed_result]
else:
is_single_sent = False
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result, output_format='Eventuality', in_order=True, **kw)
para_relations = self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw)
if in_order:
if (eventuality_output_format == 'json'):
para_eventualities = [[eventuality.encode(encoding=None) for eventuality in sent_eventualities] for sent_eventualities in para_eventualities]
if (relation_output_format == 'triple'):
relations = [list(chain.from_iterable([relation.to_triple() for relation in sent_relations])) for sent_relations in para_relations]
if is_single_sent:
return (para_eventualities[0], para_relations[0])
else:
return (para_eventualities, para_relations)
else:
eid2eventuality = dict()
for eventuality in chain.from_iterable(para_eventualities):
eid = eventuality.eid
if (eid not in eid2eventuality):
eid2eventuality[eid] = deepcopy(eventuality)
else:
eid2eventuality[eid].update(eventuality)
if (eventuality_output_format == 'Eventuality'):
eventualities = sorted(eid2eventuality.values(), key=(lambda e: e.eid))
elif (eventuality_output_format == 'json'):
eventualities = sorted([eventuality.encode(encoding=None) for eventuality in eid2eventuality.values()], key=(lambda e: e['eid']))
rid2relation = dict()
for relation in chain.from_iterable(para_relations):
if (relation.rid not in rid2relation):
rid2relation[relation.rid] = deepcopy(relation)
else:
rid2relation[relation.rid].update(relation)
if (relation_output_format == 'Relation'):
relations = sorted(rid2relation.values(), key=(lambda r: r.rid))
elif (relation_output_format == 'triple'):
relations = sorted(chain.from_iterable([relation.to_triples() for relation in rid2relation.values()]))
return (eventualities, relations) | This method extracts eventualities and relations from parsed_result of one paragraph. | aser/extract/aser_extractor.py | extract_from_parsed_result | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_from_parsed_result(self, parsed_result, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, **kw):
' \n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
if (not isinstance(parsed_result, (list, tuple, dict))):
raise NotImplementedError
if isinstance(parsed_result, dict):
is_single_sent = True
parsed_result = [parsed_result]
else:
is_single_sent = False
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result, output_format='Eventuality', in_order=True, **kw)
para_relations = self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw)
if in_order:
if (eventuality_output_format == 'json'):
para_eventualities = [[eventuality.encode(encoding=None) for eventuality in sent_eventualities] for sent_eventualities in para_eventualities]
if (relation_output_format == 'triple'):
relations = [list(chain.from_iterable([relation.to_triple() for relation in sent_relations])) for sent_relations in para_relations]
if is_single_sent:
return (para_eventualities[0], para_relations[0])
else:
return (para_eventualities, para_relations)
else:
eid2eventuality = dict()
for eventuality in chain.from_iterable(para_eventualities):
eid = eventuality.eid
if (eid not in eid2eventuality):
eid2eventuality[eid] = deepcopy(eventuality)
else:
eid2eventuality[eid].update(eventuality)
if (eventuality_output_format == 'Eventuality'):
eventualities = sorted(eid2eventuality.values(), key=(lambda e: e.eid))
elif (eventuality_output_format == 'json'):
eventualities = sorted([eventuality.encode(encoding=None) for eventuality in eid2eventuality.values()], key=(lambda e: e['eid']))
rid2relation = dict()
for relation in chain.from_iterable(para_relations):
if (relation.rid not in rid2relation):
rid2relation[relation.rid] = deepcopy(relation)
else:
rid2relation[relation.rid].update(relation)
if (relation_output_format == 'Relation'):
relations = sorted(rid2relation.values(), key=(lambda r: r.rid))
elif (relation_output_format == 'triple'):
relations = sorted(chain.from_iterable([relation.to_triples() for relation in rid2relation.values()]))
return (eventualities, relations) | def extract_from_parsed_result(self, parsed_result, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, **kw):
' \n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
if (not isinstance(parsed_result, (list, tuple, dict))):
raise NotImplementedError
if isinstance(parsed_result, dict):
is_single_sent = True
parsed_result = [parsed_result]
else:
is_single_sent = False
para_eventualities = self.extract_eventualities_from_parsed_result(parsed_result, output_format='Eventuality', in_order=True, **kw)
para_relations = self.extract_relations_from_parsed_result(parsed_result, para_eventualities, output_format='Relation', in_order=True, **kw)
if in_order:
if (eventuality_output_format == 'json'):
para_eventualities = [[eventuality.encode(encoding=None) for eventuality in sent_eventualities] for sent_eventualities in para_eventualities]
if (relation_output_format == 'triple'):
relations = [list(chain.from_iterable([relation.to_triple() for relation in sent_relations])) for sent_relations in para_relations]
if is_single_sent:
return (para_eventualities[0], para_relations[0])
else:
return (para_eventualities, para_relations)
else:
eid2eventuality = dict()
for eventuality in chain.from_iterable(para_eventualities):
eid = eventuality.eid
if (eid not in eid2eventuality):
eid2eventuality[eid] = deepcopy(eventuality)
else:
eid2eventuality[eid].update(eventuality)
if (eventuality_output_format == 'Eventuality'):
eventualities = sorted(eid2eventuality.values(), key=(lambda e: e.eid))
elif (eventuality_output_format == 'json'):
eventualities = sorted([eventuality.encode(encoding=None) for eventuality in eid2eventuality.values()], key=(lambda e: e['eid']))
rid2relation = dict()
for relation in chain.from_iterable(para_relations):
if (relation.rid not in rid2relation):
rid2relation[relation.rid] = deepcopy(relation)
else:
rid2relation[relation.rid].update(relation)
if (relation_output_format == 'Relation'):
relations = sorted(rid2relation.values(), key=(lambda r: r.rid))
elif (relation_output_format == 'triple'):
relations = sorted(chain.from_iterable([relation.to_triples() for relation in rid2relation.values()]))
return (eventualities, relations)<|docstring|>This method extracts eventualities and relations from parsed_result of one paragraph.<|endoftext|> |
db47b675e98fa64d22db363e4b7a91653dcbfc10f50a4df0e8bd2d8c1b554dc4 | def extract_from_text(self, text, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, annotators=None, **kw):
' This method extracts eventualities and relations for each sentence.\n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_from_parsed_result(parsed_result, eventuality_output_format=eventuality_output_format, relation_output_format=relation_output_format, in_order=in_order, **kw) | This method extracts eventualities and relations for each sentence. | aser/extract/aser_extractor.py | extract_from_text | HKUST-KnowComp/CSKB-Population | 13 | python | def extract_from_text(self, text, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, annotators=None, **kw):
' \n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_from_parsed_result(parsed_result, eventuality_output_format=eventuality_output_format, relation_output_format=relation_output_format, in_order=in_order, **kw) | def extract_from_text(self, text, eventuality_output_format='Eventuality', relation_output_format='Relation', in_order=True, annotators=None, **kw):
' \n '
if (eventuality_output_format not in ['Eventuality', 'json']):
raise NotImplementedError('Error: extract_eventualities only supports Eventuality or json.')
if (relation_output_format not in ['Relation', 'triple']):
raise NotImplementedError('Error: extract_relations only supports Relation or triple.')
parsed_result = self.parse_text(text, annotators=annotators)
return self.extract_from_parsed_result(parsed_result, eventuality_output_format=eventuality_output_format, relation_output_format=relation_output_format, in_order=in_order, **kw)<|docstring|>This method extracts eventualities and relations for each sentence.<|endoftext|> |
3382577cc980fd34ef2f75b8ec268606457c5a570d56da225469079441729452 | def run(params):
' Route to API method '
if (2 <= len(params) <= 4):
if (params[1] == 'widevine_install'):
widevine_install()
elif (params[1] == 'widevine_remove'):
widevine_remove()
elif (params[1] == 'check_inputstream'):
if (len(params) == 3):
check_inputstream(params[2])
elif (len(params) == 4):
check_inputstream(params[2], drm=params[3])
elif (len(params) > 4):
log('invalid API call, too many parameters')
else:
ADDON.openSettings() | Route to API method | addon.py | run | tito/script.module.inputstreamhelper | 0 | python | def run(params):
' '
if (2 <= len(params) <= 4):
if (params[1] == 'widevine_install'):
widevine_install()
elif (params[1] == 'widevine_remove'):
widevine_remove()
elif (params[1] == 'check_inputstream'):
if (len(params) == 3):
check_inputstream(params[2])
elif (len(params) == 4):
check_inputstream(params[2], drm=params[3])
elif (len(params) > 4):
log('invalid API call, too many parameters')
else:
ADDON.openSettings() | def run(params):
' '
if (2 <= len(params) <= 4):
if (params[1] == 'widevine_install'):
widevine_install()
elif (params[1] == 'widevine_remove'):
widevine_remove()
elif (params[1] == 'check_inputstream'):
if (len(params) == 3):
check_inputstream(params[2])
elif (len(params) == 4):
check_inputstream(params[2], drm=params[3])
elif (len(params) > 4):
log('invalid API call, too many parameters')
else:
ADDON.openSettings()<|docstring|>Route to API method<|endoftext|> |
8e42f417501dab9e7269c6462d8cf676f761e85b6e231bbc2a929a9b50955f17 | def check_inputstream(protocol, drm=None):
' The API interface to check inputstream '
Helper(protocol, drm=drm).check_inputstream() | The API interface to check inputstream | addon.py | check_inputstream | tito/script.module.inputstreamhelper | 0 | python | def check_inputstream(protocol, drm=None):
' '
Helper(protocol, drm=drm).check_inputstream() | def check_inputstream(protocol, drm=None):
' '
Helper(protocol, drm=drm).check_inputstream()<|docstring|>The API interface to check inputstream<|endoftext|> |
e7b9fc84b5c061270f29d4257f9e75fd213760def40bd9690bef0186a9fe3765 | def widevine_install():
' The API interface to install Widevine CDM '
Helper('mpd', drm='widevine').install_widevine() | The API interface to install Widevine CDM | addon.py | widevine_install | tito/script.module.inputstreamhelper | 0 | python | def widevine_install():
' '
Helper('mpd', drm='widevine').install_widevine() | def widevine_install():
' '
Helper('mpd', drm='widevine').install_widevine()<|docstring|>The API interface to install Widevine CDM<|endoftext|> |
816018d493dc02e5c4a26fafef15933166617a1f7161e5a10afff6faa2cc79be | def widevine_remove():
' The API interface to remove Widevine CDMs '
Helper('mpd', drm='widevine').remove_widevine() | The API interface to remove Widevine CDMs | addon.py | widevine_remove | tito/script.module.inputstreamhelper | 0 | python | def widevine_remove():
' '
Helper('mpd', drm='widevine').remove_widevine() | def widevine_remove():
' '
Helper('mpd', drm='widevine').remove_widevine()<|docstring|>The API interface to remove Widevine CDMs<|endoftext|> |
b1c99898ce5ad166e7f29465e7398139d2db67559ddc4ccb70a91d65cc2199dc | def prepare_optparser():
'Prepare optparser object. New options will be added in this\n function first.\n '
usage = 'usage: %prog -c mysample.cfg -s A01A -1 A01_1.fq -2 A02_2.fq'
description = 'Please set the sample name. e.g. L04A, L04C, L04T.'
optparser = OptionParser(version='0.0.1', description=description, usage=usage, add_help_option=False)
optparser.add_option('-h', '--help', action='help', help='Show this help message and exit.')
optparser.add_option('-c', '--config', dest='config', default='config.cfg', type='string', help='Set the config File.[config.cfg]')
optparser.add_option('-s', '--samplename', dest='samplename', type='string', help='Set the samplename.(Required)')
optparser.add_option('-f', '--case_vcf', dest='case_vcf', type='string', help='You can set this to your case vcf file path.')
optparser.add_option('-t', '--control_vcf', dest='control_vcf', type='string', default='', help='You can set this to your case vcf file path.')
optparser.add_option('-i', '--in_bam', dest='in_bam', type='string', help='Set your bam file path.(eg. case,control, or case only)')
optparser.add_option('-o', '--out_dir', dest='out_dir', type='string', default='vcf', help='Set the vcf file out_dir.[vcf]')
return optparser | Prepare optparser object. New options will be added in this
function first. | iseq/refinement.py | prepare_optparser | Miachol/iseq | 12 | python | def prepare_optparser():
'Prepare optparser object. New options will be added in this\n function first.\n '
usage = 'usage: %prog -c mysample.cfg -s A01A -1 A01_1.fq -2 A02_2.fq'
description = 'Please set the sample name. e.g. L04A, L04C, L04T.'
optparser = OptionParser(version='0.0.1', description=description, usage=usage, add_help_option=False)
optparser.add_option('-h', '--help', action='help', help='Show this help message and exit.')
optparser.add_option('-c', '--config', dest='config', default='config.cfg', type='string', help='Set the config File.[config.cfg]')
optparser.add_option('-s', '--samplename', dest='samplename', type='string', help='Set the samplename.(Required)')
optparser.add_option('-f', '--case_vcf', dest='case_vcf', type='string', help='You can set this to your case vcf file path.')
optparser.add_option('-t', '--control_vcf', dest='control_vcf', type='string', default=, help='You can set this to your case vcf file path.')
optparser.add_option('-i', '--in_bam', dest='in_bam', type='string', help='Set your bam file path.(eg. case,control, or case only)')
optparser.add_option('-o', '--out_dir', dest='out_dir', type='string', default='vcf', help='Set the vcf file out_dir.[vcf]')
return optparser | def prepare_optparser():
'Prepare optparser object. New options will be added in this\n function first.\n '
usage = 'usage: %prog -c mysample.cfg -s A01A -1 A01_1.fq -2 A02_2.fq'
description = 'Please set the sample name. e.g. L04A, L04C, L04T.'
optparser = OptionParser(version='0.0.1', description=description, usage=usage, add_help_option=False)
optparser.add_option('-h', '--help', action='help', help='Show this help message and exit.')
optparser.add_option('-c', '--config', dest='config', default='config.cfg', type='string', help='Set the config File.[config.cfg]')
optparser.add_option('-s', '--samplename', dest='samplename', type='string', help='Set the samplename.(Required)')
optparser.add_option('-f', '--case_vcf', dest='case_vcf', type='string', help='You can set this to your case vcf file path.')
optparser.add_option('-t', '--control_vcf', dest='control_vcf', type='string', default=, help='You can set this to your case vcf file path.')
optparser.add_option('-i', '--in_bam', dest='in_bam', type='string', help='Set your bam file path.(eg. case,control, or case only)')
optparser.add_option('-o', '--out_dir', dest='out_dir', type='string', default='vcf', help='Set the vcf file out_dir.[vcf]')
return optparser<|docstring|>Prepare optparser object. New options will be added in this
function first.<|endoftext|> |
d628172ef68cccfcf7f895b25aebdbf2e4c5910f922c585063b8d012e00d50e5 | def opt_validate(optparser):
'Validate options from a OptParser object.\n Ret: Validated options object.\n '
(options, args) = optparser.parse_args()
if (not options.config):
optparser.print_help()
sys.exit(1)
elif (not options.samplename):
optparser.print_help()
sys.exit(1)
elif (not options.case_vcf):
optparser.print_help()
sys.exit(1)
return options | Validate options from a OptParser object.
Ret: Validated options object. | iseq/refinement.py | opt_validate | Miachol/iseq | 12 | python | def opt_validate(optparser):
'Validate options from a OptParser object.\n Ret: Validated options object.\n '
(options, args) = optparser.parse_args()
if (not options.config):
optparser.print_help()
sys.exit(1)
elif (not options.samplename):
optparser.print_help()
sys.exit(1)
elif (not options.case_vcf):
optparser.print_help()
sys.exit(1)
return options | def opt_validate(optparser):
'Validate options from a OptParser object.\n Ret: Validated options object.\n '
(options, args) = optparser.parse_args()
if (not options.config):
optparser.print_help()
sys.exit(1)
elif (not options.samplename):
optparser.print_help()
sys.exit(1)
elif (not options.case_vcf):
optparser.print_help()
sys.exit(1)
return options<|docstring|>Validate options from a OptParser object.
Ret: Validated options object.<|endoftext|> |
faf11e71176fc6847ec6bb6bde45723d14dac6746857d5603a58eea96b9544f0 | def lambda_handler(event=None, context=None):
'\n AWS Lambda handler.\n\n '
wzdx_registry = WZDxFeedRegistry(DATASET_ID, socrata_params=json.loads(SOCRATA_PARAMS), lambda_to_trigger=LAMBDA_TO_TRIGGER, logger=logger)
wzdx_registry.ingest() | AWS Lambda handler. | lambda__wzdx_trigger_ingest.py | lambda_handler | usdot-its-jpo-data-portal/wzdx_registry | 0 | python | def lambda_handler(event=None, context=None):
'\n \n\n '
wzdx_registry = WZDxFeedRegistry(DATASET_ID, socrata_params=json.loads(SOCRATA_PARAMS), lambda_to_trigger=LAMBDA_TO_TRIGGER, logger=logger)
wzdx_registry.ingest() | def lambda_handler(event=None, context=None):
'\n \n\n '
wzdx_registry = WZDxFeedRegistry(DATASET_ID, socrata_params=json.loads(SOCRATA_PARAMS), lambda_to_trigger=LAMBDA_TO_TRIGGER, logger=logger)
wzdx_registry.ingest()<|docstring|>AWS Lambda handler.<|endoftext|> |
5d54e9e06d8118dd04f8e2af49c92f11478ec832865c8c79c8d161b21753eb70 | def main(argv):
'\n Main entry point of this utility application.\n\n This is simply a function called by the checking of namespace __main__, at\n the end of this script (in order to execute only when this script is ran\n directly).\n\n Parameters\n ------\n argv: list of str\n Arguments received from the command line.\n '
annotationsPath = 'C:/Users/luigi/Dropbox/Doutorado/dataset/annotation-all'
print('Reading data...')
data = OrderedDict()
tot = OrderedDict()
for (dirpath, _, filenames) in os.walk(annotationsPath):
for f in filenames:
name = os.path.splitext(f)[0]
parts = name.split('-')
if ((len(parts) != 2) or (parts[1] != 'face')):
continue
subject = parts[0].split('_')[1]
fileName = os.path.join(dirpath, f)
print('\tfile {}...'.format(fileName))
fails = []
lastFrame = 0
with open(fileName, 'r', newline='') as file:
reader = csv.reader(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
next(reader, None)
for row in reader:
lastFrame = int(row[0])
if (not any([float(i) for i in row[1:]])):
fails.append(int(row[0]))
tot[subject] = lastFrame
data[subject] = fails
print('Plotting data...')
subjects = []
times = []
fails = []
for (s, v) in data.items():
fail = ((len(v) / tot[s]) * 100)
fails.append([int(s), fail])
print('Subject: {} Fails: {:.2f}%'.format(s, fail))
for f in v:
subjects.append(int(s))
times.append(((f / 30) / 60))
ax = sns.stripplot(x=subjects, y=times, linewidth=1)
ax.set_xlabel('Subjects', fontsize=15)
ax.set_ylabel('Video Progress (in Minutes)', fontsize=15)
ax.set_ylim([0, 10])
fails = np.array(fails)
np.savetxt('fails.csv', fails, fmt=('%d', '%.5f'), delimiter=',', header='subject,fails (percent)')
mng = plt.get_current_fig_manager()
mng.window.state('zoomed')
plt.show() | Main entry point of this utility application.
This is simply a function called by the checking of namespace __main__, at
the end of this script (in order to execute only when this script is ran
directly).
Parameters
------
argv: list of str
Arguments received from the command line. | fsdk/reports/faces.py | main | luigivieira/fsdk | 0 | python | def main(argv):
'\n Main entry point of this utility application.\n\n This is simply a function called by the checking of namespace __main__, at\n the end of this script (in order to execute only when this script is ran\n directly).\n\n Parameters\n ------\n argv: list of str\n Arguments received from the command line.\n '
annotationsPath = 'C:/Users/luigi/Dropbox/Doutorado/dataset/annotation-all'
print('Reading data...')
data = OrderedDict()
tot = OrderedDict()
for (dirpath, _, filenames) in os.walk(annotationsPath):
for f in filenames:
name = os.path.splitext(f)[0]
parts = name.split('-')
if ((len(parts) != 2) or (parts[1] != 'face')):
continue
subject = parts[0].split('_')[1]
fileName = os.path.join(dirpath, f)
print('\tfile {}...'.format(fileName))
fails = []
lastFrame = 0
with open(fileName, 'r', newline=) as file:
reader = csv.reader(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
next(reader, None)
for row in reader:
lastFrame = int(row[0])
if (not any([float(i) for i in row[1:]])):
fails.append(int(row[0]))
tot[subject] = lastFrame
data[subject] = fails
print('Plotting data...')
subjects = []
times = []
fails = []
for (s, v) in data.items():
fail = ((len(v) / tot[s]) * 100)
fails.append([int(s), fail])
print('Subject: {} Fails: {:.2f}%'.format(s, fail))
for f in v:
subjects.append(int(s))
times.append(((f / 30) / 60))
ax = sns.stripplot(x=subjects, y=times, linewidth=1)
ax.set_xlabel('Subjects', fontsize=15)
ax.set_ylabel('Video Progress (in Minutes)', fontsize=15)
ax.set_ylim([0, 10])
fails = np.array(fails)
np.savetxt('fails.csv', fails, fmt=('%d', '%.5f'), delimiter=',', header='subject,fails (percent)')
mng = plt.get_current_fig_manager()
mng.window.state('zoomed')
plt.show() | def main(argv):
'\n Main entry point of this utility application.\n\n This is simply a function called by the checking of namespace __main__, at\n the end of this script (in order to execute only when this script is ran\n directly).\n\n Parameters\n ------\n argv: list of str\n Arguments received from the command line.\n '
annotationsPath = 'C:/Users/luigi/Dropbox/Doutorado/dataset/annotation-all'
print('Reading data...')
data = OrderedDict()
tot = OrderedDict()
for (dirpath, _, filenames) in os.walk(annotationsPath):
for f in filenames:
name = os.path.splitext(f)[0]
parts = name.split('-')
if ((len(parts) != 2) or (parts[1] != 'face')):
continue
subject = parts[0].split('_')[1]
fileName = os.path.join(dirpath, f)
print('\tfile {}...'.format(fileName))
fails = []
lastFrame = 0
with open(fileName, 'r', newline=) as file:
reader = csv.reader(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
next(reader, None)
for row in reader:
lastFrame = int(row[0])
if (not any([float(i) for i in row[1:]])):
fails.append(int(row[0]))
tot[subject] = lastFrame
data[subject] = fails
print('Plotting data...')
subjects = []
times = []
fails = []
for (s, v) in data.items():
fail = ((len(v) / tot[s]) * 100)
fails.append([int(s), fail])
print('Subject: {} Fails: {:.2f}%'.format(s, fail))
for f in v:
subjects.append(int(s))
times.append(((f / 30) / 60))
ax = sns.stripplot(x=subjects, y=times, linewidth=1)
ax.set_xlabel('Subjects', fontsize=15)
ax.set_ylabel('Video Progress (in Minutes)', fontsize=15)
ax.set_ylim([0, 10])
fails = np.array(fails)
np.savetxt('fails.csv', fails, fmt=('%d', '%.5f'), delimiter=',', header='subject,fails (percent)')
mng = plt.get_current_fig_manager()
mng.window.state('zoomed')
plt.show()<|docstring|>Main entry point of this utility application.
This is simply a function called by the checking of namespace __main__, at
the end of this script (in order to execute only when this script is ran
directly).
Parameters
------
argv: list of str
Arguments received from the command line.<|endoftext|> |
c3d2c3911806f9dcc486aab152769c80156ed1fb2466c35e9575dd319f66457c | def __init__(self, universe, selection1='protein', selection2='not resname SOL', water_selection='resname SOL', order=1, selection1_type='both', update_selection=False, update_water_selection=True, filter_first=True, distance_type='hydrogen', distance=3.0, angle=120.0, forcefield='CHARMM27', donors=None, acceptors=None, output_format='sele1_sele2', debug=None, verbose=False, pbc=False, **kwargs):
'Set up the calculation of water bridges between two selections in a\n universe.\n\n The timeseries is accessible as the attribute\n :attr:`WaterBridgeAnalysis.timeseries`.\n\n If no hydrogen bonds are detected or if the initial check fails, look\n at the log output (enable with :func:`MDAnalysis.start_logging` and set\n `verbose` ``=True``). It is likely that the default names for donors\n and acceptors are not suitable (especially for non-standard\n ligands). In this case, either change the `forcefield` or use\n customized `donors` and/or `acceptors`.\n\n Parameters\n ----------\n universe : Universe\n Universe object\n selection1 : str (optional)\n Selection string for first selection [\'protein\']\n selection2 : str (optional)\n Selection string for second selection [\'not resname SOL\']\n This string selects everything except water where water is assumed\n to have a residue name as SOL.\n water_selection : str (optional)\n Selection string for bridging water selection [\'resname SOL\']\n The default selection assumes that the water molecules have residue\n name "SOL". Change it to the appropriate selection for your\n specific force field.\n\n However, in theory, this selection can be anything which forms\n a hydrogen bond with selection 1 and selection 2.\n order : int (optional)\n The maximum number of water bridges linking both selections.\n if the order is set to 3, then all the residues linked with less than\n three water molecules will be detected. [1]\n\n Computation of high order water bridges can be very time-consuming.\n Think carefully before running the calculation, do you really want\n to compute the 20th order water bridge between domain A and domain B\n or you just want to know the third order water bridge between two residues.\n selection1_type : {"donor", "acceptor", "both"} (optional)\n Selection 1 can be \'donor\', \'acceptor\' or \'both\'. Note that the\n value for `selection1_type` automatically determines how\n `selection2` handles donors and acceptors: If `selection1` contains\n \'both\' then `selection2` will also contain \'both\'. If `selection1`\n is set to \'donor\' then `selection2` is \'acceptor\' (and vice versa).\n [\'both\'].\n update_selection : bool (optional)\n Update selection 1 and 2 at each frame. Setting to ``True`` if the\n selection is not static. Selections are filtered first to speed up\n performance. Thus, setting to ``True`` is recommended if contact\n surface between selection 1 and selection 2 is constantly\n changing. [``False``]\n update_water_selection : bool (optional)\n Update selection of water at each frame. Setting to ``False`` is\n **only** recommended when the total amount of water molecules in the\n simulation are small and when water molecules remain static across\n the simulation.\n\n However, in normal simulations, only a tiny proportion of water is\n engaged in the formation of water bridge. It is recommended to\n update the water selection and set keyword `filter_first` to\n ``True`` so as to filter out water not residing between the two\n selections. [``True``]\n filter_first : bool (optional)\n Filter the water selection to only include water within 4 Å + `order` *\n (2 Å + `distance`) away from `both` selection 1 and selection 2.\n Selection 1 and selection 2 are both filtered to only include atoms\n with the same distance away from the other selection. [``True``]\n distance : float (optional)\n Distance cutoff for hydrogen bonds; only interactions with a H-A\n distance <= `distance` (and the appropriate D-H-A angle, see\n `angle`) are recorded. (Note: `distance_type` can change this to\n the D-A distance.) [3.0]\n angle : float (optional)\n Angle cutoff for hydrogen bonds; an ideal H-bond has an angle of\n 180º. A hydrogen bond is only recorded if the D-H-A angle is\n >= `angle`. The default of 120º also finds fairly non-specific\n hydrogen interactions and possibly better value is 150º. [120.0]\n forcefield : {"CHARMM27", "GLYCAM06", "other"} (optional)\n Name of the forcefield used. Switches between different\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS` and\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS` values.\n ["CHARMM27"]\n donors : sequence (optional)\n Extra H donor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS`), must be a sequence.\n acceptors : sequence (optional)\n Extra H acceptor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS`), must be a\n sequence.\n distance_type : {"hydrogen", "heavy"} (optional)\n Measure hydrogen bond lengths between donor and acceptor heavy\n atoms ("heavy") or between donor hydrogen and acceptor heavy\n atom ("hydrogen"). If using "heavy" then one should set the\n *distance* cutoff to a higher value such as 3.5 Å. ["hydrogen"]\n output_format: {"sele1_sele2", "donor_acceptor"} (optional)\n Setting the output format for timeseries and table. If set to\n "sele1_sele2", for each hydrogen bond, the one close to selection 1\n will be placed before selection 2. If set to "donor_acceptor", the\n donor will be placed before acceptor. "sele1_sele2"]\n debug : bool (optional)\n If set to ``True`` enables per-frame debug logging. This is disabled\n by default because it generates a very large amount of output in\n the log file. (Note that a logger must have been started to see\n the output, e.g. using :func:`MDAnalysis.start_logging`.)\n verbose : bool (optional)\n Toggle progress output. (Can also be given as keyword argument to\n :meth:`run`.)\n\n Notes\n -----\n In order to speed up processing, atoms are filtered by a coarse\n distance criterion before a detailed hydrogen bonding analysis is\n performed (`filter_first` = ``True``).\n\n If selection 1 and selection 2 are very mobile during the simulation\n and the contact surface is constantly changing (i.e. residues are\n moving farther than 4 Å + `order` * (2 Å + `distance`)), you might\n consider setting the `update_selection` keywords to ``True``\n to ensure correctness.\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated\n see :attr:`WaterBridgeAnalysis.timeseries` for detail.\n This class is now based on\n :class:`~MDAnalysis.analysis.base.AnalysisBase`.\n\n\n '
super(WaterBridgeAnalysis, self).__init__(universe.trajectory, **kwargs)
self.water_selection = water_selection
self.update_water_selection = update_water_selection
self.debug = debug
self.output_format = output_format
self.u = universe
self.selection1 = selection1
self.selection2 = selection2
self.selection1_type = selection1_type
if (selection1 == selection2):
self.selection1_type = 'donor'
self.update_selection = update_selection
self.filter_first = filter_first
self.distance = distance
self.distance_type = distance_type
self.angle = angle
self.pbc = (pbc and all(self.u.dimensions[:3]))
self.order = order
if (donors is None):
donors = ()
if (acceptors is None):
acceptors = ()
self.forcefield = forcefield
self.donors = tuple(set(self.DEFAULT_DONORS[forcefield]).union(donors))
self.acceptors = tuple(set(self.DEFAULT_ACCEPTORS[forcefield]).union(acceptors))
if (self.selection1_type not in ('both', 'donor', 'acceptor')):
raise ValueError('HydrogenBondAnalysis: Invalid selection type {0!s}'.format(self.selection1_type))
self._network = []
self.timesteps = None
self._log_parameters() | Set up the calculation of water bridges between two selections in a
universe.
The timeseries is accessible as the attribute
:attr:`WaterBridgeAnalysis.timeseries`.
If no hydrogen bonds are detected or if the initial check fails, look
at the log output (enable with :func:`MDAnalysis.start_logging` and set
`verbose` ``=True``). It is likely that the default names for donors
and acceptors are not suitable (especially for non-standard
ligands). In this case, either change the `forcefield` or use
customized `donors` and/or `acceptors`.
Parameters
----------
universe : Universe
Universe object
selection1 : str (optional)
Selection string for first selection ['protein']
selection2 : str (optional)
Selection string for second selection ['not resname SOL']
This string selects everything except water where water is assumed
to have a residue name as SOL.
water_selection : str (optional)
Selection string for bridging water selection ['resname SOL']
The default selection assumes that the water molecules have residue
name "SOL". Change it to the appropriate selection for your
specific force field.
However, in theory, this selection can be anything which forms
a hydrogen bond with selection 1 and selection 2.
order : int (optional)
The maximum number of water bridges linking both selections.
if the order is set to 3, then all the residues linked with less than
three water molecules will be detected. [1]
Computation of high order water bridges can be very time-consuming.
Think carefully before running the calculation, do you really want
to compute the 20th order water bridge between domain A and domain B
or you just want to know the third order water bridge between two residues.
selection1_type : {"donor", "acceptor", "both"} (optional)
Selection 1 can be 'donor', 'acceptor' or 'both'. Note that the
value for `selection1_type` automatically determines how
`selection2` handles donors and acceptors: If `selection1` contains
'both' then `selection2` will also contain 'both'. If `selection1`
is set to 'donor' then `selection2` is 'acceptor' (and vice versa).
['both'].
update_selection : bool (optional)
Update selection 1 and 2 at each frame. Setting to ``True`` if the
selection is not static. Selections are filtered first to speed up
performance. Thus, setting to ``True`` is recommended if contact
surface between selection 1 and selection 2 is constantly
changing. [``False``]
update_water_selection : bool (optional)
Update selection of water at each frame. Setting to ``False`` is
**only** recommended when the total amount of water molecules in the
simulation are small and when water molecules remain static across
the simulation.
However, in normal simulations, only a tiny proportion of water is
engaged in the formation of water bridge. It is recommended to
update the water selection and set keyword `filter_first` to
``True`` so as to filter out water not residing between the two
selections. [``True``]
filter_first : bool (optional)
Filter the water selection to only include water within 4 Å + `order` *
(2 Å + `distance`) away from `both` selection 1 and selection 2.
Selection 1 and selection 2 are both filtered to only include atoms
with the same distance away from the other selection. [``True``]
distance : float (optional)
Distance cutoff for hydrogen bonds; only interactions with a H-A
distance <= `distance` (and the appropriate D-H-A angle, see
`angle`) are recorded. (Note: `distance_type` can change this to
the D-A distance.) [3.0]
angle : float (optional)
Angle cutoff for hydrogen bonds; an ideal H-bond has an angle of
180º. A hydrogen bond is only recorded if the D-H-A angle is
>= `angle`. The default of 120º also finds fairly non-specific
hydrogen interactions and possibly better value is 150º. [120.0]
forcefield : {"CHARMM27", "GLYCAM06", "other"} (optional)
Name of the forcefield used. Switches between different
:attr:`~HydrogenBondAnalysis.DEFAULT_DONORS` and
:attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS` values.
["CHARMM27"]
donors : sequence (optional)
Extra H donor atom types (in addition to those in
:attr:`~HydrogenBondAnalysis.DEFAULT_DONORS`), must be a sequence.
acceptors : sequence (optional)
Extra H acceptor atom types (in addition to those in
:attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS`), must be a
sequence.
distance_type : {"hydrogen", "heavy"} (optional)
Measure hydrogen bond lengths between donor and acceptor heavy
atoms ("heavy") or between donor hydrogen and acceptor heavy
atom ("hydrogen"). If using "heavy" then one should set the
*distance* cutoff to a higher value such as 3.5 Å. ["hydrogen"]
output_format: {"sele1_sele2", "donor_acceptor"} (optional)
Setting the output format for timeseries and table. If set to
"sele1_sele2", for each hydrogen bond, the one close to selection 1
will be placed before selection 2. If set to "donor_acceptor", the
donor will be placed before acceptor. "sele1_sele2"]
debug : bool (optional)
If set to ``True`` enables per-frame debug logging. This is disabled
by default because it generates a very large amount of output in
the log file. (Note that a logger must have been started to see
the output, e.g. using :func:`MDAnalysis.start_logging`.)
verbose : bool (optional)
Toggle progress output. (Can also be given as keyword argument to
:meth:`run`.)
Notes
-----
In order to speed up processing, atoms are filtered by a coarse
distance criterion before a detailed hydrogen bonding analysis is
performed (`filter_first` = ``True``).
If selection 1 and selection 2 are very mobile during the simulation
and the contact surface is constantly changing (i.e. residues are
moving farther than 4 Å + `order` * (2 Å + `distance`)), you might
consider setting the `update_selection` keywords to ``True``
to ensure correctness.
.. versionchanged 0.20.0
The :attr:`WaterBridgeAnalysis.timeseries` has been updated
see :attr:`WaterBridgeAnalysis.timeseries` for detail.
This class is now based on
:class:`~MDAnalysis.analysis.base.AnalysisBase`. | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | __init__ | dtklinh/GBRDE | 2 | python | def __init__(self, universe, selection1='protein', selection2='not resname SOL', water_selection='resname SOL', order=1, selection1_type='both', update_selection=False, update_water_selection=True, filter_first=True, distance_type='hydrogen', distance=3.0, angle=120.0, forcefield='CHARMM27', donors=None, acceptors=None, output_format='sele1_sele2', debug=None, verbose=False, pbc=False, **kwargs):
'Set up the calculation of water bridges between two selections in a\n universe.\n\n The timeseries is accessible as the attribute\n :attr:`WaterBridgeAnalysis.timeseries`.\n\n If no hydrogen bonds are detected or if the initial check fails, look\n at the log output (enable with :func:`MDAnalysis.start_logging` and set\n `verbose` ``=True``). It is likely that the default names for donors\n and acceptors are not suitable (especially for non-standard\n ligands). In this case, either change the `forcefield` or use\n customized `donors` and/or `acceptors`.\n\n Parameters\n ----------\n universe : Universe\n Universe object\n selection1 : str (optional)\n Selection string for first selection [\'protein\']\n selection2 : str (optional)\n Selection string for second selection [\'not resname SOL\']\n This string selects everything except water where water is assumed\n to have a residue name as SOL.\n water_selection : str (optional)\n Selection string for bridging water selection [\'resname SOL\']\n The default selection assumes that the water molecules have residue\n name "SOL". Change it to the appropriate selection for your\n specific force field.\n\n However, in theory, this selection can be anything which forms\n a hydrogen bond with selection 1 and selection 2.\n order : int (optional)\n The maximum number of water bridges linking both selections.\n if the order is set to 3, then all the residues linked with less than\n three water molecules will be detected. [1]\n\n Computation of high order water bridges can be very time-consuming.\n Think carefully before running the calculation, do you really want\n to compute the 20th order water bridge between domain A and domain B\n or you just want to know the third order water bridge between two residues.\n selection1_type : {"donor", "acceptor", "both"} (optional)\n Selection 1 can be \'donor\', \'acceptor\' or \'both\'. Note that the\n value for `selection1_type` automatically determines how\n `selection2` handles donors and acceptors: If `selection1` contains\n \'both\' then `selection2` will also contain \'both\'. If `selection1`\n is set to \'donor\' then `selection2` is \'acceptor\' (and vice versa).\n [\'both\'].\n update_selection : bool (optional)\n Update selection 1 and 2 at each frame. Setting to ``True`` if the\n selection is not static. Selections are filtered first to speed up\n performance. Thus, setting to ``True`` is recommended if contact\n surface between selection 1 and selection 2 is constantly\n changing. [``False``]\n update_water_selection : bool (optional)\n Update selection of water at each frame. Setting to ``False`` is\n **only** recommended when the total amount of water molecules in the\n simulation are small and when water molecules remain static across\n the simulation.\n\n However, in normal simulations, only a tiny proportion of water is\n engaged in the formation of water bridge. It is recommended to\n update the water selection and set keyword `filter_first` to\n ``True`` so as to filter out water not residing between the two\n selections. [``True``]\n filter_first : bool (optional)\n Filter the water selection to only include water within 4 Å + `order` *\n (2 Å + `distance`) away from `both` selection 1 and selection 2.\n Selection 1 and selection 2 are both filtered to only include atoms\n with the same distance away from the other selection. [``True``]\n distance : float (optional)\n Distance cutoff for hydrogen bonds; only interactions with a H-A\n distance <= `distance` (and the appropriate D-H-A angle, see\n `angle`) are recorded. (Note: `distance_type` can change this to\n the D-A distance.) [3.0]\n angle : float (optional)\n Angle cutoff for hydrogen bonds; an ideal H-bond has an angle of\n 180º. A hydrogen bond is only recorded if the D-H-A angle is\n >= `angle`. The default of 120º also finds fairly non-specific\n hydrogen interactions and possibly better value is 150º. [120.0]\n forcefield : {"CHARMM27", "GLYCAM06", "other"} (optional)\n Name of the forcefield used. Switches between different\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS` and\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS` values.\n ["CHARMM27"]\n donors : sequence (optional)\n Extra H donor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS`), must be a sequence.\n acceptors : sequence (optional)\n Extra H acceptor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS`), must be a\n sequence.\n distance_type : {"hydrogen", "heavy"} (optional)\n Measure hydrogen bond lengths between donor and acceptor heavy\n atoms ("heavy") or between donor hydrogen and acceptor heavy\n atom ("hydrogen"). If using "heavy" then one should set the\n *distance* cutoff to a higher value such as 3.5 Å. ["hydrogen"]\n output_format: {"sele1_sele2", "donor_acceptor"} (optional)\n Setting the output format for timeseries and table. If set to\n "sele1_sele2", for each hydrogen bond, the one close to selection 1\n will be placed before selection 2. If set to "donor_acceptor", the\n donor will be placed before acceptor. "sele1_sele2"]\n debug : bool (optional)\n If set to ``True`` enables per-frame debug logging. This is disabled\n by default because it generates a very large amount of output in\n the log file. (Note that a logger must have been started to see\n the output, e.g. using :func:`MDAnalysis.start_logging`.)\n verbose : bool (optional)\n Toggle progress output. (Can also be given as keyword argument to\n :meth:`run`.)\n\n Notes\n -----\n In order to speed up processing, atoms are filtered by a coarse\n distance criterion before a detailed hydrogen bonding analysis is\n performed (`filter_first` = ``True``).\n\n If selection 1 and selection 2 are very mobile during the simulation\n and the contact surface is constantly changing (i.e. residues are\n moving farther than 4 Å + `order` * (2 Å + `distance`)), you might\n consider setting the `update_selection` keywords to ``True``\n to ensure correctness.\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated\n see :attr:`WaterBridgeAnalysis.timeseries` for detail.\n This class is now based on\n :class:`~MDAnalysis.analysis.base.AnalysisBase`.\n\n\n '
super(WaterBridgeAnalysis, self).__init__(universe.trajectory, **kwargs)
self.water_selection = water_selection
self.update_water_selection = update_water_selection
self.debug = debug
self.output_format = output_format
self.u = universe
self.selection1 = selection1
self.selection2 = selection2
self.selection1_type = selection1_type
if (selection1 == selection2):
self.selection1_type = 'donor'
self.update_selection = update_selection
self.filter_first = filter_first
self.distance = distance
self.distance_type = distance_type
self.angle = angle
self.pbc = (pbc and all(self.u.dimensions[:3]))
self.order = order
if (donors is None):
donors = ()
if (acceptors is None):
acceptors = ()
self.forcefield = forcefield
self.donors = tuple(set(self.DEFAULT_DONORS[forcefield]).union(donors))
self.acceptors = tuple(set(self.DEFAULT_ACCEPTORS[forcefield]).union(acceptors))
if (self.selection1_type not in ('both', 'donor', 'acceptor')):
raise ValueError('HydrogenBondAnalysis: Invalid selection type {0!s}'.format(self.selection1_type))
self._network = []
self.timesteps = None
self._log_parameters() | def __init__(self, universe, selection1='protein', selection2='not resname SOL', water_selection='resname SOL', order=1, selection1_type='both', update_selection=False, update_water_selection=True, filter_first=True, distance_type='hydrogen', distance=3.0, angle=120.0, forcefield='CHARMM27', donors=None, acceptors=None, output_format='sele1_sele2', debug=None, verbose=False, pbc=False, **kwargs):
'Set up the calculation of water bridges between two selections in a\n universe.\n\n The timeseries is accessible as the attribute\n :attr:`WaterBridgeAnalysis.timeseries`.\n\n If no hydrogen bonds are detected or if the initial check fails, look\n at the log output (enable with :func:`MDAnalysis.start_logging` and set\n `verbose` ``=True``). It is likely that the default names for donors\n and acceptors are not suitable (especially for non-standard\n ligands). In this case, either change the `forcefield` or use\n customized `donors` and/or `acceptors`.\n\n Parameters\n ----------\n universe : Universe\n Universe object\n selection1 : str (optional)\n Selection string for first selection [\'protein\']\n selection2 : str (optional)\n Selection string for second selection [\'not resname SOL\']\n This string selects everything except water where water is assumed\n to have a residue name as SOL.\n water_selection : str (optional)\n Selection string for bridging water selection [\'resname SOL\']\n The default selection assumes that the water molecules have residue\n name "SOL". Change it to the appropriate selection for your\n specific force field.\n\n However, in theory, this selection can be anything which forms\n a hydrogen bond with selection 1 and selection 2.\n order : int (optional)\n The maximum number of water bridges linking both selections.\n if the order is set to 3, then all the residues linked with less than\n three water molecules will be detected. [1]\n\n Computation of high order water bridges can be very time-consuming.\n Think carefully before running the calculation, do you really want\n to compute the 20th order water bridge between domain A and domain B\n or you just want to know the third order water bridge between two residues.\n selection1_type : {"donor", "acceptor", "both"} (optional)\n Selection 1 can be \'donor\', \'acceptor\' or \'both\'. Note that the\n value for `selection1_type` automatically determines how\n `selection2` handles donors and acceptors: If `selection1` contains\n \'both\' then `selection2` will also contain \'both\'. If `selection1`\n is set to \'donor\' then `selection2` is \'acceptor\' (and vice versa).\n [\'both\'].\n update_selection : bool (optional)\n Update selection 1 and 2 at each frame. Setting to ``True`` if the\n selection is not static. Selections are filtered first to speed up\n performance. Thus, setting to ``True`` is recommended if contact\n surface between selection 1 and selection 2 is constantly\n changing. [``False``]\n update_water_selection : bool (optional)\n Update selection of water at each frame. Setting to ``False`` is\n **only** recommended when the total amount of water molecules in the\n simulation are small and when water molecules remain static across\n the simulation.\n\n However, in normal simulations, only a tiny proportion of water is\n engaged in the formation of water bridge. It is recommended to\n update the water selection and set keyword `filter_first` to\n ``True`` so as to filter out water not residing between the two\n selections. [``True``]\n filter_first : bool (optional)\n Filter the water selection to only include water within 4 Å + `order` *\n (2 Å + `distance`) away from `both` selection 1 and selection 2.\n Selection 1 and selection 2 are both filtered to only include atoms\n with the same distance away from the other selection. [``True``]\n distance : float (optional)\n Distance cutoff for hydrogen bonds; only interactions with a H-A\n distance <= `distance` (and the appropriate D-H-A angle, see\n `angle`) are recorded. (Note: `distance_type` can change this to\n the D-A distance.) [3.0]\n angle : float (optional)\n Angle cutoff for hydrogen bonds; an ideal H-bond has an angle of\n 180º. A hydrogen bond is only recorded if the D-H-A angle is\n >= `angle`. The default of 120º also finds fairly non-specific\n hydrogen interactions and possibly better value is 150º. [120.0]\n forcefield : {"CHARMM27", "GLYCAM06", "other"} (optional)\n Name of the forcefield used. Switches between different\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS` and\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS` values.\n ["CHARMM27"]\n donors : sequence (optional)\n Extra H donor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_DONORS`), must be a sequence.\n acceptors : sequence (optional)\n Extra H acceptor atom types (in addition to those in\n :attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS`), must be a\n sequence.\n distance_type : {"hydrogen", "heavy"} (optional)\n Measure hydrogen bond lengths between donor and acceptor heavy\n atoms ("heavy") or between donor hydrogen and acceptor heavy\n atom ("hydrogen"). If using "heavy" then one should set the\n *distance* cutoff to a higher value such as 3.5 Å. ["hydrogen"]\n output_format: {"sele1_sele2", "donor_acceptor"} (optional)\n Setting the output format for timeseries and table. If set to\n "sele1_sele2", for each hydrogen bond, the one close to selection 1\n will be placed before selection 2. If set to "donor_acceptor", the\n donor will be placed before acceptor. "sele1_sele2"]\n debug : bool (optional)\n If set to ``True`` enables per-frame debug logging. This is disabled\n by default because it generates a very large amount of output in\n the log file. (Note that a logger must have been started to see\n the output, e.g. using :func:`MDAnalysis.start_logging`.)\n verbose : bool (optional)\n Toggle progress output. (Can also be given as keyword argument to\n :meth:`run`.)\n\n Notes\n -----\n In order to speed up processing, atoms are filtered by a coarse\n distance criterion before a detailed hydrogen bonding analysis is\n performed (`filter_first` = ``True``).\n\n If selection 1 and selection 2 are very mobile during the simulation\n and the contact surface is constantly changing (i.e. residues are\n moving farther than 4 Å + `order` * (2 Å + `distance`)), you might\n consider setting the `update_selection` keywords to ``True``\n to ensure correctness.\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated\n see :attr:`WaterBridgeAnalysis.timeseries` for detail.\n This class is now based on\n :class:`~MDAnalysis.analysis.base.AnalysisBase`.\n\n\n '
super(WaterBridgeAnalysis, self).__init__(universe.trajectory, **kwargs)
self.water_selection = water_selection
self.update_water_selection = update_water_selection
self.debug = debug
self.output_format = output_format
self.u = universe
self.selection1 = selection1
self.selection2 = selection2
self.selection1_type = selection1_type
if (selection1 == selection2):
self.selection1_type = 'donor'
self.update_selection = update_selection
self.filter_first = filter_first
self.distance = distance
self.distance_type = distance_type
self.angle = angle
self.pbc = (pbc and all(self.u.dimensions[:3]))
self.order = order
if (donors is None):
donors = ()
if (acceptors is None):
acceptors = ()
self.forcefield = forcefield
self.donors = tuple(set(self.DEFAULT_DONORS[forcefield]).union(donors))
self.acceptors = tuple(set(self.DEFAULT_ACCEPTORS[forcefield]).union(acceptors))
if (self.selection1_type not in ('both', 'donor', 'acceptor')):
raise ValueError('HydrogenBondAnalysis: Invalid selection type {0!s}'.format(self.selection1_type))
self._network = []
self.timesteps = None
self._log_parameters()<|docstring|>Set up the calculation of water bridges between two selections in a
universe.
The timeseries is accessible as the attribute
:attr:`WaterBridgeAnalysis.timeseries`.
If no hydrogen bonds are detected or if the initial check fails, look
at the log output (enable with :func:`MDAnalysis.start_logging` and set
`verbose` ``=True``). It is likely that the default names for donors
and acceptors are not suitable (especially for non-standard
ligands). In this case, either change the `forcefield` or use
customized `donors` and/or `acceptors`.
Parameters
----------
universe : Universe
Universe object
selection1 : str (optional)
Selection string for first selection ['protein']
selection2 : str (optional)
Selection string for second selection ['not resname SOL']
This string selects everything except water where water is assumed
to have a residue name as SOL.
water_selection : str (optional)
Selection string for bridging water selection ['resname SOL']
The default selection assumes that the water molecules have residue
name "SOL". Change it to the appropriate selection for your
specific force field.
However, in theory, this selection can be anything which forms
a hydrogen bond with selection 1 and selection 2.
order : int (optional)
The maximum number of water bridges linking both selections.
if the order is set to 3, then all the residues linked with less than
three water molecules will be detected. [1]
Computation of high order water bridges can be very time-consuming.
Think carefully before running the calculation, do you really want
to compute the 20th order water bridge between domain A and domain B
or you just want to know the third order water bridge between two residues.
selection1_type : {"donor", "acceptor", "both"} (optional)
Selection 1 can be 'donor', 'acceptor' or 'both'. Note that the
value for `selection1_type` automatically determines how
`selection2` handles donors and acceptors: If `selection1` contains
'both' then `selection2` will also contain 'both'. If `selection1`
is set to 'donor' then `selection2` is 'acceptor' (and vice versa).
['both'].
update_selection : bool (optional)
Update selection 1 and 2 at each frame. Setting to ``True`` if the
selection is not static. Selections are filtered first to speed up
performance. Thus, setting to ``True`` is recommended if contact
surface between selection 1 and selection 2 is constantly
changing. [``False``]
update_water_selection : bool (optional)
Update selection of water at each frame. Setting to ``False`` is
**only** recommended when the total amount of water molecules in the
simulation are small and when water molecules remain static across
the simulation.
However, in normal simulations, only a tiny proportion of water is
engaged in the formation of water bridge. It is recommended to
update the water selection and set keyword `filter_first` to
``True`` so as to filter out water not residing between the two
selections. [``True``]
filter_first : bool (optional)
Filter the water selection to only include water within 4 Å + `order` *
(2 Å + `distance`) away from `both` selection 1 and selection 2.
Selection 1 and selection 2 are both filtered to only include atoms
with the same distance away from the other selection. [``True``]
distance : float (optional)
Distance cutoff for hydrogen bonds; only interactions with a H-A
distance <= `distance` (and the appropriate D-H-A angle, see
`angle`) are recorded. (Note: `distance_type` can change this to
the D-A distance.) [3.0]
angle : float (optional)
Angle cutoff for hydrogen bonds; an ideal H-bond has an angle of
180º. A hydrogen bond is only recorded if the D-H-A angle is
>= `angle`. The default of 120º also finds fairly non-specific
hydrogen interactions and possibly better value is 150º. [120.0]
forcefield : {"CHARMM27", "GLYCAM06", "other"} (optional)
Name of the forcefield used. Switches between different
:attr:`~HydrogenBondAnalysis.DEFAULT_DONORS` and
:attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS` values.
["CHARMM27"]
donors : sequence (optional)
Extra H donor atom types (in addition to those in
:attr:`~HydrogenBondAnalysis.DEFAULT_DONORS`), must be a sequence.
acceptors : sequence (optional)
Extra H acceptor atom types (in addition to those in
:attr:`~HydrogenBondAnalysis.DEFAULT_ACCEPTORS`), must be a
sequence.
distance_type : {"hydrogen", "heavy"} (optional)
Measure hydrogen bond lengths between donor and acceptor heavy
atoms ("heavy") or between donor hydrogen and acceptor heavy
atom ("hydrogen"). If using "heavy" then one should set the
*distance* cutoff to a higher value such as 3.5 Å. ["hydrogen"]
output_format: {"sele1_sele2", "donor_acceptor"} (optional)
Setting the output format for timeseries and table. If set to
"sele1_sele2", for each hydrogen bond, the one close to selection 1
will be placed before selection 2. If set to "donor_acceptor", the
donor will be placed before acceptor. "sele1_sele2"]
debug : bool (optional)
If set to ``True`` enables per-frame debug logging. This is disabled
by default because it generates a very large amount of output in
the log file. (Note that a logger must have been started to see
the output, e.g. using :func:`MDAnalysis.start_logging`.)
verbose : bool (optional)
Toggle progress output. (Can also be given as keyword argument to
:meth:`run`.)
Notes
-----
In order to speed up processing, atoms are filtered by a coarse
distance criterion before a detailed hydrogen bonding analysis is
performed (`filter_first` = ``True``).
If selection 1 and selection 2 are very mobile during the simulation
and the contact surface is constantly changing (i.e. residues are
moving farther than 4 Å + `order` * (2 Å + `distance`)), you might
consider setting the `update_selection` keywords to ``True``
to ensure correctness.
.. versionchanged 0.20.0
The :attr:`WaterBridgeAnalysis.timeseries` has been updated
see :attr:`WaterBridgeAnalysis.timeseries` for detail.
This class is now based on
:class:`~MDAnalysis.analysis.base.AnalysisBase`.<|endoftext|> |
6ae9432b0354264dc7c821cbfb882f5838fdeaa781664346855f987885f4864b | def _log_parameters(self):
'Log important parameters to the logfile.'
logger.info('WaterBridgeAnalysis: selection = %r (update: %r)', self.selection2, self.update_selection)
logger.info('WaterBridgeAnalysis: water selection = %r (update: %r)', self.water_selection, self.update_water_selection)
logger.info('WaterBridgeAnalysis: criterion: donor %s atom and acceptor atom distance <= %.3f A', self.distance_type, self.distance)
logger.info('WaterBridgeAnalysis: criterion: angle D-H-A >= %.3f degrees', self.angle)
logger.info('WaterBridgeAnalysis: force field %s to guess donor and acceptor names', self.forcefield) | Log important parameters to the logfile. | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _log_parameters | dtklinh/GBRDE | 2 | python | def _log_parameters(self):
logger.info('WaterBridgeAnalysis: selection = %r (update: %r)', self.selection2, self.update_selection)
logger.info('WaterBridgeAnalysis: water selection = %r (update: %r)', self.water_selection, self.update_water_selection)
logger.info('WaterBridgeAnalysis: criterion: donor %s atom and acceptor atom distance <= %.3f A', self.distance_type, self.distance)
logger.info('WaterBridgeAnalysis: criterion: angle D-H-A >= %.3f degrees', self.angle)
logger.info('WaterBridgeAnalysis: force field %s to guess donor and acceptor names', self.forcefield) | def _log_parameters(self):
logger.info('WaterBridgeAnalysis: selection = %r (update: %r)', self.selection2, self.update_selection)
logger.info('WaterBridgeAnalysis: water selection = %r (update: %r)', self.water_selection, self.update_water_selection)
logger.info('WaterBridgeAnalysis: criterion: donor %s atom and acceptor atom distance <= %.3f A', self.distance_type, self.distance)
logger.info('WaterBridgeAnalysis: criterion: angle D-H-A >= %.3f degrees', self.angle)
logger.info('WaterBridgeAnalysis: force field %s to guess donor and acceptor names', self.forcefield)<|docstring|>Log important parameters to the logfile.<|endoftext|> |
c13b3d608a7b41bb05165e9ce9c6e91753a57f7872e4f795e8cb62121ab449cc | def _get_bonded_hydrogens(self, atom):
'Find hydrogens bonded within cutoff to `atom`.\n\n Hydrogens are detected by either name ("H*", "[123]H*") or type ("H");\n this is not fool-proof as the atom type is not always a character but\n the name pattern should catch most typical occurrences.\n\n The distance from `atom` is calculated for all hydrogens in the residue\n and only those within a cutoff are kept. The cutoff depends on the\n heavy atom (more precisely, on its element, which is taken as the first\n letter of its name ``atom.name[0]``) and is parameterized in\n :attr:`HydrogenBondAnalysis.r_cov`. If no match is found then the\n default of 1.5 Å is used.\n\n\n Parameters\n ----------\n atom : groups.Atom\n heavy atom\n\n Returns\n -------\n hydrogen_atoms : AtomGroup or []\n list of hydrogens (can be a :class:`~MDAnalysis.core.groups.AtomGroup`)\n or empty list ``[]`` if none were found.\n '
try:
return atom.residue.atoms.select_atoms('(name H* 1H* 2H* 3H* or type H) and around {0:f} name {1!s}'.format(self.r_cov[atom.name[0]], atom.name))
except NoDataError:
return [] | Find hydrogens bonded within cutoff to `atom`.
Hydrogens are detected by either name ("H*", "[123]H*") or type ("H");
this is not fool-proof as the atom type is not always a character but
the name pattern should catch most typical occurrences.
The distance from `atom` is calculated for all hydrogens in the residue
and only those within a cutoff are kept. The cutoff depends on the
heavy atom (more precisely, on its element, which is taken as the first
letter of its name ``atom.name[0]``) and is parameterized in
:attr:`HydrogenBondAnalysis.r_cov`. If no match is found then the
default of 1.5 Å is used.
Parameters
----------
atom : groups.Atom
heavy atom
Returns
-------
hydrogen_atoms : AtomGroup or []
list of hydrogens (can be a :class:`~MDAnalysis.core.groups.AtomGroup`)
or empty list ``[]`` if none were found. | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _get_bonded_hydrogens | dtklinh/GBRDE | 2 | python | def _get_bonded_hydrogens(self, atom):
'Find hydrogens bonded within cutoff to `atom`.\n\n Hydrogens are detected by either name ("H*", "[123]H*") or type ("H");\n this is not fool-proof as the atom type is not always a character but\n the name pattern should catch most typical occurrences.\n\n The distance from `atom` is calculated for all hydrogens in the residue\n and only those within a cutoff are kept. The cutoff depends on the\n heavy atom (more precisely, on its element, which is taken as the first\n letter of its name ``atom.name[0]``) and is parameterized in\n :attr:`HydrogenBondAnalysis.r_cov`. If no match is found then the\n default of 1.5 Å is used.\n\n\n Parameters\n ----------\n atom : groups.Atom\n heavy atom\n\n Returns\n -------\n hydrogen_atoms : AtomGroup or []\n list of hydrogens (can be a :class:`~MDAnalysis.core.groups.AtomGroup`)\n or empty list ``[]`` if none were found.\n '
try:
return atom.residue.atoms.select_atoms('(name H* 1H* 2H* 3H* or type H) and around {0:f} name {1!s}'.format(self.r_cov[atom.name[0]], atom.name))
except NoDataError:
return [] | def _get_bonded_hydrogens(self, atom):
'Find hydrogens bonded within cutoff to `atom`.\n\n Hydrogens are detected by either name ("H*", "[123]H*") or type ("H");\n this is not fool-proof as the atom type is not always a character but\n the name pattern should catch most typical occurrences.\n\n The distance from `atom` is calculated for all hydrogens in the residue\n and only those within a cutoff are kept. The cutoff depends on the\n heavy atom (more precisely, on its element, which is taken as the first\n letter of its name ``atom.name[0]``) and is parameterized in\n :attr:`HydrogenBondAnalysis.r_cov`. If no match is found then the\n default of 1.5 Å is used.\n\n\n Parameters\n ----------\n atom : groups.Atom\n heavy atom\n\n Returns\n -------\n hydrogen_atoms : AtomGroup or []\n list of hydrogens (can be a :class:`~MDAnalysis.core.groups.AtomGroup`)\n or empty list ``[]`` if none were found.\n '
try:
return atom.residue.atoms.select_atoms('(name H* 1H* 2H* 3H* or type H) and around {0:f} name {1!s}'.format(self.r_cov[atom.name[0]], atom.name))
except NoDataError:
return []<|docstring|>Find hydrogens bonded within cutoff to `atom`.
Hydrogens are detected by either name ("H*", "[123]H*") or type ("H");
this is not fool-proof as the atom type is not always a character but
the name pattern should catch most typical occurrences.
The distance from `atom` is calculated for all hydrogens in the residue
and only those within a cutoff are kept. The cutoff depends on the
heavy atom (more precisely, on its element, which is taken as the first
letter of its name ``atom.name[0]``) and is parameterized in
:attr:`HydrogenBondAnalysis.r_cov`. If no match is found then the
default of 1.5 Å is used.
Parameters
----------
atom : groups.Atom
heavy atom
Returns
-------
hydrogen_atoms : AtomGroup or []
list of hydrogens (can be a :class:`~MDAnalysis.core.groups.AtomGroup`)
or empty list ``[]`` if none were found.<|endoftext|> |
32e9dfa8695301fc1501d1c18349b633965435dcaf0c98f9f040b790cba552fc | def _traverse_water_network(self, graph, current, analysis_func=None, output=None, link_func=None, **kwargs):
'\n This function recursively traverses the water network self._network and finds the hydrogen bonds which connect\n the current atom to the next atom. The newly found hydrogen bond will be appended to the hydrogen bonds\n connecting the selection 1 to the current atom via link_func. When selection 2 is reached, the full list of\n hydrogen bonds connecting the selection 1 to selection 2 will be fed into analysis_func, which will then modify\n the output in place.\n :param graph: The connection network describes the connection between the atoms in the water network.\n :param current: The hydrogen bonds from selection 1 until now.\n :param analysis_func: The analysis function which is called to analysis the hydrogen bonds.\n :param output: where the result is stored.\n :param link_func: The new hydrogen bonds will be appended to current.\n :param kwargs: the keywords which are passed into the analysis_func.\n :return:\n '
if (link_func is None):
link_func = self._full_link
if (graph is None):
if (not (analysis_func is None)):
analysis_func(current, output, self.u, **kwargs)
elif (len(current) <= self.order):
for node in graph:
new = link_func(current, node)
self._traverse_water_network(graph[node], new, analysis_func, output, link_func, **kwargs) | This function recursively traverses the water network self._network and finds the hydrogen bonds which connect
the current atom to the next atom. The newly found hydrogen bond will be appended to the hydrogen bonds
connecting the selection 1 to the current atom via link_func. When selection 2 is reached, the full list of
hydrogen bonds connecting the selection 1 to selection 2 will be fed into analysis_func, which will then modify
the output in place.
:param graph: The connection network describes the connection between the atoms in the water network.
:param current: The hydrogen bonds from selection 1 until now.
:param analysis_func: The analysis function which is called to analysis the hydrogen bonds.
:param output: where the result is stored.
:param link_func: The new hydrogen bonds will be appended to current.
:param kwargs: the keywords which are passed into the analysis_func.
:return: | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _traverse_water_network | dtklinh/GBRDE | 2 | python | def _traverse_water_network(self, graph, current, analysis_func=None, output=None, link_func=None, **kwargs):
'\n This function recursively traverses the water network self._network and finds the hydrogen bonds which connect\n the current atom to the next atom. The newly found hydrogen bond will be appended to the hydrogen bonds\n connecting the selection 1 to the current atom via link_func. When selection 2 is reached, the full list of\n hydrogen bonds connecting the selection 1 to selection 2 will be fed into analysis_func, which will then modify\n the output in place.\n :param graph: The connection network describes the connection between the atoms in the water network.\n :param current: The hydrogen bonds from selection 1 until now.\n :param analysis_func: The analysis function which is called to analysis the hydrogen bonds.\n :param output: where the result is stored.\n :param link_func: The new hydrogen bonds will be appended to current.\n :param kwargs: the keywords which are passed into the analysis_func.\n :return:\n '
if (link_func is None):
link_func = self._full_link
if (graph is None):
if (not (analysis_func is None)):
analysis_func(current, output, self.u, **kwargs)
elif (len(current) <= self.order):
for node in graph:
new = link_func(current, node)
self._traverse_water_network(graph[node], new, analysis_func, output, link_func, **kwargs) | def _traverse_water_network(self, graph, current, analysis_func=None, output=None, link_func=None, **kwargs):
'\n This function recursively traverses the water network self._network and finds the hydrogen bonds which connect\n the current atom to the next atom. The newly found hydrogen bond will be appended to the hydrogen bonds\n connecting the selection 1 to the current atom via link_func. When selection 2 is reached, the full list of\n hydrogen bonds connecting the selection 1 to selection 2 will be fed into analysis_func, which will then modify\n the output in place.\n :param graph: The connection network describes the connection between the atoms in the water network.\n :param current: The hydrogen bonds from selection 1 until now.\n :param analysis_func: The analysis function which is called to analysis the hydrogen bonds.\n :param output: where the result is stored.\n :param link_func: The new hydrogen bonds will be appended to current.\n :param kwargs: the keywords which are passed into the analysis_func.\n :return:\n '
if (link_func is None):
link_func = self._full_link
if (graph is None):
if (not (analysis_func is None)):
analysis_func(current, output, self.u, **kwargs)
elif (len(current) <= self.order):
for node in graph:
new = link_func(current, node)
self._traverse_water_network(graph[node], new, analysis_func, output, link_func, **kwargs)<|docstring|>This function recursively traverses the water network self._network and finds the hydrogen bonds which connect
the current atom to the next atom. The newly found hydrogen bond will be appended to the hydrogen bonds
connecting the selection 1 to the current atom via link_func. When selection 2 is reached, the full list of
hydrogen bonds connecting the selection 1 to selection 2 will be fed into analysis_func, which will then modify
the output in place.
:param graph: The connection network describes the connection between the atoms in the water network.
:param current: The hydrogen bonds from selection 1 until now.
:param analysis_func: The analysis function which is called to analysis the hydrogen bonds.
:param output: where the result is stored.
:param link_func: The new hydrogen bonds will be appended to current.
:param kwargs: the keywords which are passed into the analysis_func.
:return:<|endoftext|> |
96f39e4879e41079e30491e055fee82af3852ad9659db91dad065600f06b4388 | def _expand_index(self, index):
'\n Expand the index into (resname, resid, name).\n '
atom = self.u.atoms[index]
return (atom.resname, atom.resid, atom.name) | Expand the index into (resname, resid, name). | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _expand_index | dtklinh/GBRDE | 2 | python | def _expand_index(self, index):
'\n \n '
atom = self.u.atoms[index]
return (atom.resname, atom.resid, atom.name) | def _expand_index(self, index):
'\n \n '
atom = self.u.atoms[index]
return (atom.resname, atom.resid, atom.name)<|docstring|>Expand the index into (resname, resid, name).<|endoftext|> |
6860fbd9c3a1dc72e5d92190de491334ecc4fab0c140f22961de939d136f8cb0 | def _expand_timeseries(self, entry, output_format=None):
"\n Expand the compact data format into the old timeseries form.\n The old is defined as the format for release up to 0.19.2.\n As is discussed in Issue #2177, the internal storage of the hydrogen\n bond information has been changed to the compact format.\n The function takes in the argument `output_format` to see which output format will be chosen.\n if `output_format` is not specified, the value will be taken from :attr:`output_format`.\n If `output_format` is 'sele1_sele2', the output will be the old water bridge analysis format::\n\n # donor from selection 1 to acceptor in selection 2\n [sele1_index, sele2_index,\n (sele1_resname, sele1_resid, sele1_name),\n (sele2_resname, sele2_resid, sele2_name), dist, angle]\n\n If `output_format` is 'donor_acceptor', the output will be the old hydrogen bond analysis format::\n\n # From donor to acceptor\n [donor_index, acceptor_index,\n (donor_resname, donor_resid, donor_name),\n (acceptor_resname, acceptor_resid, acceptor_name), dist, angle]\n "
output_format = (output_format or self.output_format)
(atom1, heavy_atom1, atom2, heavy_atom2, dist, angle) = entry
if (output_format == 'sele1_sele2'):
(atom1, atom2) = (atom1, atom2)
elif (output_format == 'donor_acceptor'):
if (heavy_atom1 is None):
(atom1, atom2) = (atom2, atom1)
else:
(atom1, atom2) = (atom1, atom2)
else:
raise KeyError("Only 'sele1_sele2' or 'donor_acceptor' are allowed as output format")
return (atom1, atom2, self._expand_index(atom1), self._expand_index(atom2), dist, angle) | Expand the compact data format into the old timeseries form.
The old is defined as the format for release up to 0.19.2.
As is discussed in Issue #2177, the internal storage of the hydrogen
bond information has been changed to the compact format.
The function takes in the argument `output_format` to see which output format will be chosen.
if `output_format` is not specified, the value will be taken from :attr:`output_format`.
If `output_format` is 'sele1_sele2', the output will be the old water bridge analysis format::
# donor from selection 1 to acceptor in selection 2
[sele1_index, sele2_index,
(sele1_resname, sele1_resid, sele1_name),
(sele2_resname, sele2_resid, sele2_name), dist, angle]
If `output_format` is 'donor_acceptor', the output will be the old hydrogen bond analysis format::
# From donor to acceptor
[donor_index, acceptor_index,
(donor_resname, donor_resid, donor_name),
(acceptor_resname, acceptor_resid, acceptor_name), dist, angle] | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _expand_timeseries | dtklinh/GBRDE | 2 | python | def _expand_timeseries(self, entry, output_format=None):
"\n Expand the compact data format into the old timeseries form.\n The old is defined as the format for release up to 0.19.2.\n As is discussed in Issue #2177, the internal storage of the hydrogen\n bond information has been changed to the compact format.\n The function takes in the argument `output_format` to see which output format will be chosen.\n if `output_format` is not specified, the value will be taken from :attr:`output_format`.\n If `output_format` is 'sele1_sele2', the output will be the old water bridge analysis format::\n\n # donor from selection 1 to acceptor in selection 2\n [sele1_index, sele2_index,\n (sele1_resname, sele1_resid, sele1_name),\n (sele2_resname, sele2_resid, sele2_name), dist, angle]\n\n If `output_format` is 'donor_acceptor', the output will be the old hydrogen bond analysis format::\n\n # From donor to acceptor\n [donor_index, acceptor_index,\n (donor_resname, donor_resid, donor_name),\n (acceptor_resname, acceptor_resid, acceptor_name), dist, angle]\n "
output_format = (output_format or self.output_format)
(atom1, heavy_atom1, atom2, heavy_atom2, dist, angle) = entry
if (output_format == 'sele1_sele2'):
(atom1, atom2) = (atom1, atom2)
elif (output_format == 'donor_acceptor'):
if (heavy_atom1 is None):
(atom1, atom2) = (atom2, atom1)
else:
(atom1, atom2) = (atom1, atom2)
else:
raise KeyError("Only 'sele1_sele2' or 'donor_acceptor' are allowed as output format")
return (atom1, atom2, self._expand_index(atom1), self._expand_index(atom2), dist, angle) | def _expand_timeseries(self, entry, output_format=None):
"\n Expand the compact data format into the old timeseries form.\n The old is defined as the format for release up to 0.19.2.\n As is discussed in Issue #2177, the internal storage of the hydrogen\n bond information has been changed to the compact format.\n The function takes in the argument `output_format` to see which output format will be chosen.\n if `output_format` is not specified, the value will be taken from :attr:`output_format`.\n If `output_format` is 'sele1_sele2', the output will be the old water bridge analysis format::\n\n # donor from selection 1 to acceptor in selection 2\n [sele1_index, sele2_index,\n (sele1_resname, sele1_resid, sele1_name),\n (sele2_resname, sele2_resid, sele2_name), dist, angle]\n\n If `output_format` is 'donor_acceptor', the output will be the old hydrogen bond analysis format::\n\n # From donor to acceptor\n [donor_index, acceptor_index,\n (donor_resname, donor_resid, donor_name),\n (acceptor_resname, acceptor_resid, acceptor_name), dist, angle]\n "
output_format = (output_format or self.output_format)
(atom1, heavy_atom1, atom2, heavy_atom2, dist, angle) = entry
if (output_format == 'sele1_sele2'):
(atom1, atom2) = (atom1, atom2)
elif (output_format == 'donor_acceptor'):
if (heavy_atom1 is None):
(atom1, atom2) = (atom2, atom1)
else:
(atom1, atom2) = (atom1, atom2)
else:
raise KeyError("Only 'sele1_sele2' or 'donor_acceptor' are allowed as output format")
return (atom1, atom2, self._expand_index(atom1), self._expand_index(atom2), dist, angle)<|docstring|>Expand the compact data format into the old timeseries form.
The old is defined as the format for release up to 0.19.2.
As is discussed in Issue #2177, the internal storage of the hydrogen
bond information has been changed to the compact format.
The function takes in the argument `output_format` to see which output format will be chosen.
if `output_format` is not specified, the value will be taken from :attr:`output_format`.
If `output_format` is 'sele1_sele2', the output will be the old water bridge analysis format::
# donor from selection 1 to acceptor in selection 2
[sele1_index, sele2_index,
(sele1_resname, sele1_resid, sele1_name),
(sele2_resname, sele2_resid, sele2_name), dist, angle]
If `output_format` is 'donor_acceptor', the output will be the old hydrogen bond analysis format::
# From donor to acceptor
[donor_index, acceptor_index,
(donor_resname, donor_resid, donor_name),
(acceptor_resname, acceptor_resid, acceptor_name), dist, angle]<|endoftext|> |
6aeacba0419316ee0caf733495ab53250ffd25a1b01a76fa144f7d4ac03b4e6e | def _generate_timeseries(self, output_format=None):
'Time series of water bridges.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Timeseries`.\n The format of output can be changed via the output_format selection.\n If ``output_format="sele1_sele2"``, the hydrogen bond forms a directional\n link from selection 1 to selection 2. If ``output_format="donor_acceptor"``,\n for each hydrogen bond, the donor is always written before the acceptor.\n\n Note\n ----\n To find an acceptor atom in :attr:`Universe.atoms` by\n *index* one would use ``u.atoms[acceptor_index]``.\n\n The :attr:`timeseries` is a managed attribute and it is generated\n from the underlying data in :attr:`_network` every time the\n attribute is accessed. It is therefore costly to call and if\n :attr:`timeseries` is needed repeatedly it is recommended that you\n assign to a variable::\n\n w = WaterBridgeAnalysis(u)\n w.run()\n timeseries = w.timeseries\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated where\n the donor and acceptor string has been changed to tuple\n (resname string, resid, name_string).\n\n\n '
output_format = (output_format or self.output_format)
def analysis(current, output, *args, **kwargs):
output = current
timeseries = []
for frame in self._network:
new_frame = []
self._traverse_water_network(frame, new_frame, analysis_func=analysis, output=new_frame, link_func=self._compact_link)
timeseries.append([self._expand_timeseries(entry, output_format) for entry in new_frame])
return timeseries | Time series of water bridges.
The output is generated per frame as is explained in :ref:`wb_Analysis_Timeseries`.
The format of output can be changed via the output_format selection.
If ``output_format="sele1_sele2"``, the hydrogen bond forms a directional
link from selection 1 to selection 2. If ``output_format="donor_acceptor"``,
for each hydrogen bond, the donor is always written before the acceptor.
Note
----
To find an acceptor atom in :attr:`Universe.atoms` by
*index* one would use ``u.atoms[acceptor_index]``.
The :attr:`timeseries` is a managed attribute and it is generated
from the underlying data in :attr:`_network` every time the
attribute is accessed. It is therefore costly to call and if
:attr:`timeseries` is needed repeatedly it is recommended that you
assign to a variable::
w = WaterBridgeAnalysis(u)
w.run()
timeseries = w.timeseries
.. versionchanged 0.20.0
The :attr:`WaterBridgeAnalysis.timeseries` has been updated where
the donor and acceptor string has been changed to tuple
(resname string, resid, name_string). | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _generate_timeseries | dtklinh/GBRDE | 2 | python | def _generate_timeseries(self, output_format=None):
'Time series of water bridges.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Timeseries`.\n The format of output can be changed via the output_format selection.\n If ``output_format="sele1_sele2"``, the hydrogen bond forms a directional\n link from selection 1 to selection 2. If ``output_format="donor_acceptor"``,\n for each hydrogen bond, the donor is always written before the acceptor.\n\n Note\n ----\n To find an acceptor atom in :attr:`Universe.atoms` by\n *index* one would use ``u.atoms[acceptor_index]``.\n\n The :attr:`timeseries` is a managed attribute and it is generated\n from the underlying data in :attr:`_network` every time the\n attribute is accessed. It is therefore costly to call and if\n :attr:`timeseries` is needed repeatedly it is recommended that you\n assign to a variable::\n\n w = WaterBridgeAnalysis(u)\n w.run()\n timeseries = w.timeseries\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated where\n the donor and acceptor string has been changed to tuple\n (resname string, resid, name_string).\n\n\n '
output_format = (output_format or self.output_format)
def analysis(current, output, *args, **kwargs):
output = current
timeseries = []
for frame in self._network:
new_frame = []
self._traverse_water_network(frame, new_frame, analysis_func=analysis, output=new_frame, link_func=self._compact_link)
timeseries.append([self._expand_timeseries(entry, output_format) for entry in new_frame])
return timeseries | def _generate_timeseries(self, output_format=None):
'Time series of water bridges.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Timeseries`.\n The format of output can be changed via the output_format selection.\n If ``output_format="sele1_sele2"``, the hydrogen bond forms a directional\n link from selection 1 to selection 2. If ``output_format="donor_acceptor"``,\n for each hydrogen bond, the donor is always written before the acceptor.\n\n Note\n ----\n To find an acceptor atom in :attr:`Universe.atoms` by\n *index* one would use ``u.atoms[acceptor_index]``.\n\n The :attr:`timeseries` is a managed attribute and it is generated\n from the underlying data in :attr:`_network` every time the\n attribute is accessed. It is therefore costly to call and if\n :attr:`timeseries` is needed repeatedly it is recommended that you\n assign to a variable::\n\n w = WaterBridgeAnalysis(u)\n w.run()\n timeseries = w.timeseries\n\n .. versionchanged 0.20.0\n The :attr:`WaterBridgeAnalysis.timeseries` has been updated where\n the donor and acceptor string has been changed to tuple\n (resname string, resid, name_string).\n\n\n '
output_format = (output_format or self.output_format)
def analysis(current, output, *args, **kwargs):
output = current
timeseries = []
for frame in self._network:
new_frame = []
self._traverse_water_network(frame, new_frame, analysis_func=analysis, output=new_frame, link_func=self._compact_link)
timeseries.append([self._expand_timeseries(entry, output_format) for entry in new_frame])
return timeseries<|docstring|>Time series of water bridges.
The output is generated per frame as is explained in :ref:`wb_Analysis_Timeseries`.
The format of output can be changed via the output_format selection.
If ``output_format="sele1_sele2"``, the hydrogen bond forms a directional
link from selection 1 to selection 2. If ``output_format="donor_acceptor"``,
for each hydrogen bond, the donor is always written before the acceptor.
Note
----
To find an acceptor atom in :attr:`Universe.atoms` by
*index* one would use ``u.atoms[acceptor_index]``.
The :attr:`timeseries` is a managed attribute and it is generated
from the underlying data in :attr:`_network` every time the
attribute is accessed. It is therefore costly to call and if
:attr:`timeseries` is needed repeatedly it is recommended that you
assign to a variable::
w = WaterBridgeAnalysis(u)
w.run()
timeseries = w.timeseries
.. versionchanged 0.20.0
The :attr:`WaterBridgeAnalysis.timeseries` has been updated where
the donor and acceptor string has been changed to tuple
(resname string, resid, name_string).<|endoftext|> |
dfb21e365327fabf426d293f0e454d51f15cedfc64911cd7541d351a151f420a | def _get_network(self):
'Network representation of the water network.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Network`.\n Each hydrogen bond has a compact representation of ::\n\n [sele1_acceptor_idx, None, sele2_donor_idx, donor_heavy_idx, distance, angle]\n\n or ::\n\n [sele1_donor_idx, donor_heavy_idx, sele1_acceptor_idx, None, distance, angle]\n\n The donor_heavy_idx is the heavy atom bonding to the proton and atoms\n can be retrived from the universe::\n\n atom = u.atoms[idx]\n\n .. versionadded:: 0.20.0\n\n '
return self._network | Network representation of the water network.
The output is generated per frame as is explained in :ref:`wb_Analysis_Network`.
Each hydrogen bond has a compact representation of ::
[sele1_acceptor_idx, None, sele2_donor_idx, donor_heavy_idx, distance, angle]
or ::
[sele1_donor_idx, donor_heavy_idx, sele1_acceptor_idx, None, distance, angle]
The donor_heavy_idx is the heavy atom bonding to the proton and atoms
can be retrived from the universe::
atom = u.atoms[idx]
.. versionadded:: 0.20.0 | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _get_network | dtklinh/GBRDE | 2 | python | def _get_network(self):
'Network representation of the water network.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Network`.\n Each hydrogen bond has a compact representation of ::\n\n [sele1_acceptor_idx, None, sele2_donor_idx, donor_heavy_idx, distance, angle]\n\n or ::\n\n [sele1_donor_idx, donor_heavy_idx, sele1_acceptor_idx, None, distance, angle]\n\n The donor_heavy_idx is the heavy atom bonding to the proton and atoms\n can be retrived from the universe::\n\n atom = u.atoms[idx]\n\n .. versionadded:: 0.20.0\n\n '
return self._network | def _get_network(self):
'Network representation of the water network.\n\n The output is generated per frame as is explained in :ref:`wb_Analysis_Network`.\n Each hydrogen bond has a compact representation of ::\n\n [sele1_acceptor_idx, None, sele2_donor_idx, donor_heavy_idx, distance, angle]\n\n or ::\n\n [sele1_donor_idx, donor_heavy_idx, sele1_acceptor_idx, None, distance, angle]\n\n The donor_heavy_idx is the heavy atom bonding to the proton and atoms\n can be retrived from the universe::\n\n atom = u.atoms[idx]\n\n .. versionadded:: 0.20.0\n\n '
return self._network<|docstring|>Network representation of the water network.
The output is generated per frame as is explained in :ref:`wb_Analysis_Network`.
Each hydrogen bond has a compact representation of ::
[sele1_acceptor_idx, None, sele2_donor_idx, donor_heavy_idx, distance, angle]
or ::
[sele1_donor_idx, donor_heavy_idx, sele1_acceptor_idx, None, distance, angle]
The donor_heavy_idx is the heavy atom bonding to the proton and atoms
can be retrived from the universe::
atom = u.atoms[idx]
.. versionadded:: 0.20.0<|endoftext|> |
7c6160609748b2e3c30dd14f64e6540ef294b67fee40710bb5e9eea104a0d539 | @classmethod
def _full_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
result = output[:]
result.append(node)
return result | A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.
:param output: The existing hydrogen bonds from selection 1
:param node: The new hydrogen bond
:return: The hydrogen bonds from selection 1 with the new hydrogen bond added | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _full_link | dtklinh/GBRDE | 2 | python | @classmethod
def _full_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
result = output[:]
result.append(node)
return result | @classmethod
def _full_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
result = output[:]
result.append(node)
return result<|docstring|>A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.
:param output: The existing hydrogen bonds from selection 1
:param node: The new hydrogen bond
:return: The hydrogen bonds from selection 1 with the new hydrogen bond added<|endoftext|> |
d44b0627bc99657b0e450f102ea5344224c40b2b254a77e4408ca8dd5974c600 | @classmethod
def _compact_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n In this form no new list is created and thus, one bridge will only appear once.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
output.append(node)
return output | A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.
In this form no new list is created and thus, one bridge will only appear once.
:param output: The existing hydrogen bonds from selection 1
:param node: The new hydrogen bond
:return: The hydrogen bonds from selection 1 with the new hydrogen bond added | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _compact_link | dtklinh/GBRDE | 2 | python | @classmethod
def _compact_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n In this form no new list is created and thus, one bridge will only appear once.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
output.append(node)
return output | @classmethod
def _compact_link(self, output, node):
'\n A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.\n In this form no new list is created and thus, one bridge will only appear once.\n :param output: The existing hydrogen bonds from selection 1\n :param node: The new hydrogen bond\n :return: The hydrogen bonds from selection 1 with the new hydrogen bond added\n '
output.append(node)
return output<|docstring|>A function used in _traverse_water_network to add the new hydrogen bond to the existing bonds.
In this form no new list is created and thus, one bridge will only appear once.
:param output: The existing hydrogen bonds from selection 1
:param node: The new hydrogen bond
:return: The hydrogen bonds from selection 1 with the new hydrogen bond added<|endoftext|> |
29b5cae0b7c1824e494df9cb3aa9b3261fac4f1eda6e13a2e0a2e919c8a18f39 | def _count_by_type_analysis(self, current, output, *args, **kwargs):
'\n Generates the key for count_by_type analysis.\n :return:\n '
(s1_index, to_index, (s1_resname, s1_resid, s1_name), (to_resname, to_resid, to_name), dist, angle) = self._expand_timeseries(current[0])
(from_index, s2_index, (from_resname, from_resid, from_name), (s2_resname, s2_resid, s2_name), dist, angle) = self._expand_timeseries(current[(- 1)])
key = (s1_index, s2_index, s1_resname, s1_resid, s1_name, s2_resname, s2_resid, s2_name)
output[key] += 1 | Generates the key for count_by_type analysis.
:return: | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | _count_by_type_analysis | dtklinh/GBRDE | 2 | python | def _count_by_type_analysis(self, current, output, *args, **kwargs):
'\n Generates the key for count_by_type analysis.\n :return:\n '
(s1_index, to_index, (s1_resname, s1_resid, s1_name), (to_resname, to_resid, to_name), dist, angle) = self._expand_timeseries(current[0])
(from_index, s2_index, (from_resname, from_resid, from_name), (s2_resname, s2_resid, s2_name), dist, angle) = self._expand_timeseries(current[(- 1)])
key = (s1_index, s2_index, s1_resname, s1_resid, s1_name, s2_resname, s2_resid, s2_name)
output[key] += 1 | def _count_by_type_analysis(self, current, output, *args, **kwargs):
'\n Generates the key for count_by_type analysis.\n :return:\n '
(s1_index, to_index, (s1_resname, s1_resid, s1_name), (to_resname, to_resid, to_name), dist, angle) = self._expand_timeseries(current[0])
(from_index, s2_index, (from_resname, from_resid, from_name), (s2_resname, s2_resid, s2_name), dist, angle) = self._expand_timeseries(current[(- 1)])
key = (s1_index, s2_index, s1_resname, s1_resid, s1_name, s2_resname, s2_resid, s2_name)
output[key] += 1<|docstring|>Generates the key for count_by_type analysis.
:return:<|endoftext|> |
24cc9645a52aefe097c02745fb50fed28518b7085b7f31e038882ca1702c97ca | def count_by_type(self, analysis_func=None, **kwargs):
'Counts the frequency of water bridge of a specific type.\n\n If one atom *A* from *selection 1* is linked to atom *B* from\n *selection 2* through one or more bridging waters, an entity will be created and\n the proportion of time that this linkage exists in the whole simulation\n will be calculated.\n\n The identification of a specific type of water bridge can be modified by\n supplying the analysis_func function. See :ref:`wb_count_by_type`\n for detail.\n\n Returns\n -------\n counts : list\n Returns a :class:`list` containing atom indices for *A* and\n *B*, residue names, residue numbers, atom names (for both A and B) and\n the fraction of the total time during which the water bridge was\n detected. This method returns None if method\n :meth:`WaterBridgeAnalysis.run` was not executed first.\n\n\n '
output = None
if (analysis_func is None):
analysis_func = self._count_by_type_analysis
output = 'combined'
if self._network:
length = len(self._network)
result_dict = defaultdict(int)
for frame in self._network:
frame_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=frame_dict, link_func=self._full_link, **kwargs)
for (key, value) in frame_dict.items():
result_dict[key] += frame_dict[key]
if (output == 'combined'):
result = [[i for i in key] for key in result_dict]
[result[i].append((result_dict[key] / length)) for (i, key) in enumerate(result_dict)]
else:
result = [(key, (result_dict[key] / length)) for key in result_dict]
return result
else:
return None | Counts the frequency of water bridge of a specific type.
If one atom *A* from *selection 1* is linked to atom *B* from
*selection 2* through one or more bridging waters, an entity will be created and
the proportion of time that this linkage exists in the whole simulation
will be calculated.
The identification of a specific type of water bridge can be modified by
supplying the analysis_func function. See :ref:`wb_count_by_type`
for detail.
Returns
-------
counts : list
Returns a :class:`list` containing atom indices for *A* and
*B*, residue names, residue numbers, atom names (for both A and B) and
the fraction of the total time during which the water bridge was
detected. This method returns None if method
:meth:`WaterBridgeAnalysis.run` was not executed first. | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | count_by_type | dtklinh/GBRDE | 2 | python | def count_by_type(self, analysis_func=None, **kwargs):
'Counts the frequency of water bridge of a specific type.\n\n If one atom *A* from *selection 1* is linked to atom *B* from\n *selection 2* through one or more bridging waters, an entity will be created and\n the proportion of time that this linkage exists in the whole simulation\n will be calculated.\n\n The identification of a specific type of water bridge can be modified by\n supplying the analysis_func function. See :ref:`wb_count_by_type`\n for detail.\n\n Returns\n -------\n counts : list\n Returns a :class:`list` containing atom indices for *A* and\n *B*, residue names, residue numbers, atom names (for both A and B) and\n the fraction of the total time during which the water bridge was\n detected. This method returns None if method\n :meth:`WaterBridgeAnalysis.run` was not executed first.\n\n\n '
output = None
if (analysis_func is None):
analysis_func = self._count_by_type_analysis
output = 'combined'
if self._network:
length = len(self._network)
result_dict = defaultdict(int)
for frame in self._network:
frame_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=frame_dict, link_func=self._full_link, **kwargs)
for (key, value) in frame_dict.items():
result_dict[key] += frame_dict[key]
if (output == 'combined'):
result = [[i for i in key] for key in result_dict]
[result[i].append((result_dict[key] / length)) for (i, key) in enumerate(result_dict)]
else:
result = [(key, (result_dict[key] / length)) for key in result_dict]
return result
else:
return None | def count_by_type(self, analysis_func=None, **kwargs):
'Counts the frequency of water bridge of a specific type.\n\n If one atom *A* from *selection 1* is linked to atom *B* from\n *selection 2* through one or more bridging waters, an entity will be created and\n the proportion of time that this linkage exists in the whole simulation\n will be calculated.\n\n The identification of a specific type of water bridge can be modified by\n supplying the analysis_func function. See :ref:`wb_count_by_type`\n for detail.\n\n Returns\n -------\n counts : list\n Returns a :class:`list` containing atom indices for *A* and\n *B*, residue names, residue numbers, atom names (for both A and B) and\n the fraction of the total time during which the water bridge was\n detected. This method returns None if method\n :meth:`WaterBridgeAnalysis.run` was not executed first.\n\n\n '
output = None
if (analysis_func is None):
analysis_func = self._count_by_type_analysis
output = 'combined'
if self._network:
length = len(self._network)
result_dict = defaultdict(int)
for frame in self._network:
frame_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=frame_dict, link_func=self._full_link, **kwargs)
for (key, value) in frame_dict.items():
result_dict[key] += frame_dict[key]
if (output == 'combined'):
result = [[i for i in key] for key in result_dict]
[result[i].append((result_dict[key] / length)) for (i, key) in enumerate(result_dict)]
else:
result = [(key, (result_dict[key] / length)) for key in result_dict]
return result
else:
return None<|docstring|>Counts the frequency of water bridge of a specific type.
If one atom *A* from *selection 1* is linked to atom *B* from
*selection 2* through one or more bridging waters, an entity will be created and
the proportion of time that this linkage exists in the whole simulation
will be calculated.
The identification of a specific type of water bridge can be modified by
supplying the analysis_func function. See :ref:`wb_count_by_type`
for detail.
Returns
-------
counts : list
Returns a :class:`list` containing atom indices for *A* and
*B*, residue names, residue numbers, atom names (for both A and B) and
the fraction of the total time during which the water bridge was
detected. This method returns None if method
:meth:`WaterBridgeAnalysis.run` was not executed first.<|endoftext|> |
c81afcf0a4639c8a491150bb5d19dd2d91d64c6dbbd00c72b8026ea6e3bf7b03 | def count_by_time(self, analysis_func=None, **kwargs):
'Counts the number of water bridges per timestep.\n\n The counting behaviour can be adjusted by supplying analysis_func.\n See :ref:`wb_count_by_time` for details.\n\n Returns\n -------\n counts : list\n Returns a time series ``N(t)`` where ``N`` is the total\n number of observed water bridges at time ``t``.\n\n '
if (analysis_func is None):
analysis_func = self._count_by_time_analysis
if self._network:
result = []
for (time, frame) in zip(self.timesteps, self._network):
result_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result_dict, link_func=self._full_link, **kwargs)
result.append((time, sum([result_dict[key] for key in result_dict])))
return result
else:
return None | Counts the number of water bridges per timestep.
The counting behaviour can be adjusted by supplying analysis_func.
See :ref:`wb_count_by_time` for details.
Returns
-------
counts : list
Returns a time series ``N(t)`` where ``N`` is the total
number of observed water bridges at time ``t``. | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | count_by_time | dtklinh/GBRDE | 2 | python | def count_by_time(self, analysis_func=None, **kwargs):
'Counts the number of water bridges per timestep.\n\n The counting behaviour can be adjusted by supplying analysis_func.\n See :ref:`wb_count_by_time` for details.\n\n Returns\n -------\n counts : list\n Returns a time series ``N(t)`` where ``N`` is the total\n number of observed water bridges at time ``t``.\n\n '
if (analysis_func is None):
analysis_func = self._count_by_time_analysis
if self._network:
result = []
for (time, frame) in zip(self.timesteps, self._network):
result_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result_dict, link_func=self._full_link, **kwargs)
result.append((time, sum([result_dict[key] for key in result_dict])))
return result
else:
return None | def count_by_time(self, analysis_func=None, **kwargs):
'Counts the number of water bridges per timestep.\n\n The counting behaviour can be adjusted by supplying analysis_func.\n See :ref:`wb_count_by_time` for details.\n\n Returns\n -------\n counts : list\n Returns a time series ``N(t)`` where ``N`` is the total\n number of observed water bridges at time ``t``.\n\n '
if (analysis_func is None):
analysis_func = self._count_by_time_analysis
if self._network:
result = []
for (time, frame) in zip(self.timesteps, self._network):
result_dict = defaultdict(int)
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result_dict, link_func=self._full_link, **kwargs)
result.append((time, sum([result_dict[key] for key in result_dict])))
return result
else:
return None<|docstring|>Counts the number of water bridges per timestep.
The counting behaviour can be adjusted by supplying analysis_func.
See :ref:`wb_count_by_time` for details.
Returns
-------
counts : list
Returns a time series ``N(t)`` where ``N`` is the total
number of observed water bridges at time ``t``.<|endoftext|> |
547c2944cf4fa09f3aa912e7bb71ccbe33bbd22c86684c04a61d789a46a8ffdd | def timesteps_by_type(self, analysis_func=None, **kwargs):
'Frames during which each water bridges existed, sorted by each water bridges.\n\n Processes :attr:`WaterBridgeAnalysis._network` and returns a\n :class:`list` containing atom indices, residue names, residue\n numbers (from selection 1 and selection 2) and each timestep at which the\n water bridge was detected.\n\n Similar to :meth:`~WaterBridgeAnalysis.count_by_type` and\n :meth:`~WaterBridgeAnalysis.count_by_time`, the behavior can be adjusted by\n supplying an analysis_func.\n\n Returns\n -------\n data : list\n\n '
output = None
if (analysis_func is None):
analysis_func = self._timesteps_by_type_analysis
output = 'combined'
if self._network:
result = defaultdict(list)
if (self.timesteps is None):
timesteps = range(len(self._network))
else:
timesteps = self.timesteps
for (time, frame) in zip(timesteps, self._network):
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result, link_func=self._full_link, time=time, **kwargs)
result_list = []
for (key, time_list) in six.iteritems(result):
for time in time_list:
if (output == 'combined'):
key = list(key)
key.append(time)
result_list.append(key)
else:
result_list.append((key, time))
return result_list
else:
return None | Frames during which each water bridges existed, sorted by each water bridges.
Processes :attr:`WaterBridgeAnalysis._network` and returns a
:class:`list` containing atom indices, residue names, residue
numbers (from selection 1 and selection 2) and each timestep at which the
water bridge was detected.
Similar to :meth:`~WaterBridgeAnalysis.count_by_type` and
:meth:`~WaterBridgeAnalysis.count_by_time`, the behavior can be adjusted by
supplying an analysis_func.
Returns
-------
data : list | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | timesteps_by_type | dtklinh/GBRDE | 2 | python | def timesteps_by_type(self, analysis_func=None, **kwargs):
'Frames during which each water bridges existed, sorted by each water bridges.\n\n Processes :attr:`WaterBridgeAnalysis._network` and returns a\n :class:`list` containing atom indices, residue names, residue\n numbers (from selection 1 and selection 2) and each timestep at which the\n water bridge was detected.\n\n Similar to :meth:`~WaterBridgeAnalysis.count_by_type` and\n :meth:`~WaterBridgeAnalysis.count_by_time`, the behavior can be adjusted by\n supplying an analysis_func.\n\n Returns\n -------\n data : list\n\n '
output = None
if (analysis_func is None):
analysis_func = self._timesteps_by_type_analysis
output = 'combined'
if self._network:
result = defaultdict(list)
if (self.timesteps is None):
timesteps = range(len(self._network))
else:
timesteps = self.timesteps
for (time, frame) in zip(timesteps, self._network):
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result, link_func=self._full_link, time=time, **kwargs)
result_list = []
for (key, time_list) in six.iteritems(result):
for time in time_list:
if (output == 'combined'):
key = list(key)
key.append(time)
result_list.append(key)
else:
result_list.append((key, time))
return result_list
else:
return None | def timesteps_by_type(self, analysis_func=None, **kwargs):
'Frames during which each water bridges existed, sorted by each water bridges.\n\n Processes :attr:`WaterBridgeAnalysis._network` and returns a\n :class:`list` containing atom indices, residue names, residue\n numbers (from selection 1 and selection 2) and each timestep at which the\n water bridge was detected.\n\n Similar to :meth:`~WaterBridgeAnalysis.count_by_type` and\n :meth:`~WaterBridgeAnalysis.count_by_time`, the behavior can be adjusted by\n supplying an analysis_func.\n\n Returns\n -------\n data : list\n\n '
output = None
if (analysis_func is None):
analysis_func = self._timesteps_by_type_analysis
output = 'combined'
if self._network:
result = defaultdict(list)
if (self.timesteps is None):
timesteps = range(len(self._network))
else:
timesteps = self.timesteps
for (time, frame) in zip(timesteps, self._network):
self._traverse_water_network(frame, [], analysis_func=analysis_func, output=result, link_func=self._full_link, time=time, **kwargs)
result_list = []
for (key, time_list) in six.iteritems(result):
for time in time_list:
if (output == 'combined'):
key = list(key)
key.append(time)
result_list.append(key)
else:
result_list.append((key, time))
return result_list
else:
return None<|docstring|>Frames during which each water bridges existed, sorted by each water bridges.
Processes :attr:`WaterBridgeAnalysis._network` and returns a
:class:`list` containing atom indices, residue names, residue
numbers (from selection 1 and selection 2) and each timestep at which the
water bridge was detected.
Similar to :meth:`~WaterBridgeAnalysis.count_by_type` and
:meth:`~WaterBridgeAnalysis.count_by_time`, the behavior can be adjusted by
supplying an analysis_func.
Returns
-------
data : list<|endoftext|> |
5e54e5b030094cf4af646be94e40bea7550db2c4698c60b46a286d8d76ec74dd | def generate_table(self, output_format=None):
'Generate a normalised table of the results.\n\n The table is stored as a :class:`numpy.recarray` in the\n attribute :attr:`~WaterBridgeAnalysis.table`.\n\n The output format of :attr:`~WaterBridgeAnalysis.table` can also be\n changed using output_format in a fashion similar to :attr:`WaterBridgeAnalysis.timeseries`\n '
output_format = (output_format or self.output_format)
if (self._network == []):
msg = 'No data computed, do run() first.'
warnings.warn(msg, category=MissingDataWarning)
logger.warning(msg)
return None
timeseries = self._generate_timeseries(output_format)
num_records = np.sum([len(hframe) for hframe in timeseries])
if (output_format == 'sele1_sele2'):
dtype = [('time', float), ('sele1_index', int), ('sele2_index', int), ('sele1_resnm', '|U4'), ('sele1_resid', int), ('sele1_atom', '|U4'), ('sele2_resnm', '|U4'), ('sele2_resid', int), ('sele2_atom', '|U4'), ('distance', float), ('angle', float)]
elif (output_format == 'donor_acceptor'):
dtype = [('time', float), ('donor_index', int), ('acceptor_index', int), ('donor_resnm', '|U4'), ('donor_resid', int), ('donor_atom', '|U4'), ('acceptor_resnm', '|U4'), ('acceptor_resid', int), ('acceptor_atom', '|U4'), ('distance', float), ('angle', float)]
out = np.empty((num_records,), dtype=dtype)
cursor = 0
for (t, hframe) in zip(self.timesteps, timeseries):
for (donor_index, acceptor_index, donor, acceptor, distance, angle) in hframe:
out[cursor] = ((((t, donor_index, acceptor_index) + donor) + acceptor) + (distance, angle))
cursor += 1
assert (cursor == num_records), 'Internal Error: Not all wb records stored'
table = out.view(np.recarray)
logger.debug('WBridge: Stored results as table with %(num_records)d entries.', vars())
self.table = table | Generate a normalised table of the results.
The table is stored as a :class:`numpy.recarray` in the
attribute :attr:`~WaterBridgeAnalysis.table`.
The output format of :attr:`~WaterBridgeAnalysis.table` can also be
changed using output_format in a fashion similar to :attr:`WaterBridgeAnalysis.timeseries` | venv/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/wbridge_analysis.py | generate_table | dtklinh/GBRDE | 2 | python | def generate_table(self, output_format=None):
'Generate a normalised table of the results.\n\n The table is stored as a :class:`numpy.recarray` in the\n attribute :attr:`~WaterBridgeAnalysis.table`.\n\n The output format of :attr:`~WaterBridgeAnalysis.table` can also be\n changed using output_format in a fashion similar to :attr:`WaterBridgeAnalysis.timeseries`\n '
output_format = (output_format or self.output_format)
if (self._network == []):
msg = 'No data computed, do run() first.'
warnings.warn(msg, category=MissingDataWarning)
logger.warning(msg)
return None
timeseries = self._generate_timeseries(output_format)
num_records = np.sum([len(hframe) for hframe in timeseries])
if (output_format == 'sele1_sele2'):
dtype = [('time', float), ('sele1_index', int), ('sele2_index', int), ('sele1_resnm', '|U4'), ('sele1_resid', int), ('sele1_atom', '|U4'), ('sele2_resnm', '|U4'), ('sele2_resid', int), ('sele2_atom', '|U4'), ('distance', float), ('angle', float)]
elif (output_format == 'donor_acceptor'):
dtype = [('time', float), ('donor_index', int), ('acceptor_index', int), ('donor_resnm', '|U4'), ('donor_resid', int), ('donor_atom', '|U4'), ('acceptor_resnm', '|U4'), ('acceptor_resid', int), ('acceptor_atom', '|U4'), ('distance', float), ('angle', float)]
out = np.empty((num_records,), dtype=dtype)
cursor = 0
for (t, hframe) in zip(self.timesteps, timeseries):
for (donor_index, acceptor_index, donor, acceptor, distance, angle) in hframe:
out[cursor] = ((((t, donor_index, acceptor_index) + donor) + acceptor) + (distance, angle))
cursor += 1
assert (cursor == num_records), 'Internal Error: Not all wb records stored'
table = out.view(np.recarray)
logger.debug('WBridge: Stored results as table with %(num_records)d entries.', vars())
self.table = table | def generate_table(self, output_format=None):
'Generate a normalised table of the results.\n\n The table is stored as a :class:`numpy.recarray` in the\n attribute :attr:`~WaterBridgeAnalysis.table`.\n\n The output format of :attr:`~WaterBridgeAnalysis.table` can also be\n changed using output_format in a fashion similar to :attr:`WaterBridgeAnalysis.timeseries`\n '
output_format = (output_format or self.output_format)
if (self._network == []):
msg = 'No data computed, do run() first.'
warnings.warn(msg, category=MissingDataWarning)
logger.warning(msg)
return None
timeseries = self._generate_timeseries(output_format)
num_records = np.sum([len(hframe) for hframe in timeseries])
if (output_format == 'sele1_sele2'):
dtype = [('time', float), ('sele1_index', int), ('sele2_index', int), ('sele1_resnm', '|U4'), ('sele1_resid', int), ('sele1_atom', '|U4'), ('sele2_resnm', '|U4'), ('sele2_resid', int), ('sele2_atom', '|U4'), ('distance', float), ('angle', float)]
elif (output_format == 'donor_acceptor'):
dtype = [('time', float), ('donor_index', int), ('acceptor_index', int), ('donor_resnm', '|U4'), ('donor_resid', int), ('donor_atom', '|U4'), ('acceptor_resnm', '|U4'), ('acceptor_resid', int), ('acceptor_atom', '|U4'), ('distance', float), ('angle', float)]
out = np.empty((num_records,), dtype=dtype)
cursor = 0
for (t, hframe) in zip(self.timesteps, timeseries):
for (donor_index, acceptor_index, donor, acceptor, distance, angle) in hframe:
out[cursor] = ((((t, donor_index, acceptor_index) + donor) + acceptor) + (distance, angle))
cursor += 1
assert (cursor == num_records), 'Internal Error: Not all wb records stored'
table = out.view(np.recarray)
logger.debug('WBridge: Stored results as table with %(num_records)d entries.', vars())
self.table = table<|docstring|>Generate a normalised table of the results.
The table is stored as a :class:`numpy.recarray` in the
attribute :attr:`~WaterBridgeAnalysis.table`.
The output format of :attr:`~WaterBridgeAnalysis.table` can also be
changed using output_format in a fashion similar to :attr:`WaterBridgeAnalysis.timeseries`<|endoftext|> |
72c050dc5ed0a84dfdd3cd98ab5c117448cb8fc5c8f8070e1c698fb5da1aa3a1 | @register.tag('block')
def do_block(parser, token):
'\n Define a block that can be overridden by child templates.\n '
bits = token.contents.split()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' tag takes only one argument" % bits[0]))
block_name = bits[1]
try:
if (block_name in parser.__loaded_blocks):
raise TemplateSyntaxError(("'%s' tag with name '%s' appears more than once" % (bits[0], block_name)))
parser.__loaded_blocks.append(block_name)
except AttributeError:
parser.__loaded_blocks = [block_name]
nodelist = parser.parse(('endblock',))
endblock = parser.next_token()
acceptable_endblocks = ('endblock', ('endblock %s' % block_name))
if (endblock.contents not in acceptable_endblocks):
parser.invalid_block_tag(endblock, 'endblock', acceptable_endblocks)
return BlockNode(block_name, nodelist) | Define a block that can be overridden by child templates. | django/template/loader_tags.py | do_block | mavisguan/django | 61,676 | python | @register.tag('block')
def do_block(parser, token):
'\n \n '
bits = token.contents.split()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' tag takes only one argument" % bits[0]))
block_name = bits[1]
try:
if (block_name in parser.__loaded_blocks):
raise TemplateSyntaxError(("'%s' tag with name '%s' appears more than once" % (bits[0], block_name)))
parser.__loaded_blocks.append(block_name)
except AttributeError:
parser.__loaded_blocks = [block_name]
nodelist = parser.parse(('endblock',))
endblock = parser.next_token()
acceptable_endblocks = ('endblock', ('endblock %s' % block_name))
if (endblock.contents not in acceptable_endblocks):
parser.invalid_block_tag(endblock, 'endblock', acceptable_endblocks)
return BlockNode(block_name, nodelist) | @register.tag('block')
def do_block(parser, token):
'\n \n '
bits = token.contents.split()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' tag takes only one argument" % bits[0]))
block_name = bits[1]
try:
if (block_name in parser.__loaded_blocks):
raise TemplateSyntaxError(("'%s' tag with name '%s' appears more than once" % (bits[0], block_name)))
parser.__loaded_blocks.append(block_name)
except AttributeError:
parser.__loaded_blocks = [block_name]
nodelist = parser.parse(('endblock',))
endblock = parser.next_token()
acceptable_endblocks = ('endblock', ('endblock %s' % block_name))
if (endblock.contents not in acceptable_endblocks):
parser.invalid_block_tag(endblock, 'endblock', acceptable_endblocks)
return BlockNode(block_name, nodelist)<|docstring|>Define a block that can be overridden by child templates.<|endoftext|> |
fced9cc6bfb770caf0a06adb05253c8e173d17a6627e9892252ad7644c06a57f | def construct_relative_path(current_template_name, relative_name):
"\n Convert a relative path (starting with './' or '../') to the full template\n name based on the current_template_name.\n "
new_name = relative_name.strip('\'"')
if (not new_name.startswith(('./', '../'))):
return relative_name
new_name = posixpath.normpath(posixpath.join(posixpath.dirname(current_template_name.lstrip('/')), new_name))
if new_name.startswith('../'):
raise TemplateSyntaxError(("The relative path '%s' points outside the file hierarchy that template '%s' is in." % (relative_name, current_template_name)))
if (current_template_name.lstrip('/') == new_name):
raise TemplateSyntaxError(("The relative path '%s' was translated to template name '%s', the same template in which the tag appears." % (relative_name, current_template_name)))
has_quotes = (relative_name.startswith(('"', "'")) and (relative_name[0] == relative_name[(- 1)]))
return (f'"{new_name}"' if has_quotes else new_name) | Convert a relative path (starting with './' or '../') to the full template
name based on the current_template_name. | django/template/loader_tags.py | construct_relative_path | mavisguan/django | 61,676 | python | def construct_relative_path(current_template_name, relative_name):
"\n Convert a relative path (starting with './' or '../') to the full template\n name based on the current_template_name.\n "
new_name = relative_name.strip('\'"')
if (not new_name.startswith(('./', '../'))):
return relative_name
new_name = posixpath.normpath(posixpath.join(posixpath.dirname(current_template_name.lstrip('/')), new_name))
if new_name.startswith('../'):
raise TemplateSyntaxError(("The relative path '%s' points outside the file hierarchy that template '%s' is in." % (relative_name, current_template_name)))
if (current_template_name.lstrip('/') == new_name):
raise TemplateSyntaxError(("The relative path '%s' was translated to template name '%s', the same template in which the tag appears." % (relative_name, current_template_name)))
has_quotes = (relative_name.startswith(('"', "'")) and (relative_name[0] == relative_name[(- 1)]))
return (f'"{new_name}"' if has_quotes else new_name) | def construct_relative_path(current_template_name, relative_name):
"\n Convert a relative path (starting with './' or '../') to the full template\n name based on the current_template_name.\n "
new_name = relative_name.strip('\'"')
if (not new_name.startswith(('./', '../'))):
return relative_name
new_name = posixpath.normpath(posixpath.join(posixpath.dirname(current_template_name.lstrip('/')), new_name))
if new_name.startswith('../'):
raise TemplateSyntaxError(("The relative path '%s' points outside the file hierarchy that template '%s' is in." % (relative_name, current_template_name)))
if (current_template_name.lstrip('/') == new_name):
raise TemplateSyntaxError(("The relative path '%s' was translated to template name '%s', the same template in which the tag appears." % (relative_name, current_template_name)))
has_quotes = (relative_name.startswith(('"', "'")) and (relative_name[0] == relative_name[(- 1)]))
return (f'"{new_name}"' if has_quotes else new_name)<|docstring|>Convert a relative path (starting with './' or '../') to the full template
name based on the current_template_name.<|endoftext|> |
311f53f109ae9daacbcdcbe19048814cb60a1bd6024d9a582cb2544129216a53 | @register.tag('extends')
def do_extends(parser, token):
'\n Signal that this template extends a parent template.\n\n This tag may be used in two ways: ``{% extends "base" %}`` (with quotes)\n uses the literal value "base" as the name of the parent template to extend,\n or ``{% extends variable %}`` uses the value of ``variable`` as either the\n name of the parent template to extend (if it evaluates to a string) or as\n the parent template itself (if it evaluates to a Template object).\n '
bits = token.split_contents()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' takes one argument" % bits[0]))
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
parent_name = parser.compile_filter(bits[1])
nodelist = parser.parse()
if nodelist.get_nodes_by_type(ExtendsNode):
raise TemplateSyntaxError(("'%s' cannot appear more than once in the same template" % bits[0]))
return ExtendsNode(nodelist, parent_name) | Signal that this template extends a parent template.
This tag may be used in two ways: ``{% extends "base" %}`` (with quotes)
uses the literal value "base" as the name of the parent template to extend,
or ``{% extends variable %}`` uses the value of ``variable`` as either the
name of the parent template to extend (if it evaluates to a string) or as
the parent template itself (if it evaluates to a Template object). | django/template/loader_tags.py | do_extends | mavisguan/django | 61,676 | python | @register.tag('extends')
def do_extends(parser, token):
'\n Signal that this template extends a parent template.\n\n This tag may be used in two ways: ``{% extends "base" %}`` (with quotes)\n uses the literal value "base" as the name of the parent template to extend,\n or ``{% extends variable %}`` uses the value of ``variable`` as either the\n name of the parent template to extend (if it evaluates to a string) or as\n the parent template itself (if it evaluates to a Template object).\n '
bits = token.split_contents()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' takes one argument" % bits[0]))
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
parent_name = parser.compile_filter(bits[1])
nodelist = parser.parse()
if nodelist.get_nodes_by_type(ExtendsNode):
raise TemplateSyntaxError(("'%s' cannot appear more than once in the same template" % bits[0]))
return ExtendsNode(nodelist, parent_name) | @register.tag('extends')
def do_extends(parser, token):
'\n Signal that this template extends a parent template.\n\n This tag may be used in two ways: ``{% extends "base" %}`` (with quotes)\n uses the literal value "base" as the name of the parent template to extend,\n or ``{% extends variable %}`` uses the value of ``variable`` as either the\n name of the parent template to extend (if it evaluates to a string) or as\n the parent template itself (if it evaluates to a Template object).\n '
bits = token.split_contents()
if (len(bits) != 2):
raise TemplateSyntaxError(("'%s' takes one argument" % bits[0]))
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
parent_name = parser.compile_filter(bits[1])
nodelist = parser.parse()
if nodelist.get_nodes_by_type(ExtendsNode):
raise TemplateSyntaxError(("'%s' cannot appear more than once in the same template" % bits[0]))
return ExtendsNode(nodelist, parent_name)<|docstring|>Signal that this template extends a parent template.
This tag may be used in two ways: ``{% extends "base" %}`` (with quotes)
uses the literal value "base" as the name of the parent template to extend,
or ``{% extends variable %}`` uses the value of ``variable`` as either the
name of the parent template to extend (if it evaluates to a string) or as
the parent template itself (if it evaluates to a Template object).<|endoftext|> |
c86992f9212c27fc3206459883bacbbfa756aeca49eed245facddda34dbd674e | @register.tag('include')
def do_include(parser, token):
'\n Load a template and render it with the current context. You can pass\n additional context using keyword arguments.\n\n Example::\n\n {% include "foo/some_include" %}\n {% include "foo/some_include" with bar="BAZZ!" baz="BING!" %}\n\n Use the ``only`` argument to exclude the current context when rendering\n the included template::\n\n {% include "foo/some_include" only %}\n {% include "foo/some_include" with bar="1" only %}\n '
bits = token.split_contents()
if (len(bits) < 2):
raise TemplateSyntaxError(('%r tag takes at least one argument: the name of the template to be included.' % bits[0]))
options = {}
remaining_bits = bits[2:]
while remaining_bits:
option = remaining_bits.pop(0)
if (option in options):
raise TemplateSyntaxError(('The %r option was specified more than once.' % option))
if (option == 'with'):
value = token_kwargs(remaining_bits, parser, support_legacy=False)
if (not value):
raise TemplateSyntaxError(('"with" in %r tag needs at least one keyword argument.' % bits[0]))
elif (option == 'only'):
value = True
else:
raise TemplateSyntaxError(('Unknown argument for %r tag: %r.' % (bits[0], option)))
options[option] = value
isolated_context = options.get('only', False)
namemap = options.get('with', {})
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
return IncludeNode(parser.compile_filter(bits[1]), extra_context=namemap, isolated_context=isolated_context) | Load a template and render it with the current context. You can pass
additional context using keyword arguments.
Example::
{% include "foo/some_include" %}
{% include "foo/some_include" with bar="BAZZ!" baz="BING!" %}
Use the ``only`` argument to exclude the current context when rendering
the included template::
{% include "foo/some_include" only %}
{% include "foo/some_include" with bar="1" only %} | django/template/loader_tags.py | do_include | mavisguan/django | 61,676 | python | @register.tag('include')
def do_include(parser, token):
'\n Load a template and render it with the current context. You can pass\n additional context using keyword arguments.\n\n Example::\n\n {% include "foo/some_include" %}\n {% include "foo/some_include" with bar="BAZZ!" baz="BING!" %}\n\n Use the ``only`` argument to exclude the current context when rendering\n the included template::\n\n {% include "foo/some_include" only %}\n {% include "foo/some_include" with bar="1" only %}\n '
bits = token.split_contents()
if (len(bits) < 2):
raise TemplateSyntaxError(('%r tag takes at least one argument: the name of the template to be included.' % bits[0]))
options = {}
remaining_bits = bits[2:]
while remaining_bits:
option = remaining_bits.pop(0)
if (option in options):
raise TemplateSyntaxError(('The %r option was specified more than once.' % option))
if (option == 'with'):
value = token_kwargs(remaining_bits, parser, support_legacy=False)
if (not value):
raise TemplateSyntaxError(('"with" in %r tag needs at least one keyword argument.' % bits[0]))
elif (option == 'only'):
value = True
else:
raise TemplateSyntaxError(('Unknown argument for %r tag: %r.' % (bits[0], option)))
options[option] = value
isolated_context = options.get('only', False)
namemap = options.get('with', {})
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
return IncludeNode(parser.compile_filter(bits[1]), extra_context=namemap, isolated_context=isolated_context) | @register.tag('include')
def do_include(parser, token):
'\n Load a template and render it with the current context. You can pass\n additional context using keyword arguments.\n\n Example::\n\n {% include "foo/some_include" %}\n {% include "foo/some_include" with bar="BAZZ!" baz="BING!" %}\n\n Use the ``only`` argument to exclude the current context when rendering\n the included template::\n\n {% include "foo/some_include" only %}\n {% include "foo/some_include" with bar="1" only %}\n '
bits = token.split_contents()
if (len(bits) < 2):
raise TemplateSyntaxError(('%r tag takes at least one argument: the name of the template to be included.' % bits[0]))
options = {}
remaining_bits = bits[2:]
while remaining_bits:
option = remaining_bits.pop(0)
if (option in options):
raise TemplateSyntaxError(('The %r option was specified more than once.' % option))
if (option == 'with'):
value = token_kwargs(remaining_bits, parser, support_legacy=False)
if (not value):
raise TemplateSyntaxError(('"with" in %r tag needs at least one keyword argument.' % bits[0]))
elif (option == 'only'):
value = True
else:
raise TemplateSyntaxError(('Unknown argument for %r tag: %r.' % (bits[0], option)))
options[option] = value
isolated_context = options.get('only', False)
namemap = options.get('with', {})
bits[1] = construct_relative_path(parser.origin.template_name, bits[1])
return IncludeNode(parser.compile_filter(bits[1]), extra_context=namemap, isolated_context=isolated_context)<|docstring|>Load a template and render it with the current context. You can pass
additional context using keyword arguments.
Example::
{% include "foo/some_include" %}
{% include "foo/some_include" with bar="BAZZ!" baz="BING!" %}
Use the ``only`` argument to exclude the current context when rendering
the included template::
{% include "foo/some_include" only %}
{% include "foo/some_include" with bar="1" only %}<|endoftext|> |
fd232eb80a86b2ae756957fcd8aab143cda17c5c53c024cbbeec3e6e6da8bb1b | def find_template(self, template_name, context):
'\n This is a wrapper around engine.find_template(). A history is kept in\n the render_context attribute between successive extends calls and\n passed as the skip argument. This enables extends to work recursively\n without extending the same template twice.\n '
history = context.render_context.setdefault(self.context_key, [self.origin])
(template, origin) = context.template.engine.find_template(template_name, skip=history)
history.append(origin)
return template | This is a wrapper around engine.find_template(). A history is kept in
the render_context attribute between successive extends calls and
passed as the skip argument. This enables extends to work recursively
without extending the same template twice. | django/template/loader_tags.py | find_template | mavisguan/django | 61,676 | python | def find_template(self, template_name, context):
'\n This is a wrapper around engine.find_template(). A history is kept in\n the render_context attribute between successive extends calls and\n passed as the skip argument. This enables extends to work recursively\n without extending the same template twice.\n '
history = context.render_context.setdefault(self.context_key, [self.origin])
(template, origin) = context.template.engine.find_template(template_name, skip=history)
history.append(origin)
return template | def find_template(self, template_name, context):
'\n This is a wrapper around engine.find_template(). A history is kept in\n the render_context attribute between successive extends calls and\n passed as the skip argument. This enables extends to work recursively\n without extending the same template twice.\n '
history = context.render_context.setdefault(self.context_key, [self.origin])
(template, origin) = context.template.engine.find_template(template_name, skip=history)
history.append(origin)
return template<|docstring|>This is a wrapper around engine.find_template(). A history is kept in
the render_context attribute between successive extends calls and
passed as the skip argument. This enables extends to work recursively
without extending the same template twice.<|endoftext|> |
de11a21ce79f52525d01a93235aa6b667c1ffe1f9ceb68bb42cea676d7df67e4 | def render(self, context):
'\n Render the specified template and context. Cache the template object\n in render_context to avoid reparsing and loading when used in a for\n loop.\n '
template = self.template.resolve(context)
if (not callable(getattr(template, 'render', None))):
template_name = (template or ())
if isinstance(template_name, str):
template_name = (construct_relative_path(self.origin.template_name, template_name),)
else:
template_name = tuple(template_name)
cache = context.render_context.dicts[0].setdefault(self, {})
template = cache.get(template_name)
if (template is None):
template = context.template.engine.select_template(template_name)
cache[template_name] = template
elif hasattr(template, 'template'):
template = template.template
values = {name: var.resolve(context) for (name, var) in self.extra_context.items()}
if self.isolated_context:
return template.render(context.new(values))
with context.push(**values):
return template.render(context) | Render the specified template and context. Cache the template object
in render_context to avoid reparsing and loading when used in a for
loop. | django/template/loader_tags.py | render | mavisguan/django | 61,676 | python | def render(self, context):
'\n Render the specified template and context. Cache the template object\n in render_context to avoid reparsing and loading when used in a for\n loop.\n '
template = self.template.resolve(context)
if (not callable(getattr(template, 'render', None))):
template_name = (template or ())
if isinstance(template_name, str):
template_name = (construct_relative_path(self.origin.template_name, template_name),)
else:
template_name = tuple(template_name)
cache = context.render_context.dicts[0].setdefault(self, {})
template = cache.get(template_name)
if (template is None):
template = context.template.engine.select_template(template_name)
cache[template_name] = template
elif hasattr(template, 'template'):
template = template.template
values = {name: var.resolve(context) for (name, var) in self.extra_context.items()}
if self.isolated_context:
return template.render(context.new(values))
with context.push(**values):
return template.render(context) | def render(self, context):
'\n Render the specified template and context. Cache the template object\n in render_context to avoid reparsing and loading when used in a for\n loop.\n '
template = self.template.resolve(context)
if (not callable(getattr(template, 'render', None))):
template_name = (template or ())
if isinstance(template_name, str):
template_name = (construct_relative_path(self.origin.template_name, template_name),)
else:
template_name = tuple(template_name)
cache = context.render_context.dicts[0].setdefault(self, {})
template = cache.get(template_name)
if (template is None):
template = context.template.engine.select_template(template_name)
cache[template_name] = template
elif hasattr(template, 'template'):
template = template.template
values = {name: var.resolve(context) for (name, var) in self.extra_context.items()}
if self.isolated_context:
return template.render(context.new(values))
with context.push(**values):
return template.render(context)<|docstring|>Render the specified template and context. Cache the template object
in render_context to avoid reparsing and loading when used in a for
loop.<|endoftext|> |
c16f6a9858e9010100485c70d5be2024efd6df9e3ccacb5ea4b97d1c5bc25956 | def migrate_run_partition(instance, print_fn=None):
'\n Utility method to build an asset key index from the data in existing event log records.\n Takes in event_log_storage, and a print_fn to keep track of progress.\n '
if print_fn:
print_fn('Querying run storage.')
runs = instance.get_runs()
if print_fn:
runs = tqdm(runs)
for run in runs:
if (PARTITION_NAME_TAG not in run.tags):
continue
if (PARTITION_SET_TAG not in run.tags):
continue
instance.add_run_tags(run.run_id, run.tags) | Utility method to build an asset key index from the data in existing event log records.
Takes in event_log_storage, and a print_fn to keep track of progress. | python_modules/dagster/dagster/core/storage/runs/migration.py | migrate_run_partition | leftrightleft/dagster | 0 | python | def migrate_run_partition(instance, print_fn=None):
'\n Utility method to build an asset key index from the data in existing event log records.\n Takes in event_log_storage, and a print_fn to keep track of progress.\n '
if print_fn:
print_fn('Querying run storage.')
runs = instance.get_runs()
if print_fn:
runs = tqdm(runs)
for run in runs:
if (PARTITION_NAME_TAG not in run.tags):
continue
if (PARTITION_SET_TAG not in run.tags):
continue
instance.add_run_tags(run.run_id, run.tags) | def migrate_run_partition(instance, print_fn=None):
'\n Utility method to build an asset key index from the data in existing event log records.\n Takes in event_log_storage, and a print_fn to keep track of progress.\n '
if print_fn:
print_fn('Querying run storage.')
runs = instance.get_runs()
if print_fn:
runs = tqdm(runs)
for run in runs:
if (PARTITION_NAME_TAG not in run.tags):
continue
if (PARTITION_SET_TAG not in run.tags):
continue
instance.add_run_tags(run.run_id, run.tags)<|docstring|>Utility method to build an asset key index from the data in existing event log records.
Takes in event_log_storage, and a print_fn to keep track of progress.<|endoftext|> |
b95a339aa2fc65d1dda2cb097d479d0ab9de207f134b31e3032d4c5659ac8786 | def null_to_empty(val):
'Convert to empty string if the value is currently null.'
if (not val):
return ''
return val | Convert to empty string if the value is currently null. | nautobot_golden_config/models.py | null_to_empty | nniehoff/nautobot-plugin-golden-config | 0 | python | def null_to_empty(val):
if (not val):
return
return val | def null_to_empty(val):
if (not val):
return
return val<|docstring|>Convert to empty string if the value is currently null.<|endoftext|> |
98a692d9edf4901bdaa340e764f9efa058f48c9fb88ee389e4ee885c229e601e | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.name, self.slug, self.description) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.name, self.slug, self.description) | def to_csv(self):
return (self.name, self.slug, self.description)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
93dea0603195bc1719fe27c77a776e967e40eca43d40851126837ffa057dbde3 | def __str__(self):
'Return a sane string representation of the instance.'
return self.slug | Return a sane string representation of the instance. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return self.slug | def __str__(self):
return self.slug<|docstring|>Return a sane string representation of the instance.<|endoftext|> |
23b961d2151cfe9fd9891bce8bf5fb09f32feb88b418de8df644130076d478fb | def get_absolute_url(self):
'Absolute url for the ComplianceFeature instance.'
return reverse('plugins:nautobot_golden_config:compliancefeature', args=[self.pk]) | Absolute url for the ComplianceFeature instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:compliancefeature', args=[self.pk]) | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:compliancefeature', args=[self.pk])<|docstring|>Absolute url for the ComplianceFeature instance.<|endoftext|> |
69e91246522d3c70bce22cdba471b5657829f34556abbc605dadeccbbea6428d | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.platform.slug, self.feature.name, self.description, self.config_ordered, self.match_config, self.config_type) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.platform.slug, self.feature.name, self.description, self.config_ordered, self.match_config, self.config_type) | def to_csv(self):
return (self.platform.slug, self.feature.name, self.description, self.config_ordered, self.match_config, self.config_type)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
2f44bf1a950b4479697c315150f5074b1f832048bf7467d40af79100dd5a4b49 | def __str__(self):
'Return a sane string representation of the instance.'
return f'{self.platform} - {self.feature.name}' | Return a sane string representation of the instance. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return f'{self.platform} - {self.feature.name}' | def __str__(self):
return f'{self.platform} - {self.feature.name}'<|docstring|>Return a sane string representation of the instance.<|endoftext|> |
ef89129c3bb14ef6d8601cf4699d037e894d59ef9ba9c4be6a90fa04241778a1 | def get_absolute_url(self):
'Absolute url for the ComplianceRule instance.'
return reverse('plugins:nautobot_golden_config:compliancerule', args=[self.pk]) | Absolute url for the ComplianceRule instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:compliancerule', args=[self.pk]) | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:compliancerule', args=[self.pk])<|docstring|>Absolute url for the ComplianceRule instance.<|endoftext|> |
8502a11783a6c83a429a457e1049253dadcefa035d0c792e2a1470f447070086 | def clean(self):
'Verify that if cli, then match_config is set.'
if ((self.config_type == ComplianceRuleTypeChoice.TYPE_CLI) and (not self.match_config)):
raise ValidationError('CLI configuration set, but no configuration set to match.') | Verify that if cli, then match_config is set. | nautobot_golden_config/models.py | clean | nniehoff/nautobot-plugin-golden-config | 0 | python | def clean(self):
if ((self.config_type == ComplianceRuleTypeChoice.TYPE_CLI) and (not self.match_config)):
raise ValidationError('CLI configuration set, but no configuration set to match.') | def clean(self):
if ((self.config_type == ComplianceRuleTypeChoice.TYPE_CLI) and (not self.match_config)):
raise ValidationError('CLI configuration set, but no configuration set to match.')<|docstring|>Verify that if cli, then match_config is set.<|endoftext|> |
612ebcc72b7160068cd827e80c7c5055e8a21f5f196cb4c9e3c24a4093ca4119 | def get_absolute_url(self):
'Return absolute URL for instance.'
return reverse('plugins:nautobot_golden_config:configcompliance', args=[self.pk]) | Return absolute URL for instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configcompliance', args=[self.pk]) | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configcompliance', args=[self.pk])<|docstring|>Return absolute URL for instance.<|endoftext|> |
fcf4be6193325c5df7c2f9b7ca9c1ac964add8916fd42900d101096d97689a96 | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.device.name, self.rule.feature.name, self.compliance) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.device.name, self.rule.feature.name, self.compliance) | def to_csv(self):
return (self.device.name, self.rule.feature.name, self.compliance)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
1065f45a4904e98dbba65f6d962106085717038de11e90b3a94f49a0d3b01bd2 | def to_objectchange(self, action):
'Remove actual and intended configuration from changelog.'
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['actual', 'intended'])) | Remove actual and intended configuration from changelog. | nautobot_golden_config/models.py | to_objectchange | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_objectchange(self, action):
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['actual', 'intended'])) | def to_objectchange(self, action):
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['actual', 'intended']))<|docstring|>Remove actual and intended configuration from changelog.<|endoftext|> |
0f80579010b37b423f6df1ea7cf0f94492f6e69bcf571ae3e5ce2df7c77f4187 | def __str__(self):
'String representation of a the compliance.'
return f'{self.device} -> {self.rule} -> {self.compliance}' | String representation of a the compliance. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return f'{self.device} -> {self.rule} -> {self.compliance}' | def __str__(self):
return f'{self.device} -> {self.rule} -> {self.compliance}'<|docstring|>String representation of a the compliance.<|endoftext|> |
2e616c061e003959e32e02296c3777494ad50b1ff1447006957fa77230e8bfb1 | def save(self, *args, **kwargs):
'Performs the actual compliance check.'
feature = {'ordered': self.rule.config_ordered, 'name': self.rule}
if (self.rule.config_type == ComplianceRuleTypeChoice.TYPE_JSON):
feature.update({'section': self.rule.match_config})
diff = DeepDiff(self.actual, self.intended, ignore_order=self.ordered, report_repetition=True)
if (not diff):
self.compliance_int = 1
self.compliance = True
self.missing = ''
self.extra = ''
else:
self.compliance_int = 0
self.compliance = False
self.missing = null_to_empty(self._normalize_diff(diff, 'added'))
self.extra = null_to_empty(self._normalize_diff(diff, 'removed'))
else:
feature.update({'section': self.rule.match_config.splitlines()})
value = feature_compliance(feature, self.actual, self.intended, get_platform(self.device.platform.slug))
self.compliance = value['compliant']
if self.compliance:
self.compliance_int = 1
else:
self.compliance_int = 0
self.ordered = value['ordered_compliant']
self.missing = null_to_empty(value['missing'])
self.extra = null_to_empty(value['extra'])
super().save(*args, **kwargs) | Performs the actual compliance check. | nautobot_golden_config/models.py | save | nniehoff/nautobot-plugin-golden-config | 0 | python | def save(self, *args, **kwargs):
feature = {'ordered': self.rule.config_ordered, 'name': self.rule}
if (self.rule.config_type == ComplianceRuleTypeChoice.TYPE_JSON):
feature.update({'section': self.rule.match_config})
diff = DeepDiff(self.actual, self.intended, ignore_order=self.ordered, report_repetition=True)
if (not diff):
self.compliance_int = 1
self.compliance = True
self.missing =
self.extra =
else:
self.compliance_int = 0
self.compliance = False
self.missing = null_to_empty(self._normalize_diff(diff, 'added'))
self.extra = null_to_empty(self._normalize_diff(diff, 'removed'))
else:
feature.update({'section': self.rule.match_config.splitlines()})
value = feature_compliance(feature, self.actual, self.intended, get_platform(self.device.platform.slug))
self.compliance = value['compliant']
if self.compliance:
self.compliance_int = 1
else:
self.compliance_int = 0
self.ordered = value['ordered_compliant']
self.missing = null_to_empty(value['missing'])
self.extra = null_to_empty(value['extra'])
super().save(*args, **kwargs) | def save(self, *args, **kwargs):
feature = {'ordered': self.rule.config_ordered, 'name': self.rule}
if (self.rule.config_type == ComplianceRuleTypeChoice.TYPE_JSON):
feature.update({'section': self.rule.match_config})
diff = DeepDiff(self.actual, self.intended, ignore_order=self.ordered, report_repetition=True)
if (not diff):
self.compliance_int = 1
self.compliance = True
self.missing =
self.extra =
else:
self.compliance_int = 0
self.compliance = False
self.missing = null_to_empty(self._normalize_diff(diff, 'added'))
self.extra = null_to_empty(self._normalize_diff(diff, 'removed'))
else:
feature.update({'section': self.rule.match_config.splitlines()})
value = feature_compliance(feature, self.actual, self.intended, get_platform(self.device.platform.slug))
self.compliance = value['compliant']
if self.compliance:
self.compliance_int = 1
else:
self.compliance_int = 0
self.ordered = value['ordered_compliant']
self.missing = null_to_empty(value['missing'])
self.extra = null_to_empty(value['extra'])
super().save(*args, **kwargs)<|docstring|>Performs the actual compliance check.<|endoftext|> |
44971dd84b5ecf745e730c85d2ae83dd88c88834f96ddd0ac46a1091f91bea00 | @staticmethod
def _normalize_diff(diff, path_to_diff):
'Normalizes the diff to a list of keys and list indexes that have changed.'
dictionary_items = list(diff.get(f'dictionary_item_{path_to_diff}', []))
list_items = list(diff.get(f'iterable_item_{path_to_diff}', {}).keys())
values_changed = list(diff.get('values_changed', {}).keys())
type_changes = list(diff.get('type_changes', {}).keys())
return (((dictionary_items + list_items) + values_changed) + type_changes) | Normalizes the diff to a list of keys and list indexes that have changed. | nautobot_golden_config/models.py | _normalize_diff | nniehoff/nautobot-plugin-golden-config | 0 | python | @staticmethod
def _normalize_diff(diff, path_to_diff):
dictionary_items = list(diff.get(f'dictionary_item_{path_to_diff}', []))
list_items = list(diff.get(f'iterable_item_{path_to_diff}', {}).keys())
values_changed = list(diff.get('values_changed', {}).keys())
type_changes = list(diff.get('type_changes', {}).keys())
return (((dictionary_items + list_items) + values_changed) + type_changes) | @staticmethod
def _normalize_diff(diff, path_to_diff):
dictionary_items = list(diff.get(f'dictionary_item_{path_to_diff}', []))
list_items = list(diff.get(f'iterable_item_{path_to_diff}', {}).keys())
values_changed = list(diff.get('values_changed', {}).keys())
type_changes = list(diff.get('type_changes', {}).keys())
return (((dictionary_items + list_items) + values_changed) + type_changes)<|docstring|>Normalizes the diff to a list of keys and list indexes that have changed.<|endoftext|> |
30f5dc7083332e8e5fee6b3e7ed0ae7ebba37a89ff177bda5df74230e9bb9e82 | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.device, self.backup_last_attempt_date, self.backup_last_success_date, self.intended_last_attempt_date, self.intended_last_success_date, self.compliance_last_attempt_date, self.compliance_last_success_date) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.device, self.backup_last_attempt_date, self.backup_last_success_date, self.intended_last_attempt_date, self.intended_last_success_date, self.compliance_last_attempt_date, self.compliance_last_success_date) | def to_csv(self):
return (self.device, self.backup_last_attempt_date, self.backup_last_success_date, self.intended_last_attempt_date, self.intended_last_success_date, self.compliance_last_attempt_date, self.compliance_last_success_date)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
3874d0896041318e14e64ce0093c971129ea5bc7eaaf38fef0073d0a95734cca | def to_objectchange(self, action):
'Remove actual and intended configuration from changelog.'
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['backup_config', 'intended_config', 'compliance_config'])) | Remove actual and intended configuration from changelog. | nautobot_golden_config/models.py | to_objectchange | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_objectchange(self, action):
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['backup_config', 'intended_config', 'compliance_config'])) | def to_objectchange(self, action):
return ObjectChange(changed_object=self, object_repr=str(self), action=action, object_data=serialize_object(self, exclude=['backup_config', 'intended_config', 'compliance_config']))<|docstring|>Remove actual and intended configuration from changelog.<|endoftext|> |
49898db18bea2a8f173c9e0204a4ebf0bef7bd5567e4fe1c4c6d452988dd00e9 | def __str__(self):
'String representation of a the compliance.'
return f'{self.device}' | String representation of a the compliance. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return f'{self.device}' | def __str__(self):
return f'{self.device}'<|docstring|>String representation of a the compliance.<|endoftext|> |
6fca937f44390a4530f8780796e8e27302d43563602a998fb4342ab12b306edc | def get_absolute_url(self):
'Return absolute URL for instance.'
return reverse('plugins:nautobot_golden_config:goldenconfigsetting') | Return absolute URL for instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:goldenconfigsetting') | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:goldenconfigsetting')<|docstring|>Return absolute URL for instance.<|endoftext|> |
e96a4428ba892ebc9ccca4f5a433b58e78983880b2bd27d40da1b6e647bf5488 | def __str__(self):
'Return a simple string if model is called.'
return 'Golden Config Settings' | Return a simple string if model is called. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return 'Golden Config Settings' | def __str__(self):
return 'Golden Config Settings'<|docstring|>Return a simple string if model is called.<|endoftext|> |
7711a8d7a4d88bbfab2fc62f3ea33f2c8f790266a046c01b1e8cfebaaad51ab0 | def delete(self, *args, **kwargs):
'Enforce the singleton pattern, there is no way to delete the configurations.' | Enforce the singleton pattern, there is no way to delete the configurations. | nautobot_golden_config/models.py | delete | nniehoff/nautobot-plugin-golden-config | 0 | python | def delete(self, *args, **kwargs):
| def delete(self, *args, **kwargs):
<|docstring|>Enforce the singleton pattern, there is no way to delete the configurations.<|endoftext|> |
545deb73673a500ea10a0627a19dbe539cf45e6b647d25b6f78e8c3b7322f1ef | @classmethod
def load(cls):
'Enforce the singleton pattern, fail it somehow more than one instance.'
if (len(cls.objects.all()) != 1):
raise ValidationError('There was an error where more than one instance existed for a setting.')
return cls.objects.first() | Enforce the singleton pattern, fail it somehow more than one instance. | nautobot_golden_config/models.py | load | nniehoff/nautobot-plugin-golden-config | 0 | python | @classmethod
def load(cls):
if (len(cls.objects.all()) != 1):
raise ValidationError('There was an error where more than one instance existed for a setting.')
return cls.objects.first() | @classmethod
def load(cls):
if (len(cls.objects.all()) != 1):
raise ValidationError('There was an error where more than one instance existed for a setting.')
return cls.objects.first()<|docstring|>Enforce the singleton pattern, fail it somehow more than one instance.<|endoftext|> |
03c817d6eb2297bd0db5e5e2475c35839233aa92634047d6249766aaff4310bf | def clean(self):
'Validate there is only one model and if there is a GraphQL query, that it is valid.'
super().clean()
if self.sot_agg_query:
try:
LOGGER.debug('GraphQL - test query: `%s`', str(self.sot_agg_query))
backend = get_default_backend()
schema = graphene_settings.SCHEMA
backend.document_from_string(schema, str(self.sot_agg_query))
except GraphQLSyntaxError as error:
raise ValidationError(str(error))
LOGGER.debug('GraphQL - test query start with: `%s`', GRAPHQL_STR_START)
if (not str(self.sot_agg_query).startswith(GRAPHQL_STR_START)):
raise ValidationError(f'The GraphQL query must start with exactly `{GRAPHQL_STR_START}`')
if self.scope:
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
if filterset.errors:
for key in filterset.errors:
error_message = ', '.join(filterset.errors[key])
raise ValidationError({'scope': f'{key}: {error_message}'})
filterset_params = set(filterset.get_filters().keys())
for key in self.scope.keys():
if (key not in filterset_params):
raise ValidationError({'scope': f"'{key}' is not a valid filter parameter for Device object"}) | Validate there is only one model and if there is a GraphQL query, that it is valid. | nautobot_golden_config/models.py | clean | nniehoff/nautobot-plugin-golden-config | 0 | python | def clean(self):
super().clean()
if self.sot_agg_query:
try:
LOGGER.debug('GraphQL - test query: `%s`', str(self.sot_agg_query))
backend = get_default_backend()
schema = graphene_settings.SCHEMA
backend.document_from_string(schema, str(self.sot_agg_query))
except GraphQLSyntaxError as error:
raise ValidationError(str(error))
LOGGER.debug('GraphQL - test query start with: `%s`', GRAPHQL_STR_START)
if (not str(self.sot_agg_query).startswith(GRAPHQL_STR_START)):
raise ValidationError(f'The GraphQL query must start with exactly `{GRAPHQL_STR_START}`')
if self.scope:
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
if filterset.errors:
for key in filterset.errors:
error_message = ', '.join(filterset.errors[key])
raise ValidationError({'scope': f'{key}: {error_message}'})
filterset_params = set(filterset.get_filters().keys())
for key in self.scope.keys():
if (key not in filterset_params):
raise ValidationError({'scope': f"'{key}' is not a valid filter parameter for Device object"}) | def clean(self):
super().clean()
if self.sot_agg_query:
try:
LOGGER.debug('GraphQL - test query: `%s`', str(self.sot_agg_query))
backend = get_default_backend()
schema = graphene_settings.SCHEMA
backend.document_from_string(schema, str(self.sot_agg_query))
except GraphQLSyntaxError as error:
raise ValidationError(str(error))
LOGGER.debug('GraphQL - test query start with: `%s`', GRAPHQL_STR_START)
if (not str(self.sot_agg_query).startswith(GRAPHQL_STR_START)):
raise ValidationError(f'The GraphQL query must start with exactly `{GRAPHQL_STR_START}`')
if self.scope:
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
if filterset.errors:
for key in filterset.errors:
error_message = ', '.join(filterset.errors[key])
raise ValidationError({'scope': f'{key}: {error_message}'})
filterset_params = set(filterset.get_filters().keys())
for key in self.scope.keys():
if (key not in filterset_params):
raise ValidationError({'scope': f"'{key}' is not a valid filter parameter for Device object"})<|docstring|>Validate there is only one model and if there is a GraphQL query, that it is valid.<|endoftext|> |
ad7426cf53792cb840c09fa1af4347c6568ead730dd39b82371069d58fa98e5b | def get_queryset(self):
'Generate a Device QuerySet from the filter.'
if (not self.scope):
return Device.objects.all()
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
return filterset.qs | Generate a Device QuerySet from the filter. | nautobot_golden_config/models.py | get_queryset | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_queryset(self):
if (not self.scope):
return Device.objects.all()
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
return filterset.qs | def get_queryset(self):
if (not self.scope):
return Device.objects.all()
filterset_class = get_filterset_for_model(Device)
filterset = filterset_class(self.scope, Device.objects.all())
return filterset.qs<|docstring|>Generate a Device QuerySet from the filter.<|endoftext|> |
b635e1ae5cbd00910c0b6bca36e2e471890a55ec365a4edbfe9bbe0a7eb888dc | def device_count(self):
'Return the number of devices in the group.'
return self.get_queryset().count() | Return the number of devices in the group. | nautobot_golden_config/models.py | device_count | nniehoff/nautobot-plugin-golden-config | 0 | python | def device_count(self):
return self.get_queryset().count() | def device_count(self):
return self.get_queryset().count()<|docstring|>Return the number of devices in the group.<|endoftext|> |
2dd938d79a9759ae8e0bd821d4210d6653e86033c60a806752ad9606bb950572 | def get_filter_as_string(self):
'Get filter as string.'
if (not self.scope):
return None
result = ''
for (key, value) in self.scope.items():
if isinstance(value, list):
for item in value:
if (result != ''):
result += '&'
result += f'{key}={item}'
else:
result += '&'
result += f'{key}={value}'
return result | Get filter as string. | nautobot_golden_config/models.py | get_filter_as_string | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_filter_as_string(self):
if (not self.scope):
return None
result =
for (key, value) in self.scope.items():
if isinstance(value, list):
for item in value:
if (result != ):
result += '&'
result += f'{key}={item}'
else:
result += '&'
result += f'{key}={value}'
return result | def get_filter_as_string(self):
if (not self.scope):
return None
result =
for (key, value) in self.scope.items():
if isinstance(value, list):
for item in value:
if (result != ):
result += '&'
result += f'{key}={item}'
else:
result += '&'
result += f'{key}={value}'
return result<|docstring|>Get filter as string.<|endoftext|> |
2f6789ef98cdf357680a5c304bffa76504732e448bde4b1b871e25bf3d163190 | def get_url_to_filtered_device_list(self):
'Get url to all devices that are matching the filter.'
base_url = reverse('dcim:device_list')
filter_str = self.get_filter_as_string()
if filter_str:
return f'{base_url}?{filter_str}'
return base_url | Get url to all devices that are matching the filter. | nautobot_golden_config/models.py | get_url_to_filtered_device_list | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_url_to_filtered_device_list(self):
base_url = reverse('dcim:device_list')
filter_str = self.get_filter_as_string()
if filter_str:
return f'{base_url}?{filter_str}'
return base_url | def get_url_to_filtered_device_list(self):
base_url = reverse('dcim:device_list')
filter_str = self.get_filter_as_string()
if filter_str:
return f'{base_url}?{filter_str}'
return base_url<|docstring|>Get url to all devices that are matching the filter.<|endoftext|> |
1df13d43e0a46b7ad1b58ed8b8313971216ff89cd9de08c0a6ddaaaf813aef32 | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.name, self.platform.slug, self.regex) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.name, self.platform.slug, self.regex) | def to_csv(self):
return (self.name, self.platform.slug, self.regex)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
d19470e85127c01ff23c1c46775e9cc25120c40a79205b70e6f68b570cd11c56 | def __str__(self):
'Return a simple string if model is called.'
return self.name | Return a simple string if model is called. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return self.name | def __str__(self):
return self.name<|docstring|>Return a simple string if model is called.<|endoftext|> |
930abf51b3e71ef61eb2b509aab412d9d3cf900bdb736e05be0c34dbb87d53b3 | def get_absolute_url(self):
'Return absolute URL for instance.'
return reverse('plugins:nautobot_golden_config:configremove', args=[self.pk]) | Return absolute URL for instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configremove', args=[self.pk]) | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configremove', args=[self.pk])<|docstring|>Return absolute URL for instance.<|endoftext|> |
0c1b5daf1c9c610745eeb7a2f8ad907fe6a1019c5754585c6d9482027f3919d1 | def to_csv(self):
'Indicates model fields to return as csv.'
return (self.name, self.platform.slug, self.regex, self.replace) | Indicates model fields to return as csv. | nautobot_golden_config/models.py | to_csv | nniehoff/nautobot-plugin-golden-config | 0 | python | def to_csv(self):
return (self.name, self.platform.slug, self.regex, self.replace) | def to_csv(self):
return (self.name, self.platform.slug, self.regex, self.replace)<|docstring|>Indicates model fields to return as csv.<|endoftext|> |
45dc5c726fca5af373248dfb28587c74aed4574c7dfcdd5dea7d281b3b49247c | def get_absolute_url(self):
'Return absolute URL for instance.'
return reverse('plugins:nautobot_golden_config:configreplace', args=[self.pk]) | Return absolute URL for instance. | nautobot_golden_config/models.py | get_absolute_url | nniehoff/nautobot-plugin-golden-config | 0 | python | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configreplace', args=[self.pk]) | def get_absolute_url(self):
return reverse('plugins:nautobot_golden_config:configreplace', args=[self.pk])<|docstring|>Return absolute URL for instance.<|endoftext|> |
d19470e85127c01ff23c1c46775e9cc25120c40a79205b70e6f68b570cd11c56 | def __str__(self):
'Return a simple string if model is called.'
return self.name | Return a simple string if model is called. | nautobot_golden_config/models.py | __str__ | nniehoff/nautobot-plugin-golden-config | 0 | python | def __str__(self):
return self.name | def __str__(self):
return self.name<|docstring|>Return a simple string if model is called.<|endoftext|> |
709f7dade87f33167b0df3026b7cc6b3b7a07cc00d36b761f09119f6f29cfc94 | def handle(self, *args, **options):
'Automatically called when the load_questions command is given.'
base_path = settings.QUESTIONS_BASE_PATH
questions_structure_file = 'questions.yaml'
factory = LoaderFactory()
factory.create_questions_loader(structure_filename=questions_structure_file, base_path=base_path).load() | Automatically called when the load_questions command is given. | codewof/programming/management/commands/load_questions.py | handle | jimbonothing64/codewof | 3 | python | def handle(self, *args, **options):
base_path = settings.QUESTIONS_BASE_PATH
questions_structure_file = 'questions.yaml'
factory = LoaderFactory()
factory.create_questions_loader(structure_filename=questions_structure_file, base_path=base_path).load() | def handle(self, *args, **options):
base_path = settings.QUESTIONS_BASE_PATH
questions_structure_file = 'questions.yaml'
factory = LoaderFactory()
factory.create_questions_loader(structure_filename=questions_structure_file, base_path=base_path).load()<|docstring|>Automatically called when the load_questions command is given.<|endoftext|> |
40d9ccdd1353fca8abdd72421d78bbcbe8310ddd247fd4093731b38a13c0a3fa | @property
def do_store(self):
'Whether this literal should be stored for use by future backreference chunks.\n \n See the documentation of the `backreference_body` type for details about backreference chunks.\n '
if hasattr(self, '_m_do_store'):
return (self._m_do_store if hasattr(self, '_m_do_store') else None)
self._m_do_store = ((self.tag & 16) != 0)
return (self._m_do_store if hasattr(self, '_m_do_store') else None) | Whether this literal should be stored for use by future backreference chunks.
See the documentation of the `backreference_body` type for details about backreference chunks. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | do_store | Mahlet-Inc/Hobbits | 304 | python | @property
def do_store(self):
'Whether this literal should be stored for use by future backreference chunks.\n \n See the documentation of the `backreference_body` type for details about backreference chunks.\n '
if hasattr(self, '_m_do_store'):
return (self._m_do_store if hasattr(self, '_m_do_store') else None)
self._m_do_store = ((self.tag & 16) != 0)
return (self._m_do_store if hasattr(self, '_m_do_store') else None) | @property
def do_store(self):
'Whether this literal should be stored for use by future backreference chunks.\n \n See the documentation of the `backreference_body` type for details about backreference chunks.\n '
if hasattr(self, '_m_do_store'):
return (self._m_do_store if hasattr(self, '_m_do_store') else None)
self._m_do_store = ((self.tag & 16) != 0)
return (self._m_do_store if hasattr(self, '_m_do_store') else None)<|docstring|>Whether this literal should be stored for use by future backreference chunks.
See the documentation of the `backreference_body` type for details about backreference chunks.<|endoftext|> |
4a8ab5b6300690d4eee47c820e0de7a687e06599dd1e3feaaf1e19f746633bd3 | @property
def len_literal_div2(self):
'The length of the literal data,\n in two-byte units.\n \n In practice,\n this value is always greater than zero,\n as there is no use in storing a zero-length literal.\n '
if hasattr(self, '_m_len_literal_div2'):
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None)
self._m_len_literal_div2 = (self.len_literal_div2_separate if self.is_len_literal_div2_separate else self.len_literal_div2_in_tag)
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None) | The length of the literal data,
in two-byte units.
In practice,
this value is always greater than zero,
as there is no use in storing a zero-length literal. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | len_literal_div2 | Mahlet-Inc/Hobbits | 304 | python | @property
def len_literal_div2(self):
'The length of the literal data,\n in two-byte units.\n \n In practice,\n this value is always greater than zero,\n as there is no use in storing a zero-length literal.\n '
if hasattr(self, '_m_len_literal_div2'):
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None)
self._m_len_literal_div2 = (self.len_literal_div2_separate if self.is_len_literal_div2_separate else self.len_literal_div2_in_tag)
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None) | @property
def len_literal_div2(self):
'The length of the literal data,\n in two-byte units.\n \n In practice,\n this value is always greater than zero,\n as there is no use in storing a zero-length literal.\n '
if hasattr(self, '_m_len_literal_div2'):
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None)
self._m_len_literal_div2 = (self.len_literal_div2_separate if self.is_len_literal_div2_separate else self.len_literal_div2_in_tag)
return (self._m_len_literal_div2 if hasattr(self, '_m_len_literal_div2') else None)<|docstring|>The length of the literal data,
in two-byte units.
In practice,
this value is always greater than zero,
as there is no use in storing a zero-length literal.<|endoftext|> |
7e6d359983f7833dd12c7cc71f8d067fc3860b89baa03dde1624490918e4854a | @property
def len_literal(self):
'The length of the literal data,\n in bytes.\n '
if hasattr(self, '_m_len_literal'):
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None)
self._m_len_literal = (self.len_literal_div2 * 2)
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None) | The length of the literal data,
in bytes. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | len_literal | Mahlet-Inc/Hobbits | 304 | python | @property
def len_literal(self):
'The length of the literal data,\n in bytes.\n '
if hasattr(self, '_m_len_literal'):
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None)
self._m_len_literal = (self.len_literal_div2 * 2)
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None) | @property
def len_literal(self):
'The length of the literal data,\n in bytes.\n '
if hasattr(self, '_m_len_literal'):
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None)
self._m_len_literal = (self.len_literal_div2 * 2)
return (self._m_len_literal if hasattr(self, '_m_len_literal') else None)<|docstring|>The length of the literal data,
in bytes.<|endoftext|> |
37f5a17496cda9eff0aac8d6374e12dea858a5506550617b91732ad0e4ee93f9 | @property
def len_literal_div2_in_tag(self):
'The part of the tag byte that indicates the length of the literal data,\n in two-byte units.\n If this value is 0,\n the length is stored in a separate byte after the tag byte and before the literal data.\n '
if hasattr(self, '_m_len_literal_div2_in_tag'):
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None)
self._m_len_literal_div2_in_tag = (self.tag & 15)
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None) | The part of the tag byte that indicates the length of the literal data,
in two-byte units.
If this value is 0,
the length is stored in a separate byte after the tag byte and before the literal data. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | len_literal_div2_in_tag | Mahlet-Inc/Hobbits | 304 | python | @property
def len_literal_div2_in_tag(self):
'The part of the tag byte that indicates the length of the literal data,\n in two-byte units.\n If this value is 0,\n the length is stored in a separate byte after the tag byte and before the literal data.\n '
if hasattr(self, '_m_len_literal_div2_in_tag'):
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None)
self._m_len_literal_div2_in_tag = (self.tag & 15)
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None) | @property
def len_literal_div2_in_tag(self):
'The part of the tag byte that indicates the length of the literal data,\n in two-byte units.\n If this value is 0,\n the length is stored in a separate byte after the tag byte and before the literal data.\n '
if hasattr(self, '_m_len_literal_div2_in_tag'):
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None)
self._m_len_literal_div2_in_tag = (self.tag & 15)
return (self._m_len_literal_div2_in_tag if hasattr(self, '_m_len_literal_div2_in_tag') else None)<|docstring|>The part of the tag byte that indicates the length of the literal data,
in two-byte units.
If this value is 0,
the length is stored in a separate byte after the tag byte and before the literal data.<|endoftext|> |
474dc58f35658b34f13bc41f17516987c53f0bbac7fb50076e38b68cb8f21869 | @property
def is_len_literal_div2_separate(self):
'Whether the length of the literal is stored separately from the tag.\n '
if hasattr(self, '_m_is_len_literal_div2_separate'):
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None)
self._m_is_len_literal_div2_separate = (self.len_literal_div2_in_tag == 0)
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None) | Whether the length of the literal is stored separately from the tag. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | is_len_literal_div2_separate | Mahlet-Inc/Hobbits | 304 | python | @property
def is_len_literal_div2_separate(self):
'\n '
if hasattr(self, '_m_is_len_literal_div2_separate'):
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None)
self._m_is_len_literal_div2_separate = (self.len_literal_div2_in_tag == 0)
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None) | @property
def is_len_literal_div2_separate(self):
'\n '
if hasattr(self, '_m_is_len_literal_div2_separate'):
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None)
self._m_is_len_literal_div2_separate = (self.len_literal_div2_in_tag == 0)
return (self._m_is_len_literal_div2_separate if hasattr(self, '_m_is_len_literal_div2_separate') else None)<|docstring|>Whether the length of the literal is stored separately from the tag.<|endoftext|> |
10477e6a7f9f45518d68fba6f8e3ec6bcaf5b4ca20a20ed206c85de0aa729a96 | @property
def is_index_separate(self):
'Whether the index is stored separately from the tag.\n '
if hasattr(self, '_m_is_index_separate'):
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None)
self._m_is_index_separate = ((self.tag >= 32) and (self.tag <= 34))
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None) | Whether the index is stored separately from the tag. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | is_index_separate | Mahlet-Inc/Hobbits | 304 | python | @property
def is_index_separate(self):
'\n '
if hasattr(self, '_m_is_index_separate'):
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None)
self._m_is_index_separate = ((self.tag >= 32) and (self.tag <= 34))
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None) | @property
def is_index_separate(self):
'\n '
if hasattr(self, '_m_is_index_separate'):
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None)
self._m_is_index_separate = ((self.tag >= 32) and (self.tag <= 34))
return (self._m_is_index_separate if hasattr(self, '_m_is_index_separate') else None)<|docstring|>Whether the index is stored separately from the tag.<|endoftext|> |
ac0294dd560df19b16115b375b1becad7ac95254be4d1e18bd8e4ea85436d273 | @property
def index_in_tag(self):
'The index of the referenced literal chunk,\n as stored in the tag byte.\n '
if hasattr(self, '_m_index_in_tag'):
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None)
self._m_index_in_tag = (self.tag - 35)
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None) | The index of the referenced literal chunk,
as stored in the tag byte. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | index_in_tag | Mahlet-Inc/Hobbits | 304 | python | @property
def index_in_tag(self):
'The index of the referenced literal chunk,\n as stored in the tag byte.\n '
if hasattr(self, '_m_index_in_tag'):
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None)
self._m_index_in_tag = (self.tag - 35)
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None) | @property
def index_in_tag(self):
'The index of the referenced literal chunk,\n as stored in the tag byte.\n '
if hasattr(self, '_m_index_in_tag'):
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None)
self._m_index_in_tag = (self.tag - 35)
return (self._m_index_in_tag if hasattr(self, '_m_index_in_tag') else None)<|docstring|>The index of the referenced literal chunk,
as stored in the tag byte.<|endoftext|> |
a367ec0e380b61f46dc9525701d0fd7418a8eec3b1e884668f9622830bd80355 | @property
def index_separate(self):
'The index of the referenced literal chunk,\n as stored separately from the tag byte,\n with the implicit offset corrected for.\n '
if hasattr(self, '_m_index_separate'):
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None)
if self.is_index_separate:
self._m_index_separate = ((self.index_separate_minus + 40) + (256 if (self.tag == 33) else 0))
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None) | The index of the referenced literal chunk,
as stored separately from the tag byte,
with the implicit offset corrected for. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | index_separate | Mahlet-Inc/Hobbits | 304 | python | @property
def index_separate(self):
'The index of the referenced literal chunk,\n as stored separately from the tag byte,\n with the implicit offset corrected for.\n '
if hasattr(self, '_m_index_separate'):
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None)
if self.is_index_separate:
self._m_index_separate = ((self.index_separate_minus + 40) + (256 if (self.tag == 33) else 0))
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None) | @property
def index_separate(self):
'The index of the referenced literal chunk,\n as stored separately from the tag byte,\n with the implicit offset corrected for.\n '
if hasattr(self, '_m_index_separate'):
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None)
if self.is_index_separate:
self._m_index_separate = ((self.index_separate_minus + 40) + (256 if (self.tag == 33) else 0))
return (self._m_index_separate if hasattr(self, '_m_index_separate') else None)<|docstring|>The index of the referenced literal chunk,
as stored separately from the tag byte,
with the implicit offset corrected for.<|endoftext|> |
1e448596ebb6a8750d1b65708422a30522c8e6358d8ff74d91fae3f3a58f0c8c | @property
def index(self):
'The index of the referenced literal chunk.\n \n Stored literals are assigned index numbers in the order in which they appear in the compressed data,\n starting at 0.\n Non-stored literals are not counted in the numbering and cannot be referenced using backreferences.\n Once an index is assigned to a stored literal,\n it is never changed or unassigned for the entire length of the compressed data.\n \n As the name indicates,\n a backreference can only reference stored literal chunks found *before* the backreference,\n not ones that come after it.\n '
if hasattr(self, '_m_index'):
return (self._m_index if hasattr(self, '_m_index') else None)
self._m_index = (self.index_separate if self.is_index_separate else self.index_in_tag)
return (self._m_index if hasattr(self, '_m_index') else None) | The index of the referenced literal chunk.
Stored literals are assigned index numbers in the order in which they appear in the compressed data,
starting at 0.
Non-stored literals are not counted in the numbering and cannot be referenced using backreferences.
Once an index is assigned to a stored literal,
it is never changed or unassigned for the entire length of the compressed data.
As the name indicates,
a backreference can only reference stored literal chunks found *before* the backreference,
not ones that come after it. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | index | Mahlet-Inc/Hobbits | 304 | python | @property
def index(self):
'The index of the referenced literal chunk.\n \n Stored literals are assigned index numbers in the order in which they appear in the compressed data,\n starting at 0.\n Non-stored literals are not counted in the numbering and cannot be referenced using backreferences.\n Once an index is assigned to a stored literal,\n it is never changed or unassigned for the entire length of the compressed data.\n \n As the name indicates,\n a backreference can only reference stored literal chunks found *before* the backreference,\n not ones that come after it.\n '
if hasattr(self, '_m_index'):
return (self._m_index if hasattr(self, '_m_index') else None)
self._m_index = (self.index_separate if self.is_index_separate else self.index_in_tag)
return (self._m_index if hasattr(self, '_m_index') else None) | @property
def index(self):
'The index of the referenced literal chunk.\n \n Stored literals are assigned index numbers in the order in which they appear in the compressed data,\n starting at 0.\n Non-stored literals are not counted in the numbering and cannot be referenced using backreferences.\n Once an index is assigned to a stored literal,\n it is never changed or unassigned for the entire length of the compressed data.\n \n As the name indicates,\n a backreference can only reference stored literal chunks found *before* the backreference,\n not ones that come after it.\n '
if hasattr(self, '_m_index'):
return (self._m_index if hasattr(self, '_m_index') else None)
self._m_index = (self.index_separate if self.is_index_separate else self.index_in_tag)
return (self._m_index if hasattr(self, '_m_index') else None)<|docstring|>The index of the referenced literal chunk.
Stored literals are assigned index numbers in the order in which they appear in the compressed data,
starting at 0.
Non-stored literals are not counted in the numbering and cannot be referenced using backreferences.
Once an index is assigned to a stored literal,
it is never changed or unassigned for the entire length of the compressed data.
As the name indicates,
a backreference can only reference stored literal chunks found *before* the backreference,
not ones that come after it.<|endoftext|> |
d4c4c5640a82f52ff1a234979f60add79fc8e7e109c73c089109f1aad4425fd8 | @property
def lookup_table(self):
'Fixed lookup table that maps tag byte numbers to two bytes each.\n \n The entries in the lookup table are offset -\n index 0 stands for tag 0x4b, 1 for 0x4c, etc.\n '
if hasattr(self, '_m_lookup_table'):
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None)
self._m_lookup_table = [b'\x00\x00', b'N\xba', b'\x00\x08', b'Nu', b'\x00\x0c', b'N\xad', b' S', b'/\x0b', b'a\x00', b'\x00\x10', b'p\x00', b'/\x00', b'Hn', b' P', b' n', b'/.', b'\xff\xfc', b'H\xe7', b'?<', b'\x00\x04', b'\xff\xf8', b'/\x0c', b' \x06', b'N\xed', b'NV', b' h', b'N^', b'\x00\x01', b'X\x8f', b'O\xef', b'\x00\x02', b'\x00\x18', b'`\x00', b'\xff\xff', b'P\x8f', b'N\x90', b'\x00\x06', b'&n', b'\x00\x14', b'\xff\xf4', b'L\xee', b'\x00\n', b'\x00\x0e', b'A\xee', b'L\xdf', b'H\xc0', b'\xff\xf0', b'-@', b'\x00\x12', b'0.', b'p\x01', b'/(', b' T', b'g\x00', b'\x00 ', b'\x00\x1c', b' _', b'\x18\x00', b'&o', b'Hx', b'\x00\x16', b'A\xfa', b'0<', b'(@', b'r\x00', b'(n', b' \x0c', b'f\x00', b' k', b'/\x07', b'U\x8f', b'\x00(', b'\xff\xfe', b'\xff\xec', b'"\xd8', b' \x0b', b'\x00\x0f', b'Y\x8f', b'/<', b'\xff\x00', b'\x01\x18', b'\x81\xe1', b'J\x00', b'N\xb0', b'\xff\xe8', b'H\xc7', b'\x00\x03', b'\x00"', b'\x00\x07', b'\x00\x1a', b'g\x06', b'g\x08', b'N\xf9', b'\x00$', b' x', b'\x08\x00', b'f\x04', b'\x00*', b'N\xd0', b'0(', b'&_', b'g\x04', b'\x000', b'C\xee', b'?\x00', b' \x1f', b'\x00\x1e', b'\xff\xf6', b' .', b'B\xa7', b' \x07', b'\xff\xfa', b'`\x02', b'=@', b'\x0c@', b'f\x06', b'\x00&', b'-H', b'/\x01', b'p\xff', b'`\x04', b'\x18\x80', b'J@', b'\x00@', b'\x00,', b'/\x08', b'\x00\x11', b'\xff\xe4', b'!@', b'&@', b'\xff\xf2', b'Bn', b'N\xb9', b'=|', b'\x008', b'\x00\r', b'`\x06', b'B.', b' <', b'g\x0c', b'-h', b'f\x08', b'J.', b'J\xae', b'\x00.', b'H@', b'"_', b'"\x00', b'g\n', b'0\x07', b'Bg', b'\x002', b' (', b'\x00\t', b'Hz', b'\x02\x00', b'/+', b'\x00\x05', b'"n', b'f\x02', b'\xe5\x80', b'g\x0e', b'f\n', b'\x00P', b'>\x00', b'f\x0c', b'.\x00', b'\xff\xee', b' m', b' @', b'\xff\xe0', b'S@', b'`\x08', b'\x04\x80', b'\x00h', b'\x0b|', b'D\x00', b'A\xe8', b'HA']
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None) | Fixed lookup table that maps tag byte numbers to two bytes each.
The entries in the lookup table are offset -
index 0 stands for tag 0x4b, 1 for 0x4c, etc. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | lookup_table | Mahlet-Inc/Hobbits | 304 | python | @property
def lookup_table(self):
'Fixed lookup table that maps tag byte numbers to two bytes each.\n \n The entries in the lookup table are offset -\n index 0 stands for tag 0x4b, 1 for 0x4c, etc.\n '
if hasattr(self, '_m_lookup_table'):
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None)
self._m_lookup_table = [b'\x00\x00', b'N\xba', b'\x00\x08', b'Nu', b'\x00\x0c', b'N\xad', b' S', b'/\x0b', b'a\x00', b'\x00\x10', b'p\x00', b'/\x00', b'Hn', b' P', b' n', b'/.', b'\xff\xfc', b'H\xe7', b'?<', b'\x00\x04', b'\xff\xf8', b'/\x0c', b' \x06', b'N\xed', b'NV', b' h', b'N^', b'\x00\x01', b'X\x8f', b'O\xef', b'\x00\x02', b'\x00\x18', b'`\x00', b'\xff\xff', b'P\x8f', b'N\x90', b'\x00\x06', b'&n', b'\x00\x14', b'\xff\xf4', b'L\xee', b'\x00\n', b'\x00\x0e', b'A\xee', b'L\xdf', b'H\xc0', b'\xff\xf0', b'-@', b'\x00\x12', b'0.', b'p\x01', b'/(', b' T', b'g\x00', b'\x00 ', b'\x00\x1c', b' _', b'\x18\x00', b'&o', b'Hx', b'\x00\x16', b'A\xfa', b'0<', b'(@', b'r\x00', b'(n', b' \x0c', b'f\x00', b' k', b'/\x07', b'U\x8f', b'\x00(', b'\xff\xfe', b'\xff\xec', b'"\xd8', b' \x0b', b'\x00\x0f', b'Y\x8f', b'/<', b'\xff\x00', b'\x01\x18', b'\x81\xe1', b'J\x00', b'N\xb0', b'\xff\xe8', b'H\xc7', b'\x00\x03', b'\x00"', b'\x00\x07', b'\x00\x1a', b'g\x06', b'g\x08', b'N\xf9', b'\x00$', b' x', b'\x08\x00', b'f\x04', b'\x00*', b'N\xd0', b'0(', b'&_', b'g\x04', b'\x000', b'C\xee', b'?\x00', b' \x1f', b'\x00\x1e', b'\xff\xf6', b' .', b'B\xa7', b' \x07', b'\xff\xfa', b'`\x02', b'=@', b'\x0c@', b'f\x06', b'\x00&', b'-H', b'/\x01', b'p\xff', b'`\x04', b'\x18\x80', b'J@', b'\x00@', b'\x00,', b'/\x08', b'\x00\x11', b'\xff\xe4', b'!@', b'&@', b'\xff\xf2', b'Bn', b'N\xb9', b'=|', b'\x008', b'\x00\r', b'`\x06', b'B.', b' <', b'g\x0c', b'-h', b'f\x08', b'J.', b'J\xae', b'\x00.', b'H@', b'"_', b'"\x00', b'g\n', b'0\x07', b'Bg', b'\x002', b' (', b'\x00\t', b'Hz', b'\x02\x00', b'/+', b'\x00\x05', b'"n', b'f\x02', b'\xe5\x80', b'g\x0e', b'f\n', b'\x00P', b'>\x00', b'f\x0c', b'.\x00', b'\xff\xee', b' m', b' @', b'\xff\xe0', b'S@', b'`\x08', b'\x04\x80', b'\x00h', b'\x0b|', b'D\x00', b'A\xe8', b'HA']
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None) | @property
def lookup_table(self):
'Fixed lookup table that maps tag byte numbers to two bytes each.\n \n The entries in the lookup table are offset -\n index 0 stands for tag 0x4b, 1 for 0x4c, etc.\n '
if hasattr(self, '_m_lookup_table'):
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None)
self._m_lookup_table = [b'\x00\x00', b'N\xba', b'\x00\x08', b'Nu', b'\x00\x0c', b'N\xad', b' S', b'/\x0b', b'a\x00', b'\x00\x10', b'p\x00', b'/\x00', b'Hn', b' P', b' n', b'/.', b'\xff\xfc', b'H\xe7', b'?<', b'\x00\x04', b'\xff\xf8', b'/\x0c', b' \x06', b'N\xed', b'NV', b' h', b'N^', b'\x00\x01', b'X\x8f', b'O\xef', b'\x00\x02', b'\x00\x18', b'`\x00', b'\xff\xff', b'P\x8f', b'N\x90', b'\x00\x06', b'&n', b'\x00\x14', b'\xff\xf4', b'L\xee', b'\x00\n', b'\x00\x0e', b'A\xee', b'L\xdf', b'H\xc0', b'\xff\xf0', b'-@', b'\x00\x12', b'0.', b'p\x01', b'/(', b' T', b'g\x00', b'\x00 ', b'\x00\x1c', b' _', b'\x18\x00', b'&o', b'Hx', b'\x00\x16', b'A\xfa', b'0<', b'(@', b'r\x00', b'(n', b' \x0c', b'f\x00', b' k', b'/\x07', b'U\x8f', b'\x00(', b'\xff\xfe', b'\xff\xec', b'"\xd8', b' \x0b', b'\x00\x0f', b'Y\x8f', b'/<', b'\xff\x00', b'\x01\x18', b'\x81\xe1', b'J\x00', b'N\xb0', b'\xff\xe8', b'H\xc7', b'\x00\x03', b'\x00"', b'\x00\x07', b'\x00\x1a', b'g\x06', b'g\x08', b'N\xf9', b'\x00$', b' x', b'\x08\x00', b'f\x04', b'\x00*', b'N\xd0', b'0(', b'&_', b'g\x04', b'\x000', b'C\xee', b'?\x00', b' \x1f', b'\x00\x1e', b'\xff\xf6', b' .', b'B\xa7', b' \x07', b'\xff\xfa', b'`\x02', b'=@', b'\x0c@', b'f\x06', b'\x00&', b'-H', b'/\x01', b'p\xff', b'`\x04', b'\x18\x80', b'J@', b'\x00@', b'\x00,', b'/\x08', b'\x00\x11', b'\xff\xe4', b'!@', b'&@', b'\xff\xf2', b'Bn', b'N\xb9', b'=|', b'\x008', b'\x00\r', b'`\x06', b'B.', b' <', b'g\x0c', b'-h', b'f\x08', b'J.', b'J\xae', b'\x00.', b'H@', b'"_', b'"\x00', b'g\n', b'0\x07', b'Bg', b'\x002', b' (', b'\x00\t', b'Hz', b'\x02\x00', b'/+', b'\x00\x05', b'"n', b'f\x02', b'\xe5\x80', b'g\x0e', b'f\n', b'\x00P', b'>\x00', b'f\x0c', b'.\x00', b'\xff\xee', b' m', b' @', b'\xff\xe0', b'S@', b'`\x08', b'\x04\x80', b'\x00h', b'\x0b|', b'D\x00', b'A\xe8', b'HA']
return (self._m_lookup_table if hasattr(self, '_m_lookup_table') else None)<|docstring|>Fixed lookup table that maps tag byte numbers to two bytes each.
The entries in the lookup table are offset -
index 0 stands for tag 0x4b, 1 for 0x4c, etc.<|endoftext|> |
d8626b3a97eb94a3542cfb4e8f8d7760d292b4934de09a5ad64bfddcec5617fc | @property
def value(self):
'The two bytes that the tag byte expands to,\n based on the fixed lookup table.\n '
if hasattr(self, '_m_value'):
return (self._m_value if hasattr(self, '_m_value') else None)
self._m_value = self.lookup_table[(self.tag - 75)]
return (self._m_value if hasattr(self, '_m_value') else None) | The two bytes that the tag byte expands to,
based on the fixed lookup table. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | value | Mahlet-Inc/Hobbits | 304 | python | @property
def value(self):
'The two bytes that the tag byte expands to,\n based on the fixed lookup table.\n '
if hasattr(self, '_m_value'):
return (self._m_value if hasattr(self, '_m_value') else None)
self._m_value = self.lookup_table[(self.tag - 75)]
return (self._m_value if hasattr(self, '_m_value') else None) | @property
def value(self):
'The two bytes that the tag byte expands to,\n based on the fixed lookup table.\n '
if hasattr(self, '_m_value'):
return (self._m_value if hasattr(self, '_m_value') else None)
self._m_value = self.lookup_table[(self.tag - 75)]
return (self._m_value if hasattr(self, '_m_value') else None)<|docstring|>The two bytes that the tag byte expands to,
based on the fixed lookup table.<|endoftext|> |
a92ba0f3ecbf76b6eae30fb1c26ce60d3e413940ee183d60742d9b93f8478486 | @property
def segment_number(self):
'The segment number for all of the generated jump table entries.\n \n Although it is stored as a variable-length integer,\n the segment number must be in the range `0x0 <= x <= 0xffff`,\n i. e. an unsigned 16-bit integer.\n '
if hasattr(self, '_m_segment_number'):
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None)
self._m_segment_number = self.segment_number_raw.value
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None) | The segment number for all of the generated jump table entries.
Although it is stored as a variable-length integer,
the segment number must be in the range `0x0 <= x <= 0xffff`,
i. e. an unsigned 16-bit integer. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | segment_number | Mahlet-Inc/Hobbits | 304 | python | @property
def segment_number(self):
'The segment number for all of the generated jump table entries.\n \n Although it is stored as a variable-length integer,\n the segment number must be in the range `0x0 <= x <= 0xffff`,\n i. e. an unsigned 16-bit integer.\n '
if hasattr(self, '_m_segment_number'):
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None)
self._m_segment_number = self.segment_number_raw.value
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None) | @property
def segment_number(self):
'The segment number for all of the generated jump table entries.\n \n Although it is stored as a variable-length integer,\n the segment number must be in the range `0x0 <= x <= 0xffff`,\n i. e. an unsigned 16-bit integer.\n '
if hasattr(self, '_m_segment_number'):
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None)
self._m_segment_number = self.segment_number_raw.value
return (self._m_segment_number if hasattr(self, '_m_segment_number') else None)<|docstring|>The segment number for all of the generated jump table entries.
Although it is stored as a variable-length integer,
the segment number must be in the range `0x0 <= x <= 0xffff`,
i. e. an unsigned 16-bit integer.<|endoftext|> |
3359f4b80f9ab86d9fbf57e33756e11d3dee9bd39d7d5613bdd5a9020ae5b5ce | @property
def num_addresses(self):
'The number of addresses stored in this chunk.\n \n This number must be greater than 0.\n '
if hasattr(self, '_m_num_addresses'):
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None)
self._m_num_addresses = self.num_addresses_raw.value
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None) | The number of addresses stored in this chunk.
This number must be greater than 0. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | num_addresses | Mahlet-Inc/Hobbits | 304 | python | @property
def num_addresses(self):
'The number of addresses stored in this chunk.\n \n This number must be greater than 0.\n '
if hasattr(self, '_m_num_addresses'):
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None)
self._m_num_addresses = self.num_addresses_raw.value
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None) | @property
def num_addresses(self):
'The number of addresses stored in this chunk.\n \n This number must be greater than 0.\n '
if hasattr(self, '_m_num_addresses'):
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None)
self._m_num_addresses = self.num_addresses_raw.value
return (self._m_num_addresses if hasattr(self, '_m_num_addresses') else None)<|docstring|>The number of addresses stored in this chunk.
This number must be greater than 0.<|endoftext|> |
fd39e3207312d93dc66af3bd4cc58adf3268d2c28c0eab38a120b42a93f1735e | @property
def byte_count(self):
'The length in bytes of the value to be repeated.\n Regardless of the byte count,\n the value to be repeated is stored as a variable-length integer.\n '
if hasattr(self, '_m_byte_count'):
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None)
self._m_byte_count = (1 if (self.tag == 2) else (2 if (self.tag == 3) else (- 1)))
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None) | The length in bytes of the value to be repeated.
Regardless of the byte count,
the value to be repeated is stored as a variable-length integer. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | byte_count | Mahlet-Inc/Hobbits | 304 | python | @property
def byte_count(self):
'The length in bytes of the value to be repeated.\n Regardless of the byte count,\n the value to be repeated is stored as a variable-length integer.\n '
if hasattr(self, '_m_byte_count'):
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None)
self._m_byte_count = (1 if (self.tag == 2) else (2 if (self.tag == 3) else (- 1)))
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None) | @property
def byte_count(self):
'The length in bytes of the value to be repeated.\n Regardless of the byte count,\n the value to be repeated is stored as a variable-length integer.\n '
if hasattr(self, '_m_byte_count'):
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None)
self._m_byte_count = (1 if (self.tag == 2) else (2 if (self.tag == 3) else (- 1)))
return (self._m_byte_count if hasattr(self, '_m_byte_count') else None)<|docstring|>The length in bytes of the value to be repeated.
Regardless of the byte count,
the value to be repeated is stored as a variable-length integer.<|endoftext|> |
7496707606e23207e4e825119630a0af9cf410b1468d6b1b3a875138f8440642 | @property
def to_repeat(self):
'The value to repeat.\n \n Although it is stored as a variable-length integer,\n this value must fit into an unsigned big-endian integer that is as long as `byte_count`,\n i. e. either 8 or 16 bits.\n '
if hasattr(self, '_m_to_repeat'):
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None)
self._m_to_repeat = self.to_repeat_raw.value
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None) | The value to repeat.
Although it is stored as a variable-length integer,
this value must fit into an unsigned big-endian integer that is as long as `byte_count`,
i. e. either 8 or 16 bits. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | to_repeat | Mahlet-Inc/Hobbits | 304 | python | @property
def to_repeat(self):
'The value to repeat.\n \n Although it is stored as a variable-length integer,\n this value must fit into an unsigned big-endian integer that is as long as `byte_count`,\n i. e. either 8 or 16 bits.\n '
if hasattr(self, '_m_to_repeat'):
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None)
self._m_to_repeat = self.to_repeat_raw.value
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None) | @property
def to_repeat(self):
'The value to repeat.\n \n Although it is stored as a variable-length integer,\n this value must fit into an unsigned big-endian integer that is as long as `byte_count`,\n i. e. either 8 or 16 bits.\n '
if hasattr(self, '_m_to_repeat'):
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None)
self._m_to_repeat = self.to_repeat_raw.value
return (self._m_to_repeat if hasattr(self, '_m_to_repeat') else None)<|docstring|>The value to repeat.
Although it is stored as a variable-length integer,
this value must fit into an unsigned big-endian integer that is as long as `byte_count`,
i. e. either 8 or 16 bits.<|endoftext|> |
50f5b2821f36800399db77ccd872c5c593a26fa440c283327790f2dac5650d15 | @property
def repeat_count_m1(self):
'The number of times to repeat the value,\n minus one.\n \n This value must not be negative.\n '
if hasattr(self, '_m_repeat_count_m1'):
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None)
self._m_repeat_count_m1 = self.repeat_count_m1_raw.value
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None) | The number of times to repeat the value,
minus one.
This value must not be negative. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | repeat_count_m1 | Mahlet-Inc/Hobbits | 304 | python | @property
def repeat_count_m1(self):
'The number of times to repeat the value,\n minus one.\n \n This value must not be negative.\n '
if hasattr(self, '_m_repeat_count_m1'):
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None)
self._m_repeat_count_m1 = self.repeat_count_m1_raw.value
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None) | @property
def repeat_count_m1(self):
'The number of times to repeat the value,\n minus one.\n \n This value must not be negative.\n '
if hasattr(self, '_m_repeat_count_m1'):
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None)
self._m_repeat_count_m1 = self.repeat_count_m1_raw.value
return (self._m_repeat_count_m1 if hasattr(self, '_m_repeat_count_m1') else None)<|docstring|>The number of times to repeat the value,
minus one.
This value must not be negative.<|endoftext|> |
5144fce3a570db307328bce19d9bce79a8653a7c7b8b387ada02bc9a7aa8201d | @property
def repeat_count(self):
'The number of times to repeat the value.\n \n This value must be positive.\n '
if hasattr(self, '_m_repeat_count'):
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None)
self._m_repeat_count = (self.repeat_count_m1 + 1)
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None) | The number of times to repeat the value.
This value must be positive. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | repeat_count | Mahlet-Inc/Hobbits | 304 | python | @property
def repeat_count(self):
'The number of times to repeat the value.\n \n This value must be positive.\n '
if hasattr(self, '_m_repeat_count'):
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None)
self._m_repeat_count = (self.repeat_count_m1 + 1)
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None) | @property
def repeat_count(self):
'The number of times to repeat the value.\n \n This value must be positive.\n '
if hasattr(self, '_m_repeat_count'):
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None)
self._m_repeat_count = (self.repeat_count_m1 + 1)
return (self._m_repeat_count if hasattr(self, '_m_repeat_count') else None)<|docstring|>The number of times to repeat the value.
This value must be positive.<|endoftext|> |
82032f547c8af6117db0e6ede4744cf90bde7a30ac1efdd88add7b9c6dd9f2a8 | @property
def first_value(self):
'The first value in the sequence.\n \n Although it is stored as a variable-length integer,\n this value must be in the range `-0x8000 <= x <= 0x7fff`,\n i. e. a signed 16-bit integer.\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None) | The first value in the sequence.
Although it is stored as a variable-length integer,
this value must be in the range `-0x8000 <= x <= 0x7fff`,
i. e. a signed 16-bit integer. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | first_value | Mahlet-Inc/Hobbits | 304 | python | @property
def first_value(self):
'The first value in the sequence.\n \n Although it is stored as a variable-length integer,\n this value must be in the range `-0x8000 <= x <= 0x7fff`,\n i. e. a signed 16-bit integer.\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None) | @property
def first_value(self):
'The first value in the sequence.\n \n Although it is stored as a variable-length integer,\n this value must be in the range `-0x8000 <= x <= 0x7fff`,\n i. e. a signed 16-bit integer.\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None)<|docstring|>The first value in the sequence.
Although it is stored as a variable-length integer,
this value must be in the range `-0x8000 <= x <= 0x7fff`,
i. e. a signed 16-bit integer.<|endoftext|> |
71a3f490e72503c63246e85400100fc1e167910177cfc87d68b7067006340dd1 | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None) | The number of deltas stored in this chunk.
This number must not be negative. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | num_deltas | Mahlet-Inc/Hobbits | 304 | python | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None) | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)<|docstring|>The number of deltas stored in this chunk.
This number must not be negative.<|endoftext|> |
2278a1c9efd192ef85fa5fa8c7692e82f7eb2e14bd157000f62fa3b45277dc43 | @property
def first_value(self):
'The first value in the sequence.\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None) | The first value in the sequence. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | first_value | Mahlet-Inc/Hobbits | 304 | python | @property
def first_value(self):
'\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None) | @property
def first_value(self):
'\n '
if hasattr(self, '_m_first_value'):
return (self._m_first_value if hasattr(self, '_m_first_value') else None)
self._m_first_value = self.first_value_raw.value
return (self._m_first_value if hasattr(self, '_m_first_value') else None)<|docstring|>The first value in the sequence.<|endoftext|> |
71a3f490e72503c63246e85400100fc1e167910177cfc87d68b7067006340dd1 | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None) | The number of deltas stored in this chunk.
This number must not be negative. | src/hobbits-plugins/analyzers/KaitaiStruct/ksy_py/macos/resource_compression/dcmp_0.py | num_deltas | Mahlet-Inc/Hobbits | 304 | python | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None) | @property
def num_deltas(self):
'The number of deltas stored in this chunk.\n \n This number must not be negative.\n '
if hasattr(self, '_m_num_deltas'):
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)
self._m_num_deltas = self.num_deltas_raw.value
return (self._m_num_deltas if hasattr(self, '_m_num_deltas') else None)<|docstring|>The number of deltas stored in this chunk.
This number must not be negative.<|endoftext|> |
669f979aa7638e92e5498d27e20d7832f1443561fd11e02e4767c66cea93d327 | def parse_number(x):
'Parse a number from a string.'
return round(float(x), 6) | Parse a number from a string. | strongsup/tables/structure.py | parse_number | Verose/Decomposable-Attention-Model-for-Semantic-Parsing | 72 | python | def parse_number(x):
return round(float(x), 6) | def parse_number(x):
return round(float(x), 6)<|docstring|>Parse a number from a string.<|endoftext|> |
3029935944e950d06ac41022b24f3f99e489578e63a99858bcf74ca3590a1f1f | def parse_date(x):
'Parse a date from a string with format yy-mm-dd.'
x = x.split('-')
assert (len(x) == 3), 'Not a valid date: {}'.format(x)
year = ((- 1) if (x[0][0].lower() == 'x') else int(x[0]))
month = ((- 1) if (x[1][0].lower() == 'x') else int(x[1]))
day = ((- 1) if (x[2][0].lower() == 'x') else int(x[2]))
return Date(year, month, day) | Parse a date from a string with format yy-mm-dd. | strongsup/tables/structure.py | parse_date | Verose/Decomposable-Attention-Model-for-Semantic-Parsing | 72 | python | def parse_date(x):
x = x.split('-')
assert (len(x) == 3), 'Not a valid date: {}'.format(x)
year = ((- 1) if (x[0][0].lower() == 'x') else int(x[0]))
month = ((- 1) if (x[1][0].lower() == 'x') else int(x[1]))
day = ((- 1) if (x[2][0].lower() == 'x') else int(x[2]))
return Date(year, month, day) | def parse_date(x):
x = x.split('-')
assert (len(x) == 3), 'Not a valid date: {}'.format(x)
year = ((- 1) if (x[0][0].lower() == 'x') else int(x[0]))
month = ((- 1) if (x[1][0].lower() == 'x') else int(x[1]))
day = ((- 1) if (x[2][0].lower() == 'x') else int(x[2]))
return Date(year, month, day)<|docstring|>Parse a date from a string with format yy-mm-dd.<|endoftext|> |
457992056c63d814e208308df08404c06c46037854f0ed123f37f41dcf4088b4 | def parse_value(x):
'Parse the string, which may be a number, a date, or a non-numeric string.'
try:
return parse_number(x)
except:
try:
return parse_date(x)
except:
return x | Parse the string, which may be a number, a date, or a non-numeric string. | strongsup/tables/structure.py | parse_value | Verose/Decomposable-Attention-Model-for-Semantic-Parsing | 72 | python | def parse_value(x):
try:
return parse_number(x)
except:
try:
return parse_date(x)
except:
return x | def parse_value(x):
try:
return parse_number(x)
except:
try:
return parse_date(x)
except:
return x<|docstring|>Parse the string, which may be a number, a date, or a non-numeric string.<|endoftext|> |
9a2bb48e48a6e269685ed71a1a69a19974afaaa063121cc611758662ef459c94 | def get_type(x):
'Return the type signature of x. Used to prevent comparison across types.'
if isinstance(x, float):
return 'N'
elif isinstance(x, Date):
return 'D'
elif isinstance(x, basestring):
if (not x.startswith('fb:')):
raise ValueError('NameValue does not start with "fb:": {}'.format(x))
tokens = x.split('.')
if (len(tokens) != 2):
raise ValueError('{} is not an entity'.format(x))
return tokens[0]
else:
raise ValueError('Unknown type for {}'.format(type(x))) | Return the type signature of x. Used to prevent comparison across types. | strongsup/tables/structure.py | get_type | Verose/Decomposable-Attention-Model-for-Semantic-Parsing | 72 | python | def get_type(x):
if isinstance(x, float):
return 'N'
elif isinstance(x, Date):
return 'D'
elif isinstance(x, basestring):
if (not x.startswith('fb:')):
raise ValueError('NameValue does not start with "fb:": {}'.format(x))
tokens = x.split('.')
if (len(tokens) != 2):
raise ValueError('{} is not an entity'.format(x))
return tokens[0]
else:
raise ValueError('Unknown type for {}'.format(type(x))) | def get_type(x):
if isinstance(x, float):
return 'N'
elif isinstance(x, Date):
return 'D'
elif isinstance(x, basestring):
if (not x.startswith('fb:')):
raise ValueError('NameValue does not start with "fb:": {}'.format(x))
tokens = x.split('.')
if (len(tokens) != 2):
raise ValueError('{} is not an entity'.format(x))
return tokens[0]
else:
raise ValueError('Unknown type for {}'.format(type(x)))<|docstring|>Return the type signature of x. Used to prevent comparison across types.<|endoftext|> |
62a854474b16128e1c9ab989cd0c84d09c00275fdcc44a261df7784d417bbfd1 | def ensure_same_type(collection, allowed_types=None):
'Ensure that all values in the collection have the same type.\n Return the agreed type. Throw an error if the type is not agreed.\n\n Args:\n collection: A set or a dict where values are sets.\n allowed_types: Restriction on the agreed type.\n Can be a string, a collection of strings, or None (= allow all).\n Returns:\n The agreed type\n Throws:\n ValueError if one of the following happens:\n - The collection is not a set or a set-valued dict\n - The collection is empty\n - Some two items have different types\n - Some item does not agree with the allowed types (if specified)\n '
if isinstance(collection, set):
itr = iter(collection)
elif isinstance(collection, dict):
itr = (x for v in collection.itervalues() for x in v)
else:
raise ValueError('Bad data type: {}'.format(type(collection)))
if (allowed_types and isinstance(allowed_types, basestring)):
allowed_types = [allowed_types]
agreed_type = None
for value in itr:
if (agreed_type is None):
agreed_type = get_type(value)
if ((allowed_types is not None) and (agreed_type not in allowed_types)):
raise ValueError('Type {} is not in allowed types {}'.format(agreed_type, allowed_types))
else:
t = get_type(value)
if (t != agreed_type):
raise ValueError('Value {} does not have agreed type {}'.format(value, agreed_type))
if (agreed_type is None):
raise ValueError('The collection is empty: {}'.format(collection))
return agreed_type | Ensure that all values in the collection have the same type.
Return the agreed type. Throw an error if the type is not agreed.
Args:
collection: A set or a dict where values are sets.
allowed_types: Restriction on the agreed type.
Can be a string, a collection of strings, or None (= allow all).
Returns:
The agreed type
Throws:
ValueError if one of the following happens:
- The collection is not a set or a set-valued dict
- The collection is empty
- Some two items have different types
- Some item does not agree with the allowed types (if specified) | strongsup/tables/structure.py | ensure_same_type | Verose/Decomposable-Attention-Model-for-Semantic-Parsing | 72 | python | def ensure_same_type(collection, allowed_types=None):
'Ensure that all values in the collection have the same type.\n Return the agreed type. Throw an error if the type is not agreed.\n\n Args:\n collection: A set or a dict where values are sets.\n allowed_types: Restriction on the agreed type.\n Can be a string, a collection of strings, or None (= allow all).\n Returns:\n The agreed type\n Throws:\n ValueError if one of the following happens:\n - The collection is not a set or a set-valued dict\n - The collection is empty\n - Some two items have different types\n - Some item does not agree with the allowed types (if specified)\n '
if isinstance(collection, set):
itr = iter(collection)
elif isinstance(collection, dict):
itr = (x for v in collection.itervalues() for x in v)
else:
raise ValueError('Bad data type: {}'.format(type(collection)))
if (allowed_types and isinstance(allowed_types, basestring)):
allowed_types = [allowed_types]
agreed_type = None
for value in itr:
if (agreed_type is None):
agreed_type = get_type(value)
if ((allowed_types is not None) and (agreed_type not in allowed_types)):
raise ValueError('Type {} is not in allowed types {}'.format(agreed_type, allowed_types))
else:
t = get_type(value)
if (t != agreed_type):
raise ValueError('Value {} does not have agreed type {}'.format(value, agreed_type))
if (agreed_type is None):
raise ValueError('The collection is empty: {}'.format(collection))
return agreed_type | def ensure_same_type(collection, allowed_types=None):
'Ensure that all values in the collection have the same type.\n Return the agreed type. Throw an error if the type is not agreed.\n\n Args:\n collection: A set or a dict where values are sets.\n allowed_types: Restriction on the agreed type.\n Can be a string, a collection of strings, or None (= allow all).\n Returns:\n The agreed type\n Throws:\n ValueError if one of the following happens:\n - The collection is not a set or a set-valued dict\n - The collection is empty\n - Some two items have different types\n - Some item does not agree with the allowed types (if specified)\n '
if isinstance(collection, set):
itr = iter(collection)
elif isinstance(collection, dict):
itr = (x for v in collection.itervalues() for x in v)
else:
raise ValueError('Bad data type: {}'.format(type(collection)))
if (allowed_types and isinstance(allowed_types, basestring)):
allowed_types = [allowed_types]
agreed_type = None
for value in itr:
if (agreed_type is None):
agreed_type = get_type(value)
if ((allowed_types is not None) and (agreed_type not in allowed_types)):
raise ValueError('Type {} is not in allowed types {}'.format(agreed_type, allowed_types))
else:
t = get_type(value)
if (t != agreed_type):
raise ValueError('Value {} does not have agreed type {}'.format(value, agreed_type))
if (agreed_type is None):
raise ValueError('The collection is empty: {}'.format(collection))
return agreed_type<|docstring|>Ensure that all values in the collection have the same type.
Return the agreed type. Throw an error if the type is not agreed.
Args:
collection: A set or a dict where values are sets.
allowed_types: Restriction on the agreed type.
Can be a string, a collection of strings, or None (= allow all).
Returns:
The agreed type
Throws:
ValueError if one of the following happens:
- The collection is not a set or a set-valued dict
- The collection is empty
- Some two items have different types
- Some item does not agree with the allowed types (if specified)<|endoftext|> |
2f61cbdbb4c58470a8385909f60c4a064efc23c99fc6c3b71c09ad554db93f0c | def parse_program(tokens):
'\n program:\n | top_statement program\n | top_statement\n '
functions = {}
top_statements = StatementList()
while tokens.peek():
if tokens.consume_maybe('function'):
function_declaration = parse_function_declaration(tokens)
functions[function_declaration.name] = function_declaration
else:
statement = parse_statement(tokens)
top_statements.append(statement)
return (functions, top_statements) | program:
| top_statement program
| top_statement | parser/parser.py | parse_program | JamesWP/anzu | 0 | python | def parse_program(tokens):
'\n program:\n | top_statement program\n | top_statement\n '
functions = {}
top_statements = StatementList()
while tokens.peek():
if tokens.consume_maybe('function'):
function_declaration = parse_function_declaration(tokens)
functions[function_declaration.name] = function_declaration
else:
statement = parse_statement(tokens)
top_statements.append(statement)
return (functions, top_statements) | def parse_program(tokens):
'\n program:\n | top_statement program\n | top_statement\n '
functions = {}
top_statements = StatementList()
while tokens.peek():
if tokens.consume_maybe('function'):
function_declaration = parse_function_declaration(tokens)
functions[function_declaration.name] = function_declaration
else:
statement = parse_statement(tokens)
top_statements.append(statement)
return (functions, top_statements)<|docstring|>program:
| top_statement program
| top_statement<|endoftext|> |
82a8a733fdef9c0d18947a312e723f8fbc721bb4154ba72cf2a06978df385109 | def parse_function_declaration(tokens):
"\n function_declaration:\n | identifier num_literal num_literal statement_list 'end'\n | identifier num_literal num_literal 'end'\n "
name = tokens.consume()
num_input_args = int(tokens.consume())
num_output_args = int(tokens.consume())
function = FunctionDeclaration(name, num_input_args, num_output_args)
if tokens.consume_maybe('end'):
return function
function.body = parse_statement_list(tokens)
tokens.consume_only('end')
return function | function_declaration:
| identifier num_literal num_literal statement_list 'end'
| identifier num_literal num_literal 'end' | parser/parser.py | parse_function_declaration | JamesWP/anzu | 0 | python | def parse_function_declaration(tokens):
"\n function_declaration:\n | identifier num_literal num_literal statement_list 'end'\n | identifier num_literal num_literal 'end'\n "
name = tokens.consume()
num_input_args = int(tokens.consume())
num_output_args = int(tokens.consume())
function = FunctionDeclaration(name, num_input_args, num_output_args)
if tokens.consume_maybe('end'):
return function
function.body = parse_statement_list(tokens)
tokens.consume_only('end')
return function | def parse_function_declaration(tokens):
"\n function_declaration:\n | identifier num_literal num_literal statement_list 'end'\n | identifier num_literal num_literal 'end'\n "
name = tokens.consume()
num_input_args = int(tokens.consume())
num_output_args = int(tokens.consume())
function = FunctionDeclaration(name, num_input_args, num_output_args)
if tokens.consume_maybe('end'):
return function
function.body = parse_statement_list(tokens)
tokens.consume_only('end')
return function<|docstring|>function_declaration:
| identifier num_literal num_literal statement_list 'end'
| identifier num_literal num_literal 'end'<|endoftext|> |
dab2c92ce2c6eba37eb37a1025fbb25cfe8cb4cafa54307e5563306a6e052ccd | def parse_statement_list(tokens):
'\n statement_list:\n | statement\n | statement statement_list\n '
statement_list = StatementList()
while True:
statement = parse_statement(tokens)
statement_list.append(statement)
if (tokens.peek() in ['end', 'elif', 'do']):
return statement_list | statement_list:
| statement
| statement statement_list | parser/parser.py | parse_statement_list | JamesWP/anzu | 0 | python | def parse_statement_list(tokens):
'\n statement_list:\n | statement\n | statement statement_list\n '
statement_list = StatementList()
while True:
statement = parse_statement(tokens)
statement_list.append(statement)
if (tokens.peek() in ['end', 'elif', 'do']):
return statement_list | def parse_statement_list(tokens):
'\n statement_list:\n | statement\n | statement statement_list\n '
statement_list = StatementList()
while True:
statement = parse_statement(tokens)
statement_list.append(statement)
if (tokens.peek() in ['end', 'elif', 'do']):
return statement_list<|docstring|>statement_list:
| statement
| statement statement_list<|endoftext|> |
653b3605075f9421b36d83b0dcb86fad18ea6f900e21c31ac0b0353c57b807ec | def parse_statement(tokens):
"\n statement:\n | 'while' statement_list 'do' statement_list 'end'\n | 'while' statement_list 'do' 'end'\n | 'if' if_body\n | num_literal\n | string_literal\n | builtin\n | identifier\n "
if tokens.consume_maybe('while'):
condition = parse_statement_list(tokens)
tokens.consume_only('do')
statement = WhileStatement(condition)
if tokens.consume_maybe('end'):
return statement
body = parse_statement_list(tokens)
statement.body = body
tokens.consume_only('end')
return statement
if tokens.consume_maybe('if'):
return parse_if_body(tokens)
token = tokens.consume()
return Statement(token) | statement:
| 'while' statement_list 'do' statement_list 'end'
| 'while' statement_list 'do' 'end'
| 'if' if_body
| num_literal
| string_literal
| builtin
| identifier | parser/parser.py | parse_statement | JamesWP/anzu | 0 | python | def parse_statement(tokens):
"\n statement:\n | 'while' statement_list 'do' statement_list 'end'\n | 'while' statement_list 'do' 'end'\n | 'if' if_body\n | num_literal\n | string_literal\n | builtin\n | identifier\n "
if tokens.consume_maybe('while'):
condition = parse_statement_list(tokens)
tokens.consume_only('do')
statement = WhileStatement(condition)
if tokens.consume_maybe('end'):
return statement
body = parse_statement_list(tokens)
statement.body = body
tokens.consume_only('end')
return statement
if tokens.consume_maybe('if'):
return parse_if_body(tokens)
token = tokens.consume()
return Statement(token) | def parse_statement(tokens):
"\n statement:\n | 'while' statement_list 'do' statement_list 'end'\n | 'while' statement_list 'do' 'end'\n | 'if' if_body\n | num_literal\n | string_literal\n | builtin\n | identifier\n "
if tokens.consume_maybe('while'):
condition = parse_statement_list(tokens)
tokens.consume_only('do')
statement = WhileStatement(condition)
if tokens.consume_maybe('end'):
return statement
body = parse_statement_list(tokens)
statement.body = body
tokens.consume_only('end')
return statement
if tokens.consume_maybe('if'):
return parse_if_body(tokens)
token = tokens.consume()
return Statement(token)<|docstring|>statement:
| 'while' statement_list 'do' statement_list 'end'
| 'while' statement_list 'do' 'end'
| 'if' if_body
| num_literal
| string_literal
| builtin
| identifier<|endoftext|> |
414a33119768ddbcff0a9b776762ce57eb5fd9469b897ad6e03d3578d14d2f8d | def parse_if_body(tokens):
"\n if_body:\n | statement_list 'do' statement_list 'elif' if_body\n | statement_list 'do' statement_list 'end'\n "
condition = parse_statement_list(tokens)
tokens.consume_only('do')
body = parse_statement_list(tokens)
if_statement = IfStatement(condition, body)
if tokens.consume_maybe('elif'):
if_statement.else_body = parse_if_body(tokens)
return if_statement
tokens.consume_only('end')
return if_statement | if_body:
| statement_list 'do' statement_list 'elif' if_body
| statement_list 'do' statement_list 'end' | parser/parser.py | parse_if_body | JamesWP/anzu | 0 | python | def parse_if_body(tokens):
"\n if_body:\n | statement_list 'do' statement_list 'elif' if_body\n | statement_list 'do' statement_list 'end'\n "
condition = parse_statement_list(tokens)
tokens.consume_only('do')
body = parse_statement_list(tokens)
if_statement = IfStatement(condition, body)
if tokens.consume_maybe('elif'):
if_statement.else_body = parse_if_body(tokens)
return if_statement
tokens.consume_only('end')
return if_statement | def parse_if_body(tokens):
"\n if_body:\n | statement_list 'do' statement_list 'elif' if_body\n | statement_list 'do' statement_list 'end'\n "
condition = parse_statement_list(tokens)
tokens.consume_only('do')
body = parse_statement_list(tokens)
if_statement = IfStatement(condition, body)
if tokens.consume_maybe('elif'):
if_statement.else_body = parse_if_body(tokens)
return if_statement
tokens.consume_only('end')
return if_statement<|docstring|>if_body:
| statement_list 'do' statement_list 'elif' if_body
| statement_list 'do' statement_list 'end'<|endoftext|> |
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