def main(argv):
# buffer hack
sys.stdout = Unbuffered(sys.stdout)
path = 'local/config.yml'
if len(argv) >= 1:
path = argv[0]
try:
cc.loadConfig(path)
except IOError as ioe:
print("{0}".format(ioe))
for experiment in cc.cfg['experiments']:
# load configuration into global var and run it
cc.loadExperiment(experiment)
if cc.cfg['model'] == 'rnn':
if cc.cfg['grid']:
# REMOVEME: hardcoded grid for ratio
grid = [
[1, 1, 1],
# [1,1,2],
# [1,2,1],
# [2,1,1],
# [1,2,2],
# [2,1,2],
[2, 2, 1]
]
cc.exp['grid'] = {}
import rnn.rnn
reload(rnn.rnn)
comment = '[GRID][RATIO={}][A549][TDGRUGRU] performing grid search for ratio'
for ratios in grid:
cc.exp['params']['rnn']['comment'] = comment.format(
':'.join([str(x) for x in ratios]))
cc.exp['grid']['ratios'] = ratios
print(cc.cfg, cc.exp)
rnn.rnn.run()
else:
import rnn.rnn
reload(rnn.rnn)
print(cc.cfg, cc.exp)
rnn.rnn.run()
elif cc.cfg['model'] == 'dnn':
import rnn.dnn
reload(rnn.dnn)
print(cc.cfg, cc.exp)
rnn.dnn.run()
else:
raise Exception('Run: unknown model')
def initConfigs(self):
self.configs = {}
self.configs["wf"] = loadConfig("wf")
self.configs["sc"] = dict([(k,
dict([(int(kk), vv)
for kk, vv in v.items()]))
for k, v in loadConfig("sc").items()])
def main(argv):
# buffer hack
sys.stdout = Unbuffered(sys.stdout)
path = 'local/config.yml'
if len(argv) >= 1:
path = argv[0]
try:
cc.loadConfig(path)
except IOError as ioe:
print("{0}".format(ioe))
for experiment in cc.cfg['experiments']:
# load configuration into global var and run it
cc.loadExperiment(experiment)
if cc.cfg['model'] == 'rnn':
if cc.cfg['grid']:
# REMOVEME: hardcoded grid for ratio
grid = [
[1,1,1],
# [1,1,2],
# [1,2,1],
# [2,1,1],
# [1,2,2],
# [2,1,2],
[2,2,1]
]
cc.exp['grid'] = {}
import rnn.rnn
reload(rnn.rnn)
comment = '[GRID][RATIO={}][A549][TDGRUGRU] performing grid search for ratio'
for ratios in grid:
cc.exp['params']['rnn']['comment'] = comment.format(':'.join([str(x) for x in ratios]))
cc.exp['grid']['ratios'] = ratios
print(cc.cfg,cc.exp)
rnn.rnn.run()
else:
import rnn.rnn
reload(rnn.rnn)
print(cc.cfg,cc.exp)
rnn.rnn.run()
elif cc.cfg['model'] == 'dnn':
import rnn.dnn
reload(rnn.dnn)
print(cc.cfg,cc.exp)
rnn.dnn.run()
else:
raise Exception('Run: unknown model')
def main():
"""
===========================================================================
logmappper-agent **Main** function
===========================================================================
Aqui un ejemplo de documentacion
Formatos: *cursiva*
``code = True``
**Args**:
* config: configuration object
**Returns**:
None
"""
args = processArguments()
config = cfg.loadConfig(args.configfilename, args.resetconfig)
logMapperAgentConfig = cfg.loadLogMapperAgentConfig(config)
logging_util.configureLogger(logMapperAgentConfig.logFilePath)
logger.info("Start LogMapper Agent")
cfg.printConfig(config)
control.initApplication(config)
control.startApplicationTask(config)
control.mainLoop(config)
control.stopApplicationTask(config)
logger.info("Finish LogMapper Agent")
def cacheBuiltin():
global builtin
builtin = {}
commandList = config.loadConfig("src/lib/builtin_commands.json")['commands']
for c in commandList:
builtin[c['command']] = createCommand(c)
return builtin
def main(argv):
fileConfig = "config.json"
try:
opts, args = getopt.getopt(argv, "vhc:", ["version", "help", "config="])
if opts != None and args != None:
for opt, arg in opts:
if opt in ("-v", "--version"):
print info.botabout()
sys.exit()
elif opt in ("-h", "--help"):
print help_message
sys.exit()
elif opt in ("-c", "--config"):
fileConfig = arg
except getopt.GetoptError:
print help_message
sys.exit(2)
print " Starting up {0}".format(info.botaboutshort())
print "==========================="
print "Using '{0}' as the configuration file...\n".format(fileConfig)
config = loadConfig(fileConfig)
commandcore.cacheBuiltin()
general = generalConfig(config)
server = serverConfig(config)
channels = channelcore.loadChannels(config)
bots = {}
for c in channels.values():
bots[c.name] = ChatBot(general, server, c)
thread.start_new_thread(bots[c.name].run, ())
while True:
time.sleep(1)
"""
readers = cfg.getReaders(config)
for readerName in readers:
readerConfig = cfg.loadReaderConfig(config, readerName)
if readerConfig.enable:
mapperThread = mapper.MapperThread(readerConfig, th.OperationMode.NORMAL)
mapperThread.start()
def startRegister(config):
agentConfig = cfg.loadLogMapperAgentConfig(config)
j = get.getAgent(config)
r = ds.saveData(agentConfig.masterHost, agentConfig.masterPort, lmkey.DATATYPE_AGENT, j)
return str(r)
#%%
if __name__ == '__main__':
print('Start module execution:')
logging.basicConfig(level=logging.DEBUG, format='%(asctime)s - %(levelname)s - %(message)s', datefmt='%H:%M:%S')
cfg.createDefaultConfigfile()
config=cfg.loadConfig()
commandDefinition = StartCommand("start", "sta", "Help")
commandDefinition.parseArgs("start register")
response = commandDefinition.execute(config)
print(str(response))
print("End module execution")
import db
import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from rdkit import Chem
from rdkit.Chem import Descriptors
from sklearn.feature_selection import VarianceThreshold
import pylab
from config import config as cc
cc.loadConfig('../local/config.yml')
# data = db.getTarget_206_1977()
# data = db.getTarget_206_1977_features_wide()
# data = db.getTarget_geminin()
# data = db.getTarget_a549()
data = db.getTarget_206_1977_features_computed()
'''
duplicates = {}
for datum in data:
if datum[0] in duplicates:
duplicates[datum[0]].append(datum[1])
else:
duplicates[datum[0]] = [datum[1]]
#! /usr/bin/env python
import sys
sys.path.insert(0, '../')
from config import config as cc
cc.loadConfig('../local/config.yml')
import db.db as db
import pandas as pd
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import MACCSkeys
from sets import Set
LELIMIT = 10000
SICHO_RIPTORS = Set(['MinAbsPartialCharge','HeavyAtomMolWt','MaxAbsPartialCharge','MinAbsEStateIndex','Chi3n','HallKierAlpha','PEOE_VSA1','PEOE_VSA10','PEOE_VSA11','PEOE_VSA12','PEOE_VSA13','PEOE_VSA14','PEOE_VSA2','PEOE_VSA3','PEOE_VSA6','PEOE_VSA8','PEOE_VSA9','SMR_VSA1','SMR_VSA10','SMR_VSA3','SMR_VSA6','SMR_VSA9','SlogP_VSA10','SlogP_VSA3','SlogP_VSA4','SlogP_VSA6','TPSA','EState_VSA3','EState_VSA5','EState_VSA7','EState_VSA8','VSA_EState9','NHOHCount','NumAliphaticHeterocycles','NumAromaticHeterocycles','MolLogP','fr_Ar_COO','fr_C_O','fr_Imine','fr_NH1','fr_Ndealkylation2','fr_amide','fr_aryl_methyl','fr_ester','fr_ether','fr_furan','fr_imidazole','fr_methoxy','fr_piperzine','fr_pyridine','fr_sulfide','fr_thiazole','fr_urea'])
DOWNLOAD_TABLE = 'output.stitch_120ls_400lf_907d'
DOWNLOAD_COLS = ['smiles']
DOWNLOAD_QUERY = 'SELECT distinct {} FROM {} LIMIT {} OFFSET {}'
SEND_TABLE = 'output.stitch_smiles_maccs'
# DOWNLOAD_TABLE = 'output.target_geminin_deduplicated'
# DOWNLOAD_COLS = ['molregno','canonical_smiles','is_testing','standard_value_min','standard_value_max','standard_value_count','standard_value_std','standard_value_relative_std','standard_value_median']
# SEND_TABLE = 'output.target_geminin_deduplicated_rdkit_maccs'