def get_prices_from_google(item_name):
# Search for
MAGIC_WORD = "price"
# Connect to Google
browser = mechanicalsoup.StatefulBrowser()
browser.open("https://www.google.com/")
# Fill-in the form
browser.select_form('form[action="/search"]')
browser["q"] = item_name + " " + MAGIC_WORD
WEB_AGENT_NAME = "btnG"
resp = browser.submit_selected(btnName=WEB_AGENT_NAME)
item = resp.soup.find_all("div")
print("Searcing for:", item_name)
price_list = []
# sleep in order to prevent Google bot detection
time.sleep(1)
for it in item:
res = find_price_of_item(it.text)
print(it.text)
if res:
price_list.append(res)
print(price_list)
if price_list:
price = structure(mean(price_list), max(price_list), min(price_list))
return price
else:
return status.FAILURE
def report_opt_results(self):
mf = structure(self.hf_model, self.n, self.mf_opt.x, self.EI_req)
self.results['mf score'] = mf.score
self.results['mf mass'] = mf.mass
self.results['mf EI'] = mf.EI
self.results['mf equiv score'] = mf.equiv_score
self.results['mf equiv EI'] = mf.equiv_EI
hf = structure(self.hf_model, self.n, self.hf_opt.x_opt, self.EI_req)
self.results['hf score'] = hf.score
self.results['hf mass'] = hf.mass
self.results['hf EI'] = hf.EI
self.results['hf equiv score'] = hf.equiv_score
self.results['hf equiv EI'] = hf.equiv_EI
lf = structure(self.hf_model, self.n, self.lf_opt.x_opt, self.EI_req)
self.results['lf score'] = lf.score
self.results['lf mass'] = lf.mass
self.results['lf EI'] = lf.EI
self.results['lf equiv score'] = lf.equiv_score
self.results['lf equiv EI'] = lf.equiv_EI
def init(data=[], files=globe.dic['files'], replot=globe.dic['replots']):
dic = globe.dic
for i, filename in enumerate(files):
if dic['Verbose'] > 0:
print "loading", filename
sys_err = dic['sys_err_default']
if len(filename.split('#')) == 2:
sys_err = float(filename.split('#')[1].strip())
filename = filename.split('#')[0].strip()
if dic['outputs']:
output = dic['outputs'].pop()
else:
output = '.'.join(filename.split('.')[:-1])
dic['numbered'] = 0
# Now read data file
blocks = make_blocks(read_data(filename))
if blocks:
for j, b in enumerate(blocks):
if dic['GroupBy'] == 'files':
data.append([[i, j], filename, output, b, sys_err])
elif dic['GroupBy'] == 'blocks':
data.append([[j, i], filename, output, b, sys_err])
data.sort(key=lambda x: x[0])
data = structure(data)
for i, filename in enumerate(replot):
if dic['Verbose'] > 0:
print "reloading data from", filename
if len(filename.split('#')) == 2:
filename = filename.split('#')[0].strip()
data = data + reload_plot(filename)
return data
def __init__(self, string_representation): self.structure = structure( string_representation )
from sklearn.model_selection import train_test_split
from structure import structure
from preprocess import create_dataset
from model import Model
if __name__ == "__main__":
print("Downloading files")
structure()
print("Creating dataset")
X, y = create_dataset()
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.05)
model = Model()
model.fit(
X_train, y_train,
X_test, y_test,
early=4,
epoches=50
)
def main():
recipe_file = "recipes/earth.json"
params.get_params('params/params.ini', recipe_file)
structure.structure(6371000.0)
from funcoesTermosol import importa, plota, geraSaida
from knot import knot
from element import element
from structure import structure
import numpy as np
[knot_numbers, knot_coordinates, element_numbers, incidence, load_numbers, forces, restriction_numbers, restriction] = importa('entry.xlsx')
knot_list = []
element_list = []
for i in range(knot_numbers):
# melhor codigo do mundo
knot_list.append(knot(knot_coordinates[0][i], knot_coordinates[1][i], [forces[2 * i], forces[2*i + 1]]))
for i in range(element_numbers):
incidence0 = (int(incidence[i][0]) - 1)*2
incidence1 = (int(incidence[i][1]) - 1)*2
element_list.append(element(incidence[i][2], incidence[i][3], [knot_list[int(incidence[i][0]) - 1], knot_list[int(incidence[i][1]) - 1]], [[incidence0, incidence0 + 1], [incidence1, incidence1 + 1]]))
object_structure = structure(element_list, knot_numbers, restriction, element_numbers)
geraSaida(object_structure.reaction, object_structure.u_vector, object_structure.deformation, object_structure.internal_force, object_structure.tension)
def interactive_plot(data=None, load=None):
"""Interactive Mode!"""
dic = globe.dic
command = True
history = []
if not load:
files = dic['files']
mode = choose_from('load all data to plots?',
['n', 'y'],
default='y',
info=['the initial plots list will be empty and the user will create plots individually from loaded data',
'all of the data loaded will be grouped into plots as they would be in the non-interactive mode'])
if mode == 'n':
mode = 's'
plots = [[]]
elif mode == 'y':
mode = 'a'
if not dic['MULTIP']:
# multiplot flag not give, group plots by file, then block
l = lambda x: '-'.join(map(str, x))
groups = [[d for d in data if l(d[0][:2]) == f]
for f in set([l(x[0][:2]) for x in data])]
else:
groups = [data[(i * dic['MULTIP']):((i + 1) * dic['MULTIP'])]
for i in range((len(data) / dic['MULTIP']) + 1)]
plots = groups
# interact(**{'dic': dic, 'data': data, 'plots': plots})
else:
data, plots, history, mode = load
if mode == 's':
default = 'a'
if mode == 'a':
default = 'g'
blocks = list(set([x[1] + '_' + str(x[0][1]) for x in data]))
while command:
print '#=====================#'
print ['%d: %s cols by %d rows' % (i + 1, len(p), len(p[0][6]))
for i, p in enumerate(plots) if p and p[0]]
command = choose_from('?',
['!', 'g', 'G', 'f', 'a', 'd', 's', 'q'],
default=default,
info=['drops user into an interactive python shell',
'generates plots without writing them to file',
'generates plots, writes them to file, then exits',
'load new data from file',
'add data to current plots, or add data to new plot',
'delete data from plots, or delete entire plots',
'enter plot point/line style',
'exit'])
history.append(command)
if command == '!':
interact(**{'dic': dic, 'data': data, 'plots': plots})
elif command == 'g':
if mode == 'a':
for p in plots:
clplot(p)
elif mode == 's':
if len([p for p in plots if p]) > 1:
for p in plots:
c = choose_from('Plot %d: %s cols by %d rows ?' % (i + 1, len(p), len(p[0][6])),
['y', 'n'],
default='y')
if c == 'y':
clplot(p)
elif len([p for p in plots if p]) == 1:
clplot(plots[0])
elif command == 'G':
dic['interactive'] = False
if mode == 'a':
clplot(data)
elif mode == 's':
if len([p for p in plots if p]) > 1:
for p in plots:
c = choose_from('Plot %d: %s cols by %d rows ?' % (i + 1, len(p), len(p[0][6])),
['y', 'n'],
default='y')
if c == 'y':
clplot(p)
elif len([p for p in plots if p]) == 1:
clplot(plots[0])
sys.exit(1)
elif command == 'f':
new_file = raw_input('file to load: ').strip()
if os.path.isfile(new_file):
files.append(new_file)
data += structure(init(files=[new_file]))
blocks = list(set([x[1] + '_' + str(x[0][1]) for x in data]))
elif command == 'a':
print 'adding data to plot'
print 'select file:'
for i, f in enumerate(files):
n_b = len(set([' '.join(map(str, x[0][:2]))
for x in data if x[1] == f]))
print '%d- file: %s [# blocks = %d]' % (i + 1, f, n_b)
f_choice = int(choose_from("selection",
map(str,
range(1, 1 + len(files))),
default='1')) - 1
blocks = list(set([' '.join([x[1], 'block:', str(x[0][1] + 1)]) for
x in data if x[1] == files[int(f_choice)]]))
blocks.sort(key=lambda x: x.split(' ')[-1])
print '-------------'
print 'file %s' % (files[int(f_choice)])
print 'select block:'
for i, b in enumerate(blocks):
n_c = len(set([' '.join(map(str, x[0])) for x in data if
' '.join([x[1], 'block:', str(x[0][1] + 1)]) == b]))
n_r = len([x for x in data if ' '.join([x[1], 'block:', str(x[0][1] + 1)]) == b][0][6])
print '%d- [# cols = %d, # rows = %d]' % (i + 1, n_c, n_r)
choice = int(choose_from("selection",
map(str,
range(1, 1 + len(blocks))),
default='1')) - 1
cols = [d for d in data
if ' '.join([d[1], 'block:', str(d[0][1] + 1)]) ==
blocks[choice]]
print '-------------'
print 'file %s' % (files[int(f_choice)])
print 'block %d- [# cols = %d, # rows = %d]' % (choice + 1, len(cols), len(cols[0][6]))
print 'select columns:'
for i, d in enumerate(cols):
print '%d- col: %d [len %d title: %s]' % (i + 1, d[0][1] + 1, len(d[6]), d[4])
choices = choose_multiple("selections",
range(1, 1 + len(cols)),
default='1')
print '-------------'
if choices == map(str, range(1, 1 + len(cols))):
print 'adding all columns as plot'
if not plots[-1]:
plots[-1] = cols
else:
plots.append(cols)
choices = []
for choice in choices:
print choice
good = False
if check_type(choice) == 'num':
size = len(cols[int(choice) - 1][6])
choice = int(choice) - 1
if not plots[0]:
print 'No plots, starting new plot'
plots[0].append(cols[choice])
good = True
elif len([p for p in plots if p and len(p[0]) > 6
and len(p[0][6]) == size]) > 1:
# print size, [len(p[0][6]) for p in plots]
print 'Multiple plots of an appropriate dimension have',
print 'been found'
opts = [p for p in plots if p[6] == size]
for i, o in enumerate(opts):
print i, ':', o
c = choose_from("select one ('n' for new)",
map(str, range(1, 1 + len(opts))) + ['n'],
default='1')
if check_type(c) == 'num':
plots[plots.index(opts[int(c) - 1])].append(cols[choice])
good = True
elif len([p for p in plots if p and len(p[0]) > 6
and len(p[0][6]) == size]) == 1:
# print size, [len(p[0][6]) for p in plots]
print 'One plot has been found with the appropriate',
print 'dimension.'
new = choose_from('start new plot? (y/n)',
['y', 'n'],
default='n')
if new == 'n':
plots[plots.index([p for p in plots if p
and len(p[0]) > 6
and len(p[0][6]) == size][0]
)].append(cols[int(choice)])
good = True
else:
print 'no plot of appropriate dimension has been found.'
if not good:
print 'starting new plot'
plots.append([cols[int(choice)]])
blocks = list(set([x[1] + '_' + str(x[0][1]) for x in data]))
elif command == 'd':
if len(plots) > 1:
print 'select plots:'
for i, p in enumerate(plots):
# print p
print '%d- %s cols by %d rows' % (i + 1, len(p), len(p[0][6]))
choices = choose_multiple("selection",
range(1, 1 + len(plots)),
default='1')
else:
choices = ['0']
done = choose_from("delete plots:[%s] ('n' to select columns)?" % ', '.join(choices),
['y', 'n'],
default='n')
choices = map(int, choices)
if done == 'y':
for c in choices:
del(plots[c])
else:
for c in choices:
print 'plot %s' % (c)
print 'columns:'
for i, d in enumerate(plots[choice]):
print '%d- file: %s block: %d col: %d [len %d title: %s]' % (i + 1, d[1], d[0][0] + 1, d[0][1] + 1, len(d[6]), d[4])
choice2 = int(choose_from("selection",
map(str,
range(1, 1 + len(plots[choice]))),
default='1')) - 1
s = choose_from('delete?', ['y', 'n'], default='n')
if s == 'y':
del(plots[choice][choice2])
elif command == 's':
dic['Ustyle'] = [raw_input('style: ')] + dic['Ustyle']
elif command == 'q':
if dic['SavePrompt']:
save = choose_from('save?', ['y', 'n'], default='y')
if save == 'y':
default = dic['DefaultSave']
fname = raw_input('filename? [%s]: ' % (default)) or default
pickle.dump((data, plots, history, mode), open(fname, 'w'))
sys.exit(1)
def main():
"""A Python program that takes a file or list of filesand creates plots of
the data."""
dic = globe.dic
read_flags()
if dic['interactive']:
if dic['LoadFromSavePrompt']:
load = choose_from('load saved state?',
['y', 'n'],
default='n',
info=['user can load options, data, and plots from previous session',
'data will be loaded from scratch'])
if load == 'y':
default = dic['DefaultSave']
fname = raw_input('filename? [%s]: ' % (default)) or default
print 'loading from saved state, not loading files from',
print 'command line arguments'
interactive_plot(load=pickle.load(open(fname, 'r')))
return
data = init()
interactive_plot(data=data)
else:
data = init()
clplot(data)
if __name__ == '__main__':
main()
def f_lf(X):
return(structure(self.lf_model, self.n, X[0], self.EI_req).score)
def parseatom(self, line, hetatm=None):
"""
#
# Parse a single ATOM line
#"""
import typecheck, string, structure
G = structure.structure()
#
# This routine parses every atom line and stores it in self.atomlinedefs
#
self.linenumber = self.linenumber + 1
#
# Check the atomnumber
#
atomnumber = line[6:11]
if typecheck.isint(atomnumber):
atomnumber = string.atoi(atomnumber)
else:
print '\nAtom number:', atomnumber
raise ParseAtomError, 'Non-int in atonnumber'
#
# All we now about the atomname is that it must contain a nondigit character
#
atomname = string.strip(line[12:16])
if not typecheck.containsletter(atomname):
raise ParseAtomError, 'Atom name does not contain a character: %s,\nLINE: %s' % (
atomname, line)
#
# Also the residuename must contain a letter
#
residuename = string.strip(line[17:21])
if not typecheck.containsletter(residuename):
print '\nResidue name:', residuename
raise ParseAtomError, 'Residuename does not contain a character'
# ---------------------/------------------------------------------
#
# The ChainID must be a letter, a blank or a digit
#
if self.NMRmodel is False or self.readmodels == 1 or self.ignore_NMRmodel:
chainid = line[21]
else:
chainid = '%d_%s' % (self.NMRmodel, line[21])
#
# Check the chainID
#
if not typecheck.containsletter(
chainid) and chainid != ' ' and not typecheck.isint(chainid):
print '\nChainID', chainid
raise ParseAtomError, 'Chain ID must be a letter,blank or digit'
else:
chainid = string.strip(chainid)
#print 'Chainid: %s' %chainid
newchainid = chainid
#
# Check that we are still building the same chain
#
if not self.chains.has_key(chainid):
for cid in self.chains.keys():
if self.chains[cid] == 'building' or (
self.oldchainid != newchainid
and self.chains[cid] == 'building - dummy'):
self.chains[cid] = 'terminated'
self.chains[chainid] = 'building'
else:
if self.chains[chainid] != 'building':
fail = 1
if chainid == '':
#
# Find a new chainid
#
for cid in self.chains.keys():
if self.chains[cid] == 'building - dummy':
chainid = cid
fail = None
break
if chainid == '':
for cid in self.useids:
if not self.chains.has_key(cid):
self.chains[cid] = 'building - dummy'
chainid = cid
fail = None
break
if fail:
for cid in self.chains.keys():
if self.chains[
cid] == 'building - dummy' and self.oldchainid == newchainid:
chainid = cid
fail = None
break
if fail:
for cid in self.useids:
if not self.chains.has_key(cid):
self.chains[cid] = 'building - dummy'
chainid = cid
fail = None
break
if fail:
print self.chains.keys()
raise ProtoolError, 'I ran out of alternative chain ID names'
self.oldchainid = newchainid
# -------------------------------------------------------------------------------------
#
# Check the residuenumber
#
residuenumber = line[22:27]
done = False
suffix = ''
while not done:
if typecheck.isint(residuenumber):
residuenumber = string.zfill(string.atoi(residuenumber),
G.length_of_residue_numbers)
residuenumber = residuenumber + suffix
done = True
else:
suffix = residuenumber[-1] + suffix
residuenumber = residuenumber[:-1]
#
# Get and check the coordinates
#
if len(line) < 54:
xcoord = None
ycoord = None
zcoord = None
else:
xcoord = line[30:38]
ycoord = line[38:46]
zcoord = line[46:54]
if not typecheck.isnumber(xcoord) or not typecheck.isnumber(
ycoord) or not typecheck.isnumber(zcoord):
print '\nX,Y,Z', xcoord, ycoord, zcoord
raise ParseAtomError, 'All coordinates must be numbers'
else:
xcoord = string.atof(xcoord)
ycoord = string.atof(ycoord)
zcoord = string.atof(zcoord)
#
# Get the occupancy
#
if len(line) < 60:
print '\nNo occupancy for this line'
occupancy = None
else:
occupancy = line[55:60]
if not typecheck.isnumber(occupancy):
print '\nOccupancy:', occupancy
raise ParseAtomError, 'Occupancy is not a number'
else:
occupancy = string.atof(occupancy)
#
# Get the B-factor
#
if len(line) < 66:
print '\nNo B-factor for this atom', line
bfactor = None
else:
bfactor = line[60:66]
if not typecheck.isnumber(bfactor):
print 'B-factor:', bfactor
bfactor = None
else:
bfactor = string.atof(bfactor)
#
# Put the rest of the line in a junk array
#
if len(line) > 66:
junk = line[66:]
else:
junk = None
#
# Finally put everything in self.atomlinedefs
#
self.atomlinedefs[self.linenumber] = {'NUMBER': atomnumber}
self.atomlinedefs[self.linenumber]['ATNAME'] = atomname
self.atomlinedefs[self.linenumber]['CHAINID'] = chainid
self.atomlinedefs[self.linenumber]['RESNAME'] = residuename
self.atomlinedefs[self.linenumber]['RESNUM'] = residuenumber
if xcoord != None:
self.atomlinedefs[self.linenumber]['X'] = xcoord
self.atomlinedefs[self.linenumber]['Y'] = ycoord
self.atomlinedefs[self.linenumber]['Z'] = zcoord
if occupancy or occupancy == 0.0:
self.atomlinedefs[self.linenumber]['OCCUPANCY'] = occupancy
if bfactor or bfactor == 0.0:
self.atomlinedefs[self.linenumber]['B-FACTOR'] = bfactor
if hetatm:
self.atomlinedefs[self.linenumber]['HETATM'] = 1
if junk:
#
# This is a tag
#
import string
self.atomlinedefs[self.linenumber]['tag'] = string.strip(junk)
#
# What is this atom bound to?
#
self.atomlinedefs[self.linenumber]['BOUND_TO'] = []
return
