LCPQ/EMSL_Basis_Set_Exchange_Local
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New db

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This commit is contained in:
Thomas Applencourt 2015-01-09 15:44:03 +01:00
parent 5314b7b204
commit cf1e3768d7
3 changed files with 38 additions and 12 deletions
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10
EMSL_api.py
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@ -13,9 +13,9 @@ Usage:
[--db_path=db_path]
[--with_l]
[(--save [--path=path])]
EMSL_api.py get_list_formats
EMSL_api.py list_formats
EMSL_api.py create_db --db_path=db_path
--format
--format=format
[--no-contraction]
EMSL_api.py (-h | --help)
EMSL_api.py --version
@ -50,7 +50,7 @@ if __name__ == '__main__':
db_path = arguments["--db_path"]
else:
import os
db_path = os.path.dirname(sys.argv[0]) + "/db/Gausian_uk.db"
db_path = os.path.dirname(sys.argv[0]) + "/db/Gamess-us.db"
# _ _ _ ______ _
#| | (_) | | | ___ \ (_)
@ -115,7 +115,7 @@ if __name__ == '__main__':
#| | | / __| __| | _/ _ \| '__| '_ ` _ \ / _` | __/ __|
#| |___| \__ \ |_ | || (_) | | | | | | | | (_| | |_\__ \
#\_____/_|___/\__| |_| \___/|_| |_| |_| |_|\__,_|\__|___/
if arguments["get_list_formats"]:
if arguments["list_formats"]:
for i in format_dict:
print i
@ -129,7 +129,7 @@ if __name__ == '__main__':
db_path = arguments["--db_path"]
format = arguments["--format"]
if format not in format_dict:
print "Format %s doesn't exist. Run get_list_formats to get the list of formats." % (format)
print "Format %s doesn't exist. Run list_formats to get the list of formats." % (format)
sys.exit(1)
contraction = not arguments["--no-contraction"]

BIN
db/Gausian_uk.db → db/Gamess-us.db
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40
src/EMSL_utility.py
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@ -6,7 +6,17 @@ import sys
import os
import time
debug = False
debug = True
elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
with open(elt_path, "r") as f:
data = f.readlines()
dict_ele = dict()
for i in data:
l = i.split("-")
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
def cond_sql_or(table_name, l_value):
@ -118,10 +128,21 @@ class EMSL_dump:
print data
raise Exception("WARNING not DATA")
else:
data = data.replace("PHOSPHOROUS", "PHOSPHORUS")
data = data[b + 5:e].split('\n\n')
for (elt, data_elt) in zip(elts, data):
d.append((name, des, elt, data_elt))
elt_long_th = dict_ele[elt.lower()]
elt_long_exp = data_elt.split()[0].lower()
if elt_long_th == elt_long_exp:
d.append((name, des, elt, data_elt.strip()))
else:
print "th", elt_long_th
print "exp", elt_long_exp
print "abv", elt
raise Exception("WARNING not good ELEMENT")
return d
@ -139,7 +160,7 @@ class EMSL_dump:
import threading
num_worker_threads = 7
num_try_of_dwl = 2
attemps_max = 20
q_in = Queue.Queue(num_worker_threads)
q_out = Queue.Queue(num_worker_threads)
@ -150,7 +171,8 @@ class EMSL_dump:
[name, url, des, elts] = q_in.get()
url = self.create_url(url, name, elts)
for i in range(num_try_of_dwl):
attemps = 0
while attemps < attemps_max:
text = self.requests.get(url).text
try:
basis_data = self.basis_data_row_to_array(
@ -158,10 +180,14 @@ class EMSL_dump:
break
except:
time.sleep(0.1)
pass
attemps += 1
q_out.put(([name, url, des, elts], basis_data))
q_in.task_done()
try:
q_out.put(([name, url, des, elts], basis_data))
q_in.task_done()
except:
print name,url,des
raise
def enqueue():
for [name, url, des, elts] in list_basis_array: