def neutralize_get_rules():
conn = mysql.connect2server('', 'webuser', 'purchasable')
cursor = conn.cursor()
command = "SELECT smirks, type, pka, comment, id FROM purchasable.definition_neutralize_compounds order by id"
print command
cursor.execute(command)
rows = cursor.fetchall()
rules = []
for row in rows:
rules.append([[row[0]], row[1], float(row[2]), row[3]])
#OPENEYE has got a problem with writting [NH3+], ...
rule_counter = 0
for rule in rules:
trans_counter = 0
for transformation in rule[0]:
educt, product = transformation.split('>>')
#primary amines
product = product.replace('[NH3+]', '[N+]([H])([H])[H]')
#secundary amines
product = product.replace('[NH2+]', '[N+]([H])([H])')
#tertary amines
product = product.replace('[NH+]', '[N+]([H])')
product = product.replace('[nH+]', '[n+]([H])')
product = product.replace('[nH]', '[n]([H])')
reaction = educt + '>>' + product
#print reaction
rules[rule_counter][0][trans_counter] = reaction
trans_counter = trans_counter + 1
rule_counter = rule_counter + 1
return rules
def get_smartslist(table):
conn = mysql.connect2server('', 'webuser', 'purchasable')
cursor = conn.cursor()
rule = []
command = 'select smarts_string, name from purchasable.' + table + ' order by name'
print command
cursor.execute(command)
rules = cursor.fetchall()
for i in rules:
smarts = i[0]
name = i[1]
name = name.replace(' ', '_')
name = name.replace('-', '_')
name = name.replace('/', '_')
name = name.replace(',', '_')
name = name.replace('=', '_')
rule.append([smarts, name])
return rule
def read_rules():
conn = mysql.connect2server('', 'webuser', 'purchasable')
cursor = conn.cursor()
command = "SELECT smirks, direction, type, comment, id, kek, known_error_string FROM definition_tautomer_rules order by id"
cursor.execute(command)
rows = cursor.fetchall()
rules = []
for row in rows:
if row[2] == 'equal':
equal = True
elif row[2] == 'unequal':
equal = False
else:
print 'typo'
rules.append([[row[0]], float(row[1]), equal, row[3], row[5], row[6]])
cursor.close()
conn.close()
return rules
import string, os, sys
import my_mysql as mysql
import MySQLdb
if len(sys.argv) <> 5:
print 'mysql_load_unwanted_groups.py <username> <password> <data file> <project>'
sys.exit(1)
username = sys.argv[1]
password = sys.argv[2]
data_file = open(sys.argv[3], 'r')
project = sys.argv[4]
#-------------------------------------
conn = mysql.connect2server(password, username, 'purchasable')
cursor = conn.cursor()
#get table names
command = 'select unwanted_groups from projects where project = "' + project + '"'
print command
cursor.execute(command)
results = cursor.fetchall()
if len(results) == 0:
print 'project does not exist'
sys.exit(1)
table = results[0][0]
#get id,
size = int(sys.argv[3])
mfc_codes = sys.argv[4]
prefix_file = sys.argv[5]
out_file = open(prefix_file + '_1.smi', 'w')
print mfc_codes
if mfc_codes == 'True':
mfc_codes = True
else:
mfc_codes = False
#-------------------------------------
conn = mysql.connect2server('', 'webuser', 'purchasable')
cursor = conn.cursor()
command = query.readline()
command = command.strip()
list = []
print command
#some options from the original match.py file
usa = 1
asym = 1
exph = 0
max = 0
