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
if username == 'webuser' or password == '':
print('need username and password to load compounds')
failed = True
if not project:
print('need project to upload compounds')
failed = True
if not initial:
print('need initial to upload compounds')
failed = True
if failed:
sys.exit()
#check db
conn = mysql.connect2server(password, username, 'purchasable')
cursor = conn.cursor()
if load:
#check project
command = 'select unique_compounds, supplier_info_table, supplier_table from projects where project = "' + project + '"'
#print (command)
cursor.execute(command)
results = cursor.fetchall()
if len(results) == 0:
print('project not valid')
conn.close()
sys.exit(1)
conn.close()
path_cpd_upload = path.replace(