def run_subs_query(subs):
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi,
rhs_smi.cmpd_size-context_table.context_size
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
core_table rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s""" % (subs,max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
#make sure it is not the same core on both sides
if(r[2] != r[5]):
#cansmirk
smirks,context = cansmirk(str(r[2]),str(r[5]),str(r[6]))
if(have_id):
print "%s,%s,%s,%s,%s,%s,%s,%s" % (subs,id,r[0],r[3],r[1],r[4],smirks,context)
else:
print "%s,%s,%s,%s,%s,%s,%s" % (subs,r[0],r[3],r[1],r[4],smirks,context)
def run_subs_query(subs):
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi,
rhs_smi.cmpd_size-context_table.context_size
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
core_table rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s""" % (subs, max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
#make sure it is not the same core on both sides
if (r[2] != r[5]):
#cansmirk
smirks, context = cansmirk(str(r[2]), str(r[5]), str(r[6]))
if (have_id):
print("%s,%s,%s,%s,%s,%s,%s,%s" % (subs, id, r[0], r[3], r[1], r[4], smirks, context))
else:
print("%s,%s,%s,%s,%s,%s,%s" % (subs, r[0], r[3], r[1], r[4], smirks, context))
def run_trans_smarts_query(transform):
lhs,rhs = transform.split(">>")
matching_lhs = []
matching_rhs = []
#set os enviroment for rdkit to use sqllite
os.environ['RD_USESQLLITE'] = '1'
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent" % (pre,lhs)
p1 = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
output = p1.communicate()[0].rstrip()
matching_lhs=output.split("\n")
#sys.stderr.write("rhs: %s\n" % (len(matching_lhs)) )
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent" % (pre,rhs)
p1 = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
output = p1.communicate()[0].rstrip()
matching_rhs=output.split("\n")
#sys.stderr.write("rhs: %s\n" % (len(matching_rhs)) )
#sys.stderr.write('SQLlite method\n')
lhs_q_string = "','".join(matching_lhs)
lhs_q_string = "'%s'" % (lhs_q_string)
rhs_q_string = "','".join(matching_rhs)
rhs_q_string = "'%s'" % (rhs_q_string)
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni in (%s) ) lhs,
(select cmpd_id,core_smi,context_id from core_table where core_smi_ni in (%s) ) rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s
and lhs_smi.cmpd_size-context_table.context_size <= %s """ % (lhs_q_string,rhs_q_string,max_size,max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
smirks,context = cansmirk(str(r[2]),str(r[5]),str(r[6]))
if(have_id):
print "%s,%s,%s,%s,%s,%s,%s,%s" % (transform,id,r[0],r[3],r[1],r[4],smirks,context)
else:
print "%s,%s,%s,%s,%s,%s,%s" % (transform,r[0],r[3],r[1],r[4],smirks,context)
def run_subs_smarts_query(subs_smarts):
#set os enviroment for rdkit to use sqllite
os.environ['RD_USESQLLITE'] = '1'
temp_core_ni_file = 'temp_core_ni_file_%s' % (os.getpid())
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent >%s" % (
pre, subs_smarts, temp_core_ni_file)
subprocess.Popen(cmd, shell=True).wait()
infile = open(temp_core_ni_file, 'r')
for row in infile:
row = row.rstrip()
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi,
rhs_smi.cmpd_size-context_table.context_size
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
core_table rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s
and lhs_smi.cmpd_size-context_table.context_size <= %s""" % (
row, max_size, max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
#cansmirk
smirks, context = cansmirk(str(r[2]), str(r[5]), str(r[6]))
if (have_id):
print("%s,%s,%s,%s,%s,%s,%s" %
(id, r[0], r[3], r[1], r[4], smirks, context))
else:
print("%s,%s,%s,%s,%s,%s" %
(r[0], r[3], r[1], r[4], smirks, context))
infile.close()
#remove temporary files
os.unlink(temp_core_ni_file)
def run_subs_smarts_query(subs_smarts):
#set os enviroment for rdkit to use sqllite
os.environ['RD_USESQLLITE'] = '1'
temp_core_ni_file = 'temp_core_ni_file_%s' % (os.getpid())
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent >%s" % (
pre, subs_smarts, temp_core_ni_file)
subprocess.Popen(cmd, shell=True).wait()
infile = open(temp_core_ni_file, 'r')
for row in infile:
row = row.rstrip()
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi,
rhs_smi.cmpd_size-context_table.context_size
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
core_table rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s
and lhs_smi.cmpd_size-context_table.context_size <= %s""" % (row, max_size,
max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
#cansmirk
smirks, context = cansmirk(str(r[2]), str(r[5]), str(r[6]))
if (have_id):
print("%s,%s,%s,%s,%s,%s,%s" % (id, r[0], r[3], r[1], r[4], smirks, context))
else:
print("%s,%s,%s,%s,%s,%s" % (r[0], r[3], r[1], r[4], smirks, context))
infile.close()
#remove temporary files
os.unlink(temp_core_ni_file)
def run_trans_query(transform):
lhs, rhs = transform.split(">>")
#remove connectivity info
lhs_ni = remove_numbers(lhs)
rhs_ni = remove_numbers(rhs)
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
(select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id""" % (lhs_ni, rhs_ni)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
smirks, context = cansmirk(str(r[2]), str(r[5]), str(r[6]))
#make sure connectivity is correct
if (smirks == transform):
if (have_id):
print("%s,%s,%s,%s,%s,%s,%s" %
(id, r[0], r[3], r[1], r[4], smirks, context))
else:
print("%s,%s,%s,%s,%s,%s" %
(r[0], r[3], r[1], r[4], smirks, context))
def run_trans_query(transform):
lhs,rhs = transform.split(">>")
#remove connectivity info
lhs_ni = remove_numbers(lhs)
rhs_ni = remove_numbers(rhs)
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') lhs,
(select cmpd_id,core_smi,context_id from core_table where core_smi_ni = '%s') rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id""" % (lhs_ni,rhs_ni)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
smirks,context = cansmirk(str(r[2]),str(r[5]),str(r[6]))
#make sure connectivity is correct
if(smirks == transform):
if(have_id):
print "%s,%s,%s,%s,%s,%s,%s" % (id,r[0],r[3],r[1],r[4],smirks,context)
else:
print "%s,%s,%s,%s,%s,%s" % (r[0],r[3],r[1],r[4],smirks,context)
def run_trans_smarts_query(transform):
lhs, rhs = transform.split(">>")
matching_lhs = []
matching_rhs = []
#set os enviroment for rdkit to use sqllite
os.environ['RD_USESQLLITE'] = '1'
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent" % (
pre, lhs)
p1 = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
output = p1.communicate()[0].rstrip()
matching_lhs = output.split("\n")
#sys.stderr.write("rhs: %s\n" % (len(matching_lhs)) )
cmd = "python $RDBASE/Projects/DbCLI/SearchDb.py --dbDir=%s_smarts --smarts='%s' --silent" % (
pre, rhs)
p1 = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
output = p1.communicate()[0].rstrip()
matching_rhs = output.split("\n")
#sys.stderr.write("rhs: %s\n" % (len(matching_rhs)) )
#sys.stderr.write('SQLlite method\n')
lhs_q_string = "','".join(matching_lhs)
lhs_q_string = "'%s'" % (lhs_q_string)
rhs_q_string = "','".join(matching_rhs)
rhs_q_string = "'%s'" % (rhs_q_string)
query_sql = """
select lhs_smi.smiles,
lhs.cmpd_id,
lhs.core_smi,
rhs_smi.smiles,
rhs.cmpd_id,
rhs.core_smi,
context_table.context_smi
from (select cmpd_id,core_smi,context_id from core_table where core_smi_ni in (%s) ) lhs,
(select cmpd_id,core_smi,context_id from core_table where core_smi_ni in (%s) ) rhs,
cmpd_smisp lhs_smi,
cmpd_smisp rhs_smi,
context_table
where lhs.context_id = rhs.context_id
and context_table.context_id = rhs.context_id
and lhs_smi.cmpd_id = lhs.cmpd_id
and rhs_smi.cmpd_id = rhs.cmpd_id
and lhs.cmpd_id != rhs.cmpd_id
and rhs_smi.cmpd_size-context_table.context_size <= %s
and lhs_smi.cmpd_size-context_table.context_size <= %s """ % (
lhs_q_string, rhs_q_string, max_size, max_size)
cursor.execute(query_sql)
results = cursor.fetchall()
for r in results:
smirks, context = cansmirk(str(r[2]), str(r[5]), str(r[6]))
if (have_id):
print("%s,%s,%s,%s,%s,%s,%s,%s" %
(transform, id, r[0], r[3], r[1], r[4], smirks, context))
else:
print("%s,%s,%s,%s,%s,%s,%s" %
(transform, r[0], r[3], r[1], r[4], smirks, context))
id = line_fields[1]
lhs, rhs = smirks.split(">>")
l = Chem.MolFromSmiles(lhs)
if (l == None):
sys.stderr.write("Can't generate mol for: %s\n" % (lhs))
continue
r = Chem.MolFromSmiles(rhs)
if (r == None):
sys.stderr.write("Can't generate mol for: %s\n" % (rhs))
continue
clhs = Chem.MolToSmiles(l, isomericSmiles=True)
crhs = Chem.MolToSmiles(r, isomericSmiles=True)
#just need to take care of [*H:1]
if (clhs == '[*H:1]'):
clhs = '[*:1][H]'
if (crhs == '[*H:1]'):
crhs = '[*:1][H]'
#print clhs
#print crhs
csmirk, context = cansmirk(clhs, crhs, "")
print("%s %s" % (csmirk, id))
id = line_fields[1]
lhs, rhs = smirks.split(">>")
l = Chem.MolFromSmiles(lhs)
if (l == None):
sys.stderr.write("Can't generate mol for: %s\n" % (lhs))
continue
r = Chem.MolFromSmiles(rhs)
if (r == None):
sys.stderr.write("Can't generate mol for: %s\n" % (rhs))
continue
clhs = Chem.MolToSmiles(l, isomericSmiles=True)
crhs = Chem.MolToSmiles(r, isomericSmiles=True)
#just need to take care of [*H:1]
if (clhs == '[*H:1]'):
clhs = '[*:1][H]'
if (crhs == '[*H:1]'):
crhs = '[*:1][H]'
#print clhs
#print crhs
csmirk, context = cansmirk(clhs, crhs, "")
print("%s %s" % (csmirk, id))