def GetFingerprints(details):
""" returns an iterable sequence of fingerprints
each fingerprint will have a _fieldsFromDb member whose first entry is
the id.
"""
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
except:
import traceback
FingerprintMols.error(
'Error: Problems establishing connection to database: %s|%s\n'
% (details.dbName, details.tableName))
traceback.print_exc()
cmd = _ConstructSQL(details, extraFields=details.fpColName)
curs = conn.GetCursor()
#curs.execute(cmd)
#print 'CURSOR:',curs,curs.closed
if _dataSeq:
suppl = _dataSeq(curs,
cmd,
depickle=not details.noPickle,
klass=DataStructs.ExplicitBitVect)
_dataSeq._conn = conn
else:
suppl = DbFpSupplier.ForwardDbFpSupplier(
data, fpColName=details.fpColName)
elif details.inFileName:
conn = None
try:
inF = open(details.inFileName, 'r')
except IOError:
import traceback
FingerprintMols.error('Error: Problems reading from file %s\n' %
(details.inFileName))
traceback.print_exc()
supple = []
done = 0
while not done:
try:
id, fp = cPickle.load(inF)
except:
done = 1
else:
fp._fieldsFromDb = [id]
suppl.append(fp)
else:
suppl = None
return suppl
def ScreenInDb(details, mol):
try:
probeFp = apply(FingerprintMols.FingerprintMol, (mol, ),
details.__dict__)
except:
import traceback
FingerprintMols.error('Error: problems fingerprinting molecule.\n')
traceback.print_exc()
return []
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
except:
import traceback
FingerprintMols.error(
'Error: Problems establishing connection to database: %s|%s\n'
% (details.dbName, details.tableName))
traceback.print_exc()
if details.metric not in (DataStructs.TanimotoSimilarity,
DataStructs.DiceSimilarity,
DataStructs.CosineSimilarity):
data = GetFingerprints(details)
res = ScreenFingerprints(details, data, mol)
else:
res = []
if details.metric == DataStructs.TanimotoSimilarity:
func = 'rd_tanimoto'
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.DiceSimilarity:
func = 'rd_dice'
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.CosineSimilarity:
func = 'rd_cosine'
pkl = probeFp.ToBitString()
extraFields = "%s(%s,%s) as tani" % (func, DbModule.placeHolder,
details.fpColName)
cmd = _ConstructSQL(details, extraFields=extraFields)
if details.doThreshold:
# we need to do a subquery here:
cmd = "select * from (%s) tmp where tani>%f" % (
cmd, details.screenThresh)
cmd += " order by tani desc"
if not details.doThreshold and details.topN > 0:
cmd += " limit %d" % details.topN
curs = conn.GetCursor()
curs.execute(cmd, (pkl, ))
res = curs.fetchall()
return res
def GetFingerprints(details):
""" returns an iterable sequence of fingerprints
each fingerprint will have a _fieldsFromDb member whose first entry is
the id.
"""
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, "dbUser"):
conn.user = details.dbUser
if hasattr(details, "dbPassword"):
conn.password = details.dbPassword
except Exception:
import traceback
FingerprintMols.error(
"Error: Problems establishing connection to database: %s|%s\n" % (details.dbName, details.tableName)
)
traceback.print_exc()
cmd = _ConstructSQL(details, extraFields=details.fpColName)
curs = conn.GetCursor()
# curs.execute(cmd)
# print 'CURSOR:',curs,curs.closed
if _dataSeq:
suppl = _dataSeq(curs, cmd, depickle=not details.noPickle, klass=DataStructs.ExplicitBitVect)
_dataSeq._conn = conn
else:
suppl = DbFpSupplier.ForwardDbFpSupplier(data, fpColName=details.fpColName)
elif details.inFileName:
conn = None
try:
inF = open(details.inFileName, "r")
except IOError:
import traceback
FingerprintMols.error("Error: Problems reading from file %s\n" % (details.inFileName))
traceback.print_exc()
suppl = []
done = 0
while not done:
try:
ID, fp = cPickle.load(inF)
except Exception:
done = 1
else:
fp._fieldsFromDb = [ID]
suppl.append(fp)
else:
suppl = None
return suppl
def ScreenInDb(details, mol):
try:
probeFp = apply(FingerprintMols.FingerprintMol, (mol,), details.__dict__)
except Exception:
import traceback
FingerprintMols.error("Error: problems fingerprinting molecule.\n")
traceback.print_exc()
return []
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, "dbUser"):
conn.user = details.dbUser
if hasattr(details, "dbPassword"):
conn.password = details.dbPassword
except Exception:
import traceback
FingerprintMols.error(
"Error: Problems establishing connection to database: %s|%s\n" % (details.dbName, details.tableName)
)
traceback.print_exc()
if details.metric not in (DataStructs.TanimotoSimilarity, DataStructs.DiceSimilarity, DataStructs.CosineSimilarity):
data = GetFingerprints(details)
res = ScreenFingerprints(details, data, mol)
else:
res = []
if details.metric == DataStructs.TanimotoSimilarity:
func = "rd_tanimoto"
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.DiceSimilarity:
func = "rd_dice"
pkl = probeFp.ToBitString()
elif details.metric == DataStructs.CosineSimilarity:
func = "rd_cosine"
pkl = probeFp.ToBitString()
extraFields = "%s(%s,%s) as tani" % (func, DbModule.placeHolder, details.fpColName)
cmd = _ConstructSQL(details, extraFields=extraFields)
if details.doThreshold:
# we need to do a subquery here:
cmd = "select * from (%s) tmp where tani>%f" % (cmd, details.screenThresh)
cmd += " order by tani desc"
if not details.doThreshold and details.topN > 0:
cmd += " limit %d" % details.topN
curs = conn.GetCursor()
curs.execute(cmd, (pkl,))
res = curs.fetchall()
return res
def _ConnectToDatabase(details) -> DbConnect:
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
return conn
except Exception:
import traceback
FingerprintMols.error(f'Error: Problems establishing connection to '
f'database:{details.dbName}|{details.tableName}\n')
traceback.print_exc()
return None
