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# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code for BitEnsembles
"""
import os
import shutil
import tempfile
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import SparseBitVect
# This import is important to initialize the BitEnsemble module
from rdkit.DataStructs import BitEnsembleDb
from rdkit.DataStructs.BitEnsemble import BitEnsemble
class TestCase(unittest.TestCase):
def test1(self):
ensemble = BitEnsemble()
ensemble.SetBits([1, 11, 21, 31])
self.assertEqual(ensemble.GetNumBits(), 4)
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def test2(self):
ensemble = BitEnsemble([1, 11, 21, 31])
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def test3(self):
ensemble = BitEnsemble()
for bit in [1, 11, 21, 31]:
ensemble.AddBit(bit)
bv = SparseBitVect(100)
bv.SetBit(1)
bv.SetBit(11)
bv.SetBit(13)
score = ensemble.ScoreWithOnBits(bv)
assert score == 2, 'bad score: %d' % (score)
score = ensemble.ScoreWithIndex(bv)
assert score == 2, 'bad score: %d' % (score)
def _setupDb(self):
from rdkit.Dbase.DbConnection import DbConnect
fName = RDConfig.RDTestDatabase
if RDConfig.useSqlLite:
_, tempName = tempfile.mkstemp(suffix='sqlt')
self.tempDbName = tempName
shutil.copyfile(fName, tempName)
else: # pragma: nocover
tempName = '::RDTests'
self.conn = DbConnect(tempName)
self.dbTblName = 'bit_ensemble_test'
return self.conn
def tearDown(self):
if hasattr(self, 'tempDbName') and RDConfig.useSqlLite and os.path.exists(self.tempDbName):
try:
os.unlink(self.tempDbName)
except: # pragma: nocover
import traceback
traceback.print_exc()
def testdb1(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1, 3, 4]:
ensemble.AddBit(bit)
sigBs = [([0, 0, 0, 0, 0, 0], (0, 0, 0)),
([0, 1, 0, 1, 0, 0], (1, 1, 0)),
([0, 1, 0, 0, 1, 0], (1, 0, 1)),
([0, 1, 0, 0, 1, 1], (1, 0, 1)), ]
ensemble.InitScoreTable(conn, self.dbTblName)
for bs, tgt in sigBs:
ensemble.ScoreToDb(bs, conn)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs), 'bad number of results returned'
for i in range(len(sigBs)):
bs, tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes == tgt, 'bad bits returned: %s != %s' % (str(dbRes), str(tgt))
d = None
self.conn = None
def testdb2(self):
""" test the sig - db functionality """
conn = self._setupDb()
ensemble = BitEnsemble()
for bit in [1, 3, 4]:
ensemble.AddBit(bit)
sigBs = [([0, 0, 0, 0, 0, 0], (0, 0, 0)),
([0, 1, 0, 1, 0, 0], (1, 1, 0)),
([0, 1, 0, 0, 1, 0], (1, 0, 1)),
([0, 1, 0, 0, 1, 1], (1, 0, 1)), ]
ensemble.InitScoreTable(conn, self.dbTblName, idInfo='id varchar(10)', actInfo='act int')
for bs, tgt in sigBs:
ensemble.ScoreToDb(bs, conn, id='foo', act=1)
conn.Commit()
d = conn.GetData(table=self.dbTblName)
assert len(d) == len(sigBs), 'bad number of results returned'
for i in range(len(sigBs)):
bs, tgt = tuple(sigBs[i])
dbRes = tuple(d[i])
assert dbRes[1:-1] == tgt, 'bad bits returned: %s != %s' % (str(dbRes[1:-1]), str(tgt))
d = None
self.conn = None
if __name__ == '__main__': # pragma: nocover
unittest.main()
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