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from collections import namedtuple
import doctest
import os.path
import unittest
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem import QED
doLong = False
TestData = namedtuple('TestData', 'lineNo,smiles,mol,expected')
dataNCI200 = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'QED', 'NCI_200_qed.csv')
dataRegression = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'QED', 'Regression_qed.csv')
def load_tests(loader, tests, ignore):
""" Add the Doctests from the module """
tests.addTests(doctest.DocTestSuite(QED, optionflags=doctest.ELLIPSIS))
return tests
class TestCase(unittest.TestCase):
def testQED(self):
self.assertEqual(QED.qed.version, '1.1.0',
msg='QED version has changed. Update the regression tests if required.')
def testNCI200(self):
for d in readTestData(dataNCI200):
self.assertAlmostEqual(QED.qed(d.mol), d.expected,
msg='QED not equal to expected in line {}'.format(d.lineNo))
# Check that adding hydrogens will not change the result
# This is currently not the case. Hydrogens change the number of rotatable bonds and the
# number of alerts.
mol = Chem.AddHs(d.mol)
self.assertAlmostEqual(QED.qed(mol), d.expected,
msg='QED not equal to expected in line {}'.format(d.lineNo))
def testRegression(self):
if not doLong:
raise unittest.SkipTest('long test')
for d in readTestData(dataRegression):
self.assertAlmostEqual(QED.qed(d.mol), d.expected,
msg='QED not equal to expected in line {}'.format(d.lineNo))
def test_properties(self):
m = Chem.MolFromSmiles('N=C(CCSCc1csc(N=C(N)N)n1)NS(N)(=O)=O')
p = QED.properties(m)
self.assertAlmostEqual(p.MW, 337.456)
self.assertAlmostEqual(p.ALOGP, -0.55833)
self.assertAlmostEqual(p.HBA, 6)
self.assertAlmostEqual(p.HBD, 5)
self.assertAlmostEqual(p.PSA, 173.33)
self.assertAlmostEqual(p.ROTB, 7)
self.assertAlmostEqual(p.AROM, 1)
self.assertAlmostEqual(p.ALERTS, 3)
p = QED.properties(Chem.AddHs(m))
self.assertAlmostEqual(p.MW, 337.456)
self.assertAlmostEqual(p.ALOGP, -0.55833)
self.assertAlmostEqual(p.HBA, 6)
self.assertAlmostEqual(p.HBD, 5)
self.assertAlmostEqual(p.PSA, 173.33)
self.assertAlmostEqual(p.ROTB, 7)
self.assertAlmostEqual(p.AROM, 1)
self.assertAlmostEqual(p.ALERTS, 3)
def test_examples(self):
# Paroxetine 0.935
self.assertAlmostEqual(QED.qed(Chem.MolFromSmiles('c1cc2OCOc2cc1OCC1CNCCC1c1ccc(F)cc1')), 0.934,
places=3)
# Leflunomide 0.929
self.assertAlmostEqual(QED.qed(Chem.MolFromSmiles('C1=NOC(C)=C1C(=O)Nc1ccc(cc1)C(F)(F)F')),
0.911, places=3)
# Clomipramine 0.779
self.assertAlmostEqual(QED.qed(Chem.MolFromSmiles('CN(C)CCCN1c2ccccc2CCc2ccc(Cl)cc21')),
0.818, places=3)
# Tegaserod 0.213
self.assertAlmostEqual(QED.qed(Chem.MolFromSmiles('CCCCCNC(=N)NN=CC1=CNc2ccc(CO)cc21')),
0.235, places=3)
def readTestData(filename):
""" Read test data from file """
with open(filename, 'r') as f:
for lineNo, line in enumerate(f, 1):
if line[0] == '#':
continue
smiles, expected = line.strip().split(',')
mol = Chem.MolFromSmiles(smiles)
if not mol:
raise AssertionError('molecule construction failed on line %d' % lineNo)
yield TestData(lineNo, smiles, mol, float(expected))
def updateTestData():
""" Update the test data. This should only be done if the method changes! """
for filename in (dataNCI200, dataRegression,):
data = list(readTestData(filename))
with open(filename, 'w') as f:
print('# Test data for QED descriptor', file=f)
for d in data:
expected = QED.qed(d.mol)
print('{0.smiles},{1}'.format(d, expected), file=f)
if __name__ == '__main__': # pragma: nocover
import argparse
import sys
parser = argparse.ArgumentParser()
parser.add_argument('-l', default=False, action='store_true', dest='doLong')
parser.add_argument('-u', default=False, action='store_true', dest='updateTestData')
args = parser.parse_args()
# Handle possible arguments
doLong = args.doLong
if args.doLong:
sys.argv.remove('-l')
if args.updateTestData:
updateTestData()
sys.argv.remove('-u')
unittest.main()
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