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# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ 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.
#
import unittest
import doctest
from rdkit.DataStructs import BitUtils, VectCollection, LazySignature, FingerprintSimilarity
from rdkit import DataStructs, Chem
from rdkit.Chem.Fingerprints.FingerprintMols import FingerprinterDetails
def load_tests(loader, tests, ignore):
""" Add the Doctests from the module """
tests.addTests(doctest.DocTestSuite(BitUtils, optionflags=doctest.ELLIPSIS))
tests.addTests(doctest.DocTestSuite(LazySignature, optionflags=doctest.ELLIPSIS))
tests.addTests(doctest.DocTestSuite(VectCollection, optionflags=doctest.ELLIPSIS))
return tests
class TestCaseAdditional(unittest.TestCase):
def test_VectCollection(self):
# We mainly test the use of Reset
bv1 = DataStructs.ExplicitBitVect(10)
bv1.SetBitsFromList((1, 3, 5))
bv2 = DataStructs.ExplicitBitVect(10)
bv2.SetBitsFromList((6, 8))
vc = VectCollection.VectCollection()
self.assertEqual(vc.GetOrVect(), None)
vc.AddVect(1, bv1)
vc.AddVect(2, bv2)
onBits = set([1, 3, 5, 6, 8])
for i, onOff in enumerate(vc.GetOrVect()):
self.assertEqual(i in onBits, onOff == 1)
vc.Reset()
self.assertEqual(onBits, set(vc.GetOnBits()))
vc = VectCollection.VectCollection()
self.assertEqual(vc.GetOrVect(), None)
vc.AddVect(1, bv1)
vc.AddVect(2, bv2)
for i in onBits:
self.assertEqual(vc[i], 1)
def test_LazySig(self):
self.assertRaises(ValueError, LazySignature.LazySig, lambda x: 1, 0)
# Check cache works
obj = LazySignature.LazySig(lambda x: x, 10)
self.assertNotIn(8, obj._cache)
self.assertEqual(obj[8], 8)
self.assertIn(8, obj._cache)
obj._cache[8] = 'cached'
self.assertEqual(obj[8], 'cached')
def test__init__(self):
from rdkit.Chem.Fingerprints import FingerprintMols
ms = [Chem.MolFromSmiles('CCOC'), Chem.MolFromSmiles('CCO'), Chem.MolFromSmiles('COC')]
fps = [FingerprintMols.FingerprintMol(x) for x in ms]
self.assertAlmostEqual(FingerprintSimilarity(fps[0], fps[1]), 0.6, places=2)
details = FingerprinterDetails()
fpArgs = details.__dict__
fps = []
for i, x in enumerate(ms, 1):
fpArgs['fpSize'] = 16 * i
fps.append(FingerprintMols.FingerprintMol(x, **fpArgs))
self.assertAlmostEqual(FingerprintSimilarity(fps[0], fps[1]), 0.555, places=2)
self.assertAlmostEqual(FingerprintSimilarity(fps[1], fps[0]), 0.555, places=2)
fpArgs['fpSize'] = 1024
fpArgs['tgtDensity'] = 0.8
fp = FingerprintMols.FingerprintMol(ms[0], **fpArgs)
self.assertEqual(len(fp), 64)
fp = DataStructs.FoldToTargetDensity(fp, density=0.1, minLength=2)
self.assertEqual(len(fp), 4)
if __name__ == '__main__': # pragma: nocover
unittest.main()
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