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314 lines
8.1 KiB
Python
Executable File
314 lines
8.1 KiB
Python
Executable File
# $Id$
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#
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# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
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#
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# @@ All Rights Reserved @@
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#
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""" unit testing code for the python BitVects
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"""
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import unittest
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from DataStructs import BitVect
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def feq(v1,v2,tol=1e-4):
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return abs(v1-v2)<tol
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class TestCase(unittest.TestCase):
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def testVectIdx(self):
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""" test indexing into BitVects
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"""
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v = BitVect.BitVect(10)
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ok = 1
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try:
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v[0] = 1
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v[2] = 1
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except:
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ok = 0
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assert ok, 'setting bits failed'
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try:
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v[10] = 1
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'setting high bit should have failed'
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try:
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v[-1] = 1
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'setting negative bit should have failed'
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assert v[0] == 1, 'bad bit'
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assert v[1] == 0, 'bad bit'
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assert v[2] == 1, 'bad bit'
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try:
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foo = v[10]
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'getting high bit should have failed'
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try:
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foo = v[-1]
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'getting negative bit should have failed'
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def testSparseIdx(self):
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""" test indexing into SparseBitVects
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"""
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v = BitVect.SparseBitVect(10)
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ok = 1
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try:
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v[0] = 1
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v[2] = 1
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except:
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ok = 0
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assert ok, 'setting bits failed'
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try:
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v[10] = 1
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'setting high bit should have failed'
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try:
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v[-1] = 1
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'setting negative bit should have failed'
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assert v[0] == 1, 'bad bit'
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assert v[1] == 0, 'bad bit'
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assert v[2] == 1, 'bad bit'
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try:
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foo = v[10]
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'getting high bit should have failed'
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try:
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foo = v[-1]
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except:
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ok = 1
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else:
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ok = 0
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assert ok, 'getting negative bit should have failed'
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def testVectBitGet(self):
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""" test operations to get bits
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"""
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v = BitVect.BitVect(10)
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v[0] = 1
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v[2] = 1
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v[6] = 1
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assert len(v)==10,'len(BitVect) failed'
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assert v.NumOnBits()==3,'NumOnBits failed'
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assert v.GetOnBits()==[0,2,6], 'GetOnBits failed'
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assert v.GetOnBits(reverse=1)==[6,2,0], 'GetOnBits(reverse) failed'
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def testSparseBitGet(self):
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""" test operations to get sparse bits
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"""
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v = BitVect.BitVect(10)
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v[0] = 1
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v[2] = 1
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v[6] = 1
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assert len(v)==10,'len(SparseBitVect) failed'
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assert v.NumOnBits()==3,'NumOnBits failed'
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assert v.GetOnBits()==[0,2,6], 'GetOnBits failed'
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assert v.GetOnBits(reverse=1)==[6,2,0], 'GetOnBits(reverse) failed'
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def testVectBitOps(self):
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""" test bit operations on BitVects
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"""
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v1 = BitVect.BitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.BitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1&v2 == [0,6],'binary & failed'
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assert v1|v2 == [0,2,3,6],'binary | failed'
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assert v1^v2 == [2,3],'binary ^ failed'
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def testCrossBitOps(self):
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""" test bit operations between BitVects and SparseBitVects
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"""
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v1 = BitVect.SparseBitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.BitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1&v2 == [0,6],'binary & failed'
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assert v1|v2 == [0,2,3,6],'binary | failed'
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assert v1^v2 == [2,3],'binary ^ failed'
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def testSparseBitOps(self):
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""" test bit operations on SparseBitVects
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"""
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v1 = BitVect.SparseBitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.SparseBitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1&v2 == [0,6],'binary & failed'
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assert v1|v2 == [0,2,3,6],'binary | failed'
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assert v1^v2 == [2,3],'binary ^ failed'
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def testVectTanimoto(self):
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v1 = BitVect.BitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.BitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1.TanimotoSimilarity(v2)==0.5,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v1)==0.5,'TanimotoSimilarity failed'
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assert v1.TanimotoSimilarity(v1)==1.0,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v2)==1.0,'TanimotoSimilarity failed'
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def testSparseTanimoto(self):
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v1 = BitVect.SparseBitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.SparseBitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1.TanimotoSimilarity(v2)==0.5,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v1)==0.5,'TanimotoSimilarity failed'
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assert v1.TanimotoSimilarity(v1)==1.0,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v2)==1.0,'TanimotoSimilarity failed'
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def testCrossTanimoto(self):
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v1 = BitVect.SparseBitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.BitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert v1.TanimotoSimilarity(v2)==0.5,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v1)==0.5,'TanimotoSimilarity failed'
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assert v1.TanimotoSimilarity(v1)==1.0,'TanimotoSimilarity failed'
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assert v2.TanimotoSimilarity(v2)==1.0,'TanimotoSimilarity failed'
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def testVectEuclid(self):
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v1 = BitVect.BitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.BitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert abs(v1.EuclideanDistance(v2)-.14142)<.0001, 'EuclideanDistance failed'
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assert abs(v2.EuclideanDistance(v1)-.14142)<.0001, 'EuclideanDistance failed'
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assert v1.EuclideanDistance(v1)==0.0, 'EuclideanDistance failed'
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assert v2.EuclideanDistance(v2)==0.0, 'EuclideanDistance failed'
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def testSparseEuclid(self):
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v1 = BitVect.SparseBitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.SparseBitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert abs(v1.EuclideanDistance(v2)-.14142)<.0001, 'EuclideanDistance failed'
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assert abs(v2.EuclideanDistance(v1)-.14142)<.0001, 'EuclideanDistance failed'
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assert v1.EuclideanDistance(v1)==0.0, 'EuclideanDistance failed'
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assert v2.EuclideanDistance(v2)==0.0, 'EuclideanDistance failed'
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def testCrossEuclid(self):
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v1 = BitVect.BitVect(10)
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v1[0] = 1
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v1[2] = 1
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v1[6] = 1
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v2 = BitVect.SparseBitVect(10)
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v2[0] = 1
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v2[3] = 1
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v2[6] = 1
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assert abs(v1.EuclideanDistance(v2)-.14142)<.0001, 'EuclideanDistance failed'
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assert abs(v2.EuclideanDistance(v1)-.14142)<.0001, 'EuclideanDistance failed'
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assert v1.EuclideanDistance(v1)==0.0, 'EuclideanDistance failed'
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assert v2.EuclideanDistance(v2)==0.0, 'EuclideanDistance failed'
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def test90BulkDistances(self):
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"""
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verify that the base similarity (tanimoto) works using an 18 fp regression
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panel of pubchem compounds (chosen to have different lengths: 5x2048,
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5x1024, 5x512, 3x256)
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"""
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import DataStructs
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import cPickle,os
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import RDConfig
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fps = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
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'pubchem_fps.pkl'),'rb'))
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dm = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
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'pubchem_fps.dm.pkl'),'rb'))
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dmIdx=0
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for i in range(len(fps)):
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nmi,fpi = fps[i]
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for j in range(i+1,len(fps)):
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nmj,fpj = fps[j]
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sim = DataStructs.FingerprintSimilarity(fpi,fpj)
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self.failUnless(feq(sim,dm[dmIdx]))
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dmIdx+=1
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def test91BoundDistances(self):
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"""
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verify that the bounded similarity (tanimoto) works
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"""
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import DataStructs
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import cPickle,os
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import RDConfig
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fps = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
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'pubchem_fps.pkl'),'rb'))
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dm = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
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'pubchem_fps.dm.pkl'),'rb'))
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dmIdx=0
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for i in range(len(fps)):
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nmi,fpi = fps[i]
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for j in range(i+1,len(fps)):
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nmj,fpj = fps[j]
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sim = DataStructs.FingerprintSimilarity(fpi,fpj)
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self.failUnless(feq(sim,dm[dmIdx]))
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dmIdx+=1
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if __name__ == '__main__':
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unittest.main()
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