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port over some changes made on Subshape branch (r179:218)

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This commit is contained in:
Greg Landrum
2007-04-18 03:47:40 +00:00
parent 783f220443
commit 6cd195ad0b
9 changed files with 552 additions and 24 deletions
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45
Python/DataStructs/UnitTestBitVect.py
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@@ -10,6 +10,9 @@
import unittest
from DataStructs import BitVect
def feq(v1,v2,tol=1e-4):
return abs(v1-v2)<tol
class TestCase(unittest.TestCase):
def testVectIdx(self):
""" test indexing into BitVects
@@ -264,5 +267,47 @@ class TestCase(unittest.TestCase):
assert v2.EuclideanDistance(v2)==0.0, 'EuclideanDistance failed'
def test90BulkDistances(self):
"""
verify that the base similarity (tanimoto) works using an 18 fp regression
panel of pubchem compounds (chosen to have different lengths: 5x2048,
5x1024, 5x512, 3x256)
"""
import DataStructs
import cPickle,os
import RDConfig
fps = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
'pubchem_fps.pkl'),'rb'))
dm = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
'pubchem_fps.dm.pkl'),'rb'))
dmIdx=0
for i in range(len(fps)):
nmi,fpi = fps[i]
for j in range(i+1,len(fps)):
nmj,fpj = fps[j]
sim = DataStructs.FingerprintSimilarity(fpi,fpj)
self.failUnless(feq(sim,dm[dmIdx]))
dmIdx+=1
def test91BoundDistances(self):
"""
verify that the bounded similarity (tanimoto) works
"""
import DataStructs
import cPickle,os
import RDConfig
fps = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
'pubchem_fps.pkl'),'rb'))
dm = cPickle.load(file(os.path.join(RDConfig.RDCodeDir,'DataStructs','test_data',
'pubchem_fps.dm.pkl'),'rb'))
dmIdx=0
for i in range(len(fps)):
nmi,fpi = fps[i]
for j in range(i+1,len(fps)):
nmj,fpj = fps[j]
sim = DataStructs.FingerprintSimilarity(fpi,fpj)
self.failUnless(feq(sim,dm[dmIdx]))
dmIdx+=1
if __name__ == '__main__':
unittest.main()