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from __future__ import division
from rdkit import RDConfig
import unittest
from rdkit.DataManip.Metric import rdMetricMatrixCalc as rdmmc
import numpy
import random
from rdkit import DataStructs
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test0DistsArray(self):
exp = numpy.array([1., 1.414213, 1.0], 'd')
# initialize a double array and check if get back the expected distances
desc = numpy.zeros((3, 2), 'd')
desc[1, 0] = 1.0
desc[2, 0] = 1.0
desc[2, 1] = 1.0
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
# repeat with an flaot array
desc = numpy.zeros((3, 2), 'f')
desc[1, 0] = 1.0
desc[2, 0] = 1.0
desc[2, 1] = 1.0
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
# finally with an interger array
desc = numpy.zeros((3, 2), 'i')
desc[1, 0] = 1
desc[2, 0] = 1
desc[2, 1] = 1
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
def ctest1DistsListArray(self):
exp = numpy.array([1., 1.414213, 1.0], 'd')
desc = [numpy.array([0.0, 0.0], 'd'), numpy.array([1.0, 0.0], 'd'),
numpy.array([1.0, 1.0], 'd')]
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
# repeat the test with a list of numpy.arrays of floats
desc = [numpy.array([0.0, 0.0], 'f'), numpy.array([1.0, 0.0], 'f'),
numpy.array([1.0, 1.0], 'f')]
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
# repeat the test with a list of numpy.arrays of ints
desc = [numpy.array([0, 0], 'i'), numpy.array([1, 0], 'i'), numpy.array([1, 1], 'i')]
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
def test2DistListList(self):
exp = numpy.array([1., 1.414213, 1.0], 'd')
desc = [[0.0, 0.0], [1.0, 0.0], [1.0, 1.0]]
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
#test with ints
desc = [[0, 0], [1, 0], [1, 1]]
dmat = rdmmc.GetEuclideanDistMat(desc)
for i in range(numpy.shape(dmat)[0]):
assert feq(dmat[i], exp[i])
def test3Compare(self):
n = 30
m = 5
dscArr = numpy.zeros((n, m), 'd')
for i in range(n):
for j in range(m):
dscArr[i, j] = random.random()
dmatArr = rdmmc.GetEuclideanDistMat(dscArr)
dscLL = []
for i in range(n):
row = []
for j in range(m):
row.append(dscArr[i, j])
dscLL.append(row)
dmatLL = rdmmc.GetEuclideanDistMat(dscLL)
assert numpy.shape(dmatArr) == numpy.shape(dmatLL)
for i in range(n * (n - 1) // 2):
assert feq(dmatArr[i], dmatLL[i])
def test4ebv(self):
n = 30
m = 2048
dm = 800
lst = []
for i in range(n):
v = DataStructs.ExplicitBitVect(m)
for j in range(dm):
v.SetBit(random.randrange(0, m))
lst.append(v)
dMat = rdmmc.GetTanimotoDistMat(lst)
sMat = rdmmc.GetTanimotoSimMat(lst)
for i in range(n * (n - 1) // 2):
assert feq(sMat[i] + dMat[i], 1.0)
def test5sbv(self):
n = 30
m = 2048
dm = 800
lst = []
for i in range(n):
v = DataStructs.SparseBitVect(m)
for j in range(dm):
v.SetBit(random.randrange(0, m))
lst.append(v)
dMat = rdmmc.GetTanimotoDistMat(lst)
sMat = rdmmc.GetTanimotoSimMat(lst)
for i in range(n * (n - 1) // 2):
assert feq(sMat[i] + dMat[i], 1.0)
if __name__ == '__main__':
unittest.main()
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