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## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
import rdkit.Numerics.rdAlignment as rdAlg
from rdkit import Geometry
from rdkit import RDConfig
import os,sys
import unittest
import numpy.oldnumeric as Numeric
import math
import copy
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
for i in range(len(list(l1))):
if not feq(l1[i], l2[i], tol):
return 0
return 1
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def transformPoint(trans, pt):
pt2 = copy.copy(list(pt))
pt2.append(1.0)
pt2 = Numeric.array(pt2)
res = Numeric.dot(trans, pt2)
return res[:3]
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1Basic(self):
# passing two numeric arrays
refPts = Numeric.zeros((2,3), Numeric.Float)
prbPts = Numeric.zeros((2,3), Numeric.Float)
refPts[1,0] = 1.0
prbPts[0,0] = 2.0
prbPts[0,1] = 2.0
prbPts[1,0] = 2.0
prbPts[1,1] = 3.0
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
refLst = list(refPts)
cnt = 0
for item in list(prbPts):
self.failUnless(lstFeq(transformPoint(res[1], item), refLst[cnt]))
cnt+= 1
# repeat with with lists or tuples
refPts = ((0.0, 0.0, 0.0), (1.0, 0.0, 0.0))
prbPts = ((2.0, 2.0, 0.0), (2.0, 3.0, 0.0))
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
refPts = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]
prbPts = [[2.0, 2.0, 0.0], [2.0, 3.0, 0.0]]
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
# mix it up
refPts = Numeric.zeros((2,3), Numeric.Float)
refPts[1,0] = 1.0
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
def test2Weights(self) :
refPts = Numeric.array([[-math.cos(math.pi/6), -math.sin(math.pi/6), 0.0],
[math.cos(math.pi/6), -math.sin(math.pi/6), 0.0],
[0.0, 1.0, 0.0]], Numeric.Float)
prbPts = Numeric.array([[-2*math.sin(math.pi/6) + 3.0, 2*math.cos(math.pi/6), 4.0],
[-2*math.sin(math.pi/6) + 3.0, -2*math.cos(math.pi/6), 4.0],
[5.0, 0.0, 4.0]], Numeric.Float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 3.0))
target = [[-1.732, -1., 0.],
[1.732, -1., 0.],
[0., 2., 0.]]
cnt = 0
for item in list(prbPts):
self.failUnless(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = Numeric.array([1.0, 1.0, 2.0], Numeric.Float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.failUnless(feq(res[0], 3.75))
cnt = 0
target = [[-1.732, -1.25, 0.],
[1.732, -1.25, 0.],
[0., 1.75, 0.]]
for item in list(prbPts):
self.failUnless(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = [1.0, 1.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.failUnless(feq(res[0], 3.75))
weights = [1.0, 2.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.failUnless(feq(res[0], 4.8))
def test3tetra(self) :
refPts = Numeric.array([[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]], Numeric.Float)
prbPts = Numeric.array([[2.0, 2.0, 3.0],
[3.0, 2.0, 3.0],
[2.0, 3.0, 3.0]], Numeric.Float)
self.failUnlessRaises(ValueError,lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = Numeric.array([[2.0, 2.0, 3.0],
[3.0, 2.0, 3.0],
[2.0, 3.0, 3.0],
[2.0, 2.0, 4.0]], Numeric.Float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
wts = [1.0, 1.0, 1.0]
self.failUnlessRaises(ValueError,lambda : rdAlg.GetAlignmentTransform(refPts, prbPts, wts))
wts = [1.0, 1.0, 1.0, 1.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.failUnless(feq(res[0], 0.0))
# test reflection
prbPts = Numeric.array([[2.0, 2.0, 3.0],
[3.0, 2.0, 3.0],
[2.0, 2.0, 4.0],
[2.0, 3.0, 3.0]], Numeric.Float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.failUnless(feq(res[0], 1.0))
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts, 1)
self.failUnless(feq(res[0], 0.0))
cnt = 0
refLst = list(refPts)
for item in list(prbPts):
self.failUnless(lstFeq(transformPoint(res[1], item), refLst[cnt]))
cnt += 1
def test4points(self) :
refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
Geometry.Point3D(1.0, 0.0, 0.0),
Geometry.Point3D(0.0, 1.0, 0.0),
Geometry.Point3D(0.0, 0.0, 1.0),
)
prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
Geometry.Point3D(3.0, 2.0, 3.0),
Geometry.Point3D(2.0, 3.0, 3.0),
Geometry.Point3D(2.0, 2.0, 4.0),
)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.failUnless(feq(res[0], 0.0))
def test5errorHandling(self) :
refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
Geometry.Point3D(1.0, 0.0, 0.0),
Geometry.Point3D(0.0, 1.0, 0.0),
Geometry.Point3D(0.0, 0.0, 1.0),
)
prbPts = (1,2,3,4,)
self.failUnlessRaises(ValueError,
lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = ()
self.failUnlessRaises(ValueError,
lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = 1
self.failUnlessRaises(ValueError,
lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
Geometry.Point3D(3.0, 2.0, 3.0),
Geometry.Point3D(2.0, 3.0, 3.0),
(2.0, 2.0, 5.0),
)
self.failUnlessRaises(ValueError,
lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
if __name__ == '__main__':
print "Testing Alignment Wrapper code:"
unittest.main()
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