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"""
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
Replaced numpy.oldnumeric with numpy methods - Jan 2015, PGedeck
"""
#pylint: disable=E1101,C0111,R0904
from __future__ import print_function
import rdkit.Numerics.rdAlignment as rdAlg
from rdkit import Geometry
import unittest
import numpy as np
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 = np.array(pt2)
res = np.dot(trans, pt2)
return res[:3]
class TestCase(unittest.TestCase):
def test1Basic(self):
# passing two numeric arrays
refPts = np.zeros((2, 3), np.float)
prbPts = np.zeros((2, 3), np.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.assertTrue(feq(res[0], 0.0))
refLst = list(refPts)
cnt = 0
for item in list(prbPts):
self.assertTrue(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.assertTrue(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.assertTrue(feq(res[0], 0.0))
# mix it up
refPts = np.zeros((2, 3), np.float)
refPts[1, 0] = 1.0
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
def test2Weights(self):
refPts = np.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]],
np.float)
prbPts = np.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]], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(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.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = np.array([1.0, 1.0, 2.0], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(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.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = [1.0, 1.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(feq(res[0], 3.75))
weights = [1.0, 2.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(feq(res[0], 4.8))
def test3tetra(self):
refPts = np.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]],
np.float)
prbPts = np.array([[2.0, 2.0, 3.0], [3.0, 2.0, 3.0], [2.0, 3.0, 3.0]], np.float)
self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = np.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]],
np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
wts = [1.0, 1.0, 1.0]
self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts, wts))
wts = [1.0, 1.0, 1.0, 1.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.assertTrue(feq(res[0], 0.0))
# test reflection
prbPts = np.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]],
np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.assertTrue(feq(res[0], 1.0))
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts, 1)
self.assertTrue(feq(res[0], 0.0))
cnt = 0
refLst = list(refPts)
for item in list(prbPts):
self.assertTrue(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.assertTrue(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.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = ()
self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = 1
self.assertRaises(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.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
if __name__ == '__main__':
print("Testing Alignment Wrapper code:")
unittest.main()
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