mirror of
https://github.com/rdkit/rdkit.git
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24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
178 lines
5.8 KiB
Python
178 lines
5.8 KiB
Python
"""
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## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
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Replaced numpy.oldnumeric with numpy methods - Jan 2015, PGedeck
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"""
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#pylint: disable=E1101,C0111,R0904
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import rdkit.Numerics.rdAlignment as rdAlg
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from rdkit import Geometry
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import unittest
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import numpy as np
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import math
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import copy
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def lstFeq(l1, l2, tol=1.e-4):
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if len(list(l1)) != len(list(l2)):
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return 0
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for i in range(len(list(l1))):
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if not feq(l1[i], l2[i], tol):
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return 0
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return 1
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def feq(v1, v2, tol2=1e-4):
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return abs(v1 - v2) <= tol2
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def transformPoint(trans, pt):
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pt2 = copy.copy(list(pt))
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pt2.append(1.0)
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pt2 = np.array(pt2)
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res = np.dot(trans, pt2)
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return res[:3]
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class TestCase(unittest.TestCase):
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def test1Basic(self):
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# passing two numeric arrays
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refPts = np.zeros((2, 3), np.float)
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prbPts = np.zeros((2, 3), np.float)
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refPts[1, 0] = 1.0
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prbPts[0, 0] = 2.0
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prbPts[0, 1] = 2.0
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prbPts[1, 0] = 2.0
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prbPts[1, 1] = 3.0
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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refLst = list(refPts)
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cnt = 0
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
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cnt += 1
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# repeat with with lists or tuples
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refPts = ((0.0, 0.0, 0.0), (1.0, 0.0, 0.0))
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prbPts = ((2.0, 2.0, 0.0), (2.0, 3.0, 0.0))
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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refPts = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]
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prbPts = [[2.0, 2.0, 0.0], [2.0, 3.0, 0.0]]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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# mix it up
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refPts = np.zeros((2, 3), np.float)
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refPts[1, 0] = 1.0
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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def test2Weights(self):
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refPts = np.array([[-math.cos(math.pi / 6), -math.sin(math.pi / 6), 0.0],
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[math.cos(math.pi / 6), -math.sin(math.pi / 6), 0.0], [0.0, 1.0, 0.0]],
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np.float)
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prbPts = np.array([[-2 * math.sin(math.pi / 6) + 3.0, 2 * math.cos(math.pi / 6), 4.0],
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[-2 * math.sin(math.pi / 6) + 3.0, -2 * math.cos(math.pi / 6), 4.0],
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[5.0, 0.0, 4.0]], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 3.0))
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target = [[-1.732, -1., 0.], [1.732, -1., 0.], [0., 2., 0.]]
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cnt = 0
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
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cnt += 1
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weights = np.array([1.0, 1.0, 2.0], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 3.75))
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cnt = 0
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target = [[-1.732, -1.25, 0.], [1.732, -1.25, 0.], [0., 1.75, 0.]]
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
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cnt += 1
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weights = [1.0, 1.0, 2.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 3.75))
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weights = [1.0, 2.0, 2.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 4.8))
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def test3tetra(self):
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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]],
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np.float)
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prbPts = np.array([[2.0, 2.0, 3.0], [3.0, 2.0, 3.0], [2.0, 3.0, 3.0]], np.float)
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
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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]],
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np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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wts = [1.0, 1.0, 1.0]
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts, wts))
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wts = [1.0, 1.0, 1.0, 1.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
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self.assertTrue(feq(res[0], 0.0))
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# test reflection
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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]],
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np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
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self.assertTrue(feq(res[0], 1.0))
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts, 1)
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self.assertTrue(feq(res[0], 0.0))
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cnt = 0
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refLst = list(refPts)
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
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cnt += 1
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def test4points(self):
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refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
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Geometry.Point3D(1.0, 0.0, 0.0),
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Geometry.Point3D(0.0, 1.0, 0.0),
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Geometry.Point3D(0.0, 0.0, 1.0), )
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prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
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Geometry.Point3D(3.0, 2.0, 3.0),
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Geometry.Point3D(2.0, 3.0, 3.0),
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Geometry.Point3D(2.0, 2.0, 4.0), )
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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def test5errorHandling(self):
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refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
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Geometry.Point3D(1.0, 0.0, 0.0),
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Geometry.Point3D(0.0, 1.0, 0.0),
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Geometry.Point3D(0.0, 0.0, 1.0), )
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prbPts = (1,
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2,
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3,
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4, )
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = ()
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = 1
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
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Geometry.Point3D(3.0, 2.0, 3.0),
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Geometry.Point3D(2.0, 3.0, 3.0),
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(2.0, 2.0, 5.0), )
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self.assertRaises(ValueError, lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
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if __name__ == '__main__':
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print("Testing Alignment Wrapper code:")
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unittest.main()
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