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113 lines
3.4 KiB
Python
113 lines
3.4 KiB
Python
"""
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## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
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# $Id$
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#
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# Copyright (C) 2004 Rational Discovery LLC
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# All Rights Reserved
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#
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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 unittest
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import numpy as np
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from rdkit import DistanceGeometry as DG
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def feq(v1, v2, tol2=1e-4):
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return abs(v1 - v2) <= tol2
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test1SmoothPass(self):
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arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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self.assertTrue(feq(arr[0, 2], 2.0))
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self.assertTrue(feq(arr[2, 0], 0.0))
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self.assertTrue(feq(arr[0, 1], 1.0))
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self.assertTrue(feq(arr[1, 0], 1.0))
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self.assertTrue(feq(arr[1, 2], 1.0))
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def test2SmoothFail(self):
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arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], float)
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self.assertFalse(DG.DoTriangleSmoothing(arr))
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def test3SmoothPass(self):
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arr = np.array([[0, 1.1, 5.0], [0.9, 0, 1.1], [0.0, 0.9, 0]], float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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self.assertTrue(feq(arr[0, 2], 2.2))
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self.assertTrue(feq(arr[2, 0], 0.0))
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self.assertTrue(feq(arr[0, 1], 1.1))
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self.assertTrue(feq(arr[1, 0], 0.9))
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self.assertTrue(feq(arr[1, 2], 1.1))
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def test4Embed(self):
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arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
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v1 = coords[0] - coords[1]
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v2 = coords[1] - coords[2]
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d1 = np.dot(v1, v1)
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self.assertTrue(feq(d1, 1.0, 0.001))
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d2 = np.dot(v2, v2)
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self.assertTrue(feq(d2, 1.0, 0.001))
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def test5EmbedFail(self):
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arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], float)
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self.assertRaises(ValueError, lambda: DG.EmbedBoundsMatrix(arr))
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#DG.EmbedBoundsMatrix(arr,randomizeOnFailure=0,randomSeed=1)
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DG.EmbedBoundsMatrix(arr, randomizeOnFailure=1)
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def test6EmbedConstraints(self):
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arr = np.array([[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [0.99, 1.0, 0.0]], float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
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v1 = coords[0] - coords[1]
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v2 = coords[1] - coords[2]
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d1 = np.dot(v1, v1)
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self.assertTrue(feq(d1, 1.0, 2e-3))
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d2 = np.dot(v2, v2)
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self.assertTrue(feq(d2, 1.0, 2e-3))
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arr = np.array(
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[[0.0, 1.0, 1.0, 1.01], [1.0, 0.0, 1.0, 1.0], [1.0, 1.0, 0.0, 1.0], [0.99, 1.0, 1.0, 0.0]],
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float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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coords = DG.EmbedBoundsMatrix(arr)
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v1 = coords[0] - coords[1]
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v2 = coords[1] - coords[2]
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d1 = np.dot(v1, v1)
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self.assertTrue(feq(d1, 1.0, 1e-3))
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d2 = np.dot(v2, v2)
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self.assertTrue(feq(d2, 1.0, 1e-3))
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return
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# this test is currently (rev:4769) passing on windows and
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# failing on linux. It's kind of dependent on fp precision, so
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# it's probably ok to ditch it.
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arr = np.array([
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[0.0, 1.0, 1.0, 1.0],
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[1.0, 0.0, 1.0, 1.0],
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[1.0, 1.0, 0.0, 1.0],
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[1.0, 1.0, 1.0, 0.0],
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], float)
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self.assertTrue(DG.DoTriangleSmoothing(arr))
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coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
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v1 = coords[0] - coords[1]
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v2 = coords[1] - coords[2]
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d1 = np.dot(v1, v1)
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self.assertTrue(feq(d1, 1.0, 1e-3))
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d2 = np.dot(v2, v2)
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self.assertTrue(feq(d2, 1.0, 1e-3))
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if __name__ == '__main__':
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unittest.main()
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