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127 lines
3.9 KiB
Python
127 lines
3.9 KiB
Python
## 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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from rdkit import RDConfig
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import os,sys
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import unittest
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import numpy.oldnumeric as Numeric
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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 = Numeric.array([[0,1.0,5.0],
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[1.0,0,1.0],
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[0.0,1.0,0]],Numeric.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 = Numeric.array([[0,1.0,5.0],
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[1.0,0,1.0],
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[3.0,1.0,0]],Numeric.Float)
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self.assertFalse(DG.DoTriangleSmoothing(arr))
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def test3SmoothPass(self):
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arr = Numeric.array([[0,1.1,5.0],
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[0.9,0,1.1],
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[0.0,0.9,0]],Numeric.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 = Numeric.array([[0,1.0,5.0],
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[1.0,0,1.0],
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[0.0,1.0,0]],Numeric.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 = Numeric.dot(v1,v1)
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self.assertTrue(feq(d1,1.0, 0.001));
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d2 = Numeric.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 = Numeric.array([[0,1.0,5.0],
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[1.0,0,1.0],
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[3.0,1.0,0]],Numeric.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 = Numeric.array([[0.0,1.0,1.0],
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[1.0,0.0,1.0],
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[0.99,1.0,0.0]],
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Numeric.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 = Numeric.dot(v1,v1)
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self.assertTrue(feq(d1,1.0,2e-3));
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d2 = Numeric.dot(v2,v2)
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self.assertTrue(feq(d2,1.0,2e-3));
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arr = Numeric.array([[0.0,1.0,1.0,1.01],
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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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[0.99,1.0,1.0,0.0],
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],Numeric.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 = Numeric.dot(v1,v1)
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self.assertTrue(feq(d1,1.0,1e-3));
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d2 = Numeric.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 = Numeric.array([[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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],Numeric.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 = Numeric.dot(v1,v1)
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self.assertTrue(feq(d1,1.0,1e-3));
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d2 = Numeric.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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