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"""
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
Replaced numpy.oldnumeric with numpy methods - Jan 2015, PGedeck
"""
#pylint: disable=E1101,C0111,R0904
import unittest
import numpy as np
from rdkit import DistanceGeometry as DG
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1SmoothPass(self):
arr = np.array([[0, 1.0, 5.0],
[1.0, 0, 1.0],
[0.0, 1.0, 0]], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
self.assertTrue(feq(arr[0, 2], 2.0))
self.assertTrue(feq(arr[2, 0], 0.0))
self.assertTrue(feq(arr[0, 1], 1.0))
self.assertTrue(feq(arr[1, 0], 1.0))
self.assertTrue(feq(arr[1, 2], 1.0))
def test2SmoothFail(self):
arr = np.array([[0, 1.0, 5.0],
[1.0, 0, 1.0],
[3.0, 1.0, 0]], np.float)
self.assertFalse(DG.DoTriangleSmoothing(arr))
def test3SmoothPass(self):
arr = np.array([[0, 1.1, 5.0],
[0.9, 0, 1.1],
[0.0, 0.9, 0]], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
self.assertTrue(feq(arr[0, 2], 2.2))
self.assertTrue(feq(arr[2, 0], 0.0))
self.assertTrue(feq(arr[0, 1], 1.1))
self.assertTrue(feq(arr[1, 0], 0.9))
self.assertTrue(feq(arr[1, 2], 1.1))
def test4Embed(self):
arr = np.array([[0, 1.0, 5.0],
[1.0, 0, 1.0],
[0.0, 1.0, 0]], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
v1 = coords[0] - coords[1]
v2 = coords[1] - coords[2]
d1 = np.dot(v1, v1)
self.assertTrue(feq(d1, 1.0, 0.001))
d2 = np.dot(v2, v2)
self.assertTrue(feq(d2, 1.0, 0.001))
def test5EmbedFail(self):
arr = np.array([[0, 1.0, 5.0],
[1.0, 0, 1.0],
[3.0, 1.0, 0]], np.float)
self.assertRaises(ValueError, lambda : DG.EmbedBoundsMatrix(arr))
#DG.EmbedBoundsMatrix(arr,randomizeOnFailure=0,randomSeed=1)
DG.EmbedBoundsMatrix(arr, randomizeOnFailure=1)
def test6EmbedConstraints(self):
arr = np.array([[0.0, 1.0, 1.0],
[1.0, 0.0, 1.0],
[0.99, 1.0, 0.0]], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
v1 = coords[0] - coords[1]
v2 = coords[1] - coords[2]
d1 = np.dot(v1, v1)
self.assertTrue(feq(d1, 1.0, 2e-3))
d2 = np.dot(v2, v2)
self.assertTrue(feq(d2, 1.0, 2e-3))
arr = np.array([[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]], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr)
v1 = coords[0] - coords[1]
v2 = coords[1] - coords[2]
d1 = np.dot(v1, v1)
self.assertTrue(feq(d1, 1.0, 1e-3))
d2 = np.dot(v2, v2)
self.assertTrue(feq(d2, 1.0, 1e-3))
return
# this test is currently (rev:4769) passing on windows and
# failing on linux. It's kind of dependent on fp precision, so
# it's probably ok to ditch it.
arr = np.array([[0.0, 1.0, 1.0, 1.0],
[1.0, 0.0, 1.0, 1.0],
[1.0, 1.0, 0.0, 1.0],
[1.0, 1.0, 1.0, 0.0],
], np.float)
self.assertTrue(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
v1 = coords[0] - coords[1]
v2 = coords[1] - coords[2]
d1 = np.dot(v1, v1)
self.assertTrue(feq(d1, 1.0, 1e-3))
d2 = np.dot(v2, v2)
self.assertTrue(feq(d2, 1.0, 1e-3))
if __name__ == '__main__':
unittest.main()
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