mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
e9af48ffd7
* Issue #1071: add yapf configuration file * yapf formatting of Code directory * yapf formatting of Contrib directory * yapf formatting of Data directory * yapf formatting of Docs directory * yapf formatting of External directory * yapf formatting of Projects directory * yapf formatting of Regress directory * yapf formatting of Scripts directory * yapf formatting of Web directory * yapf formatting of rdkit directory
108 lines
3.5 KiB
Python
108 lines
3.5 KiB
Python
"""
|
|
## 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()
|