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## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id: rough_test.py 997 2009-02-25 06:12:43Z glandrum $
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import os,sys
import unittest
import numpy.oldnumeric as Numeric
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 = Numeric.array([[0,1.0,5.0],
[1.0,0,1.0],
[0.0,1.0,0]],Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
self.failUnless(feq(arr[0,2],2.0))
self.failUnless(feq(arr[2,0],0.0))
self.failUnless(feq(arr[0,1],1.0))
self.failUnless(feq(arr[1,0],1.0))
self.failUnless(feq(arr[1,2],1.0))
def test2SmoothFail(self):
arr = Numeric.array([[0,1.0,5.0],
[1.0,0,1.0],
[3.0,1.0,0]],Numeric.Float)
self.failIf(DG.DoTriangleSmoothing(arr))
def test3SmoothPass(self):
arr = Numeric.array([[0,1.1,5.0],
[0.9,0,1.1],
[0.0,0.9,0]],Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
self.failUnless(feq(arr[0,2],2.2))
self.failUnless(feq(arr[2,0],0.0))
self.failUnless(feq(arr[0,1],1.1))
self.failUnless(feq(arr[1,0],0.9))
self.failUnless(feq(arr[1,2],1.1))
def test4Embed(self):
arr = Numeric.array([[0,1.0,5.0],
[1.0,0,1.0],
[0.0,1.0,0]],Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr,randomSeed=100);
v1 = coords[0]-coords[1]
v2 = coords[1]-coords[2]
d1 = Numeric.dot(v1,v1)
self.failUnless(feq(d1,1.0, 0.001));
d2 = Numeric.dot(v2,v2)
self.failUnless(feq(d2,1.0, 0.001));
def test5EmbedFail(self):
arr = Numeric.array([[0,1.0,5.0],
[1.0,0,1.0],
[3.0,1.0,0]],Numeric.Float)
self.failUnlessRaises(ValueError,lambda : DG.EmbedBoundsMatrix(arr))
#DG.EmbedBoundsMatrix(arr,randomizeOnFailure=0,randomSeed=1)
DG.EmbedBoundsMatrix(arr,randomizeOnFailure=1);
def test6EmbedConstraints(self):
arr = Numeric.array([[0.0,1.0,1.0],
[1.0,0.0,1.0],
[0.99,1.0,0.0]],
Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr, randomSeed=100)
v1 = coords[0]-coords[1]
v2 = coords[1]-coords[2]
d1 = Numeric.dot(v1,v1)
self.failUnless(feq(d1,1.0,2e-3));
d2 = Numeric.dot(v2,v2)
self.failUnless(feq(d2,1.0,2e-3));
arr = Numeric.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],
],Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr)
v1 = coords[0]-coords[1]
v2 = coords[1]-coords[2]
d1 = Numeric.dot(v1,v1)
self.failUnless(feq(d1,1.0,1e-3));
d2 = Numeric.dot(v2,v2)
self.failUnless(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 = Numeric.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],
],Numeric.Float)
self.failUnless(DG.DoTriangleSmoothing(arr))
coords = DG.EmbedBoundsMatrix(arr,randomSeed=100)
v1 = coords[0]-coords[1]
v2 = coords[1]-coords[2]
d1 = Numeric.dot(v1,v1)
self.failUnless(feq(d1,1.0,1e-3));
d2 = Numeric.dot(v2,v2)
self.failUnless(feq(d2,1.0,1e-3));
if __name__ == '__main__':
unittest.main()
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