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191 lines
6.7 KiB
Python
191 lines
6.7 KiB
Python
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
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from __future__ import print_function
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import rdkit.Numerics.rdAlignment as rdAlg
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from rdkit import Geometry
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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 as np
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import math
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def lstFeq(l1, l2, tol=1.e-4):
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if (len(list(l1)) != len(list(l2))):
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return 0
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for i in range(len(list(l1))):
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if not feq(l1[i], l2[i], tol):
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return 0
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return 1
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def feq(v1,v2,tol2=1e-4):
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return abs(v1-v2)<=tol2
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def transformPoint(trans, pt):
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pt2 = list(pt)
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pt2.append(1.0)
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pt2 = np.array(pt2)
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res = np.dot(trans, pt2)
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return res[:3]
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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 test1Basic(self):
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# passing two numeric arrays
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refPts = np.zeros((2,3), np.float)
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prbPts = np.zeros((2,3), np.float)
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refPts[1,0] = 1.0
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prbPts[0,0] = 2.0
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prbPts[0,1] = 2.0
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prbPts[1,0] = 2.0
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prbPts[1,1] = 3.0
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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refLst = list(refPts)
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cnt = 0
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
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cnt+= 1
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# repeat with with lists or tuples
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refPts = ((0.0, 0.0, 0.0), (1.0, 0.0, 0.0))
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prbPts = ((2.0, 2.0, 0.0), (2.0, 3.0, 0.0))
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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refPts = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]
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prbPts = [[2.0, 2.0, 0.0], [2.0, 3.0, 0.0]]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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# mix it up
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refPts = np.zeros((2,3), np.float)
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refPts[1,0] = 1.0
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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def test2Weights(self) :
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refPts = np.array([[-math.cos(math.pi/6), -math.sin(math.pi/6), 0.0],
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[math.cos(math.pi/6), -math.sin(math.pi/6), 0.0],
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[0.0, 1.0, 0.0]], np.float)
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prbPts = np.array([[-2*math.sin(math.pi/6) + 3.0, 2*math.cos(math.pi/6), 4.0],
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[-2*math.sin(math.pi/6) + 3.0, -2*math.cos(math.pi/6), 4.0],
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[5.0, 0.0, 4.0]], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 3.0))
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target = [[-1.732, -1., 0.],
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[1.732, -1., 0.],
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[0., 2., 0.]]
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cnt = 0
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
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cnt += 1
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weights = np.array([1.0, 1.0, 2.0], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 3.75))
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cnt = 0
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target = [[-1.732, -1.25, 0.],
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[1.732, -1.25, 0.],
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[0., 1.75, 0.]]
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
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cnt += 1
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weights = [1.0, 1.0, 2.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 3.75))
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weights = [1.0, 2.0, 2.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
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self.assertTrue(feq(res[0], 4.8))
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def test3tetra(self) :
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refPts = np.array([[0.0, 0.0, 0.0],
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[1.0, 0.0, 0.0],
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[0.0, 1.0, 0.0],
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[0.0, 0.0, 1.0]], np.float)
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prbPts = np.array([[2.0, 2.0, 3.0],
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[3.0, 2.0, 3.0],
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[2.0, 3.0, 3.0]], np.float)
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self.assertRaises(ValueError,lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = np.array([[2.0, 2.0, 3.0],
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[3.0, 2.0, 3.0],
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[2.0, 3.0, 3.0],
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[2.0, 2.0, 4.0]], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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wts = [1.0, 1.0, 1.0]
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self.assertRaises(ValueError,lambda : rdAlg.GetAlignmentTransform(refPts, prbPts, wts))
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wts = [1.0, 1.0, 1.0, 1.0]
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
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self.assertTrue(feq(res[0], 0.0))
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# test reflection
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prbPts = np.array([[2.0, 2.0, 3.0],
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[3.0, 2.0, 3.0],
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[2.0, 2.0, 4.0],
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[2.0, 3.0, 3.0]], np.float)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
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self.assertTrue(feq(res[0], 1.0))
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res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts, 1)
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self.assertTrue(feq(res[0], 0.0))
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cnt = 0
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refLst = list(refPts)
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for item in list(prbPts):
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self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
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cnt += 1
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def test4points(self) :
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refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
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Geometry.Point3D(1.0, 0.0, 0.0),
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Geometry.Point3D(0.0, 1.0, 0.0),
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Geometry.Point3D(0.0, 0.0, 1.0),
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)
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prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
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Geometry.Point3D(3.0, 2.0, 3.0),
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Geometry.Point3D(2.0, 3.0, 3.0),
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Geometry.Point3D(2.0, 2.0, 4.0),
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)
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res = rdAlg.GetAlignmentTransform(refPts, prbPts)
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self.assertTrue(feq(res[0], 0.0))
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def test5errorHandling(self) :
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refPts = (Geometry.Point3D(0.0, 0.0, 0.0),
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Geometry.Point3D(1.0, 0.0, 0.0),
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Geometry.Point3D(0.0, 1.0, 0.0),
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Geometry.Point3D(0.0, 0.0, 1.0),
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)
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prbPts = (1,2,3,4,)
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self.assertRaises(ValueError,
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lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = ()
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self.assertRaises(ValueError,
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lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = 1
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self.assertRaises(ValueError,
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lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
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prbPts = (Geometry.Point3D(2.0, 2.0, 3.0),
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Geometry.Point3D(3.0, 2.0, 3.0),
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Geometry.Point3D(2.0, 3.0, 3.0),
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(2.0, 2.0, 5.0),
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)
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self.assertRaises(ValueError,
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lambda : rdAlg.GetAlignmentTransform(refPts, prbPts))
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if __name__ == '__main__':
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print("Testing Alignment Wrapper code:")
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unittest.main()
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