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8bf7a4c187cd4613d8a483c422b82e9db2fac2eb
rdkit/Code/Geometry/Wrap/testGeometry.py
Greg Landrum 8bf7a4c187 now all tests pass here as well
2009-02-03 05:26:10 +00:00

349 lines
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Python
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from rdkit import RDConfig
import os,sys
import unittest
from rdkit import DataStructs
from rdkit.Geometry import rdGeometry as geom
import cPickle,copy
import math
def feq(v1, v2, tol=1.0e-4):
return abs(v1-v2) < tol
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1aPoint3D(self):
pt = geom.Point3D();
self.failUnless(feq(pt.x, 0.0))
self.failUnless(feq(pt.y, 0.0))
self.failUnless(feq(pt.z, 0.0))
pt = geom.Point3D(3., 4., 5.)
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt.z, 5.0))
self.failUnless(feq(pt[0], 3.0))
self.failUnless(feq(pt[1], 4.0))
self.failUnless(feq(pt[2], 5.0))
self.failUnless(feq(pt[-3], 3.0))
self.failUnless(feq(pt[-2], 4.0))
self.failUnless(feq(pt[-1], 5.0))
lst = list(pt)
self.failUnless(feq(lst[0], 3.0))
self.failUnless(feq(lst[1], 4.0))
self.failUnless(feq(lst[2], 5.0))
pt2 = geom.Point3D(1., 1., 1.)
pt3 = pt+pt2
self.failUnless(feq(pt3.x, 4.0))
self.failUnless(feq(pt3.y, 5.0))
self.failUnless(feq(pt3.z, 6.0))
pt += pt2
self.failUnless(feq(pt.x, 4.0))
self.failUnless(feq(pt.y, 5.0))
self.failUnless(feq(pt.z, 6.0))
pt3 = pt-pt2
self.failUnless(feq(pt3.x, 3.0))
self.failUnless(feq(pt3.y, 4.0))
self.failUnless(feq(pt3.z, 5.0))
pt -= pt2
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt.z, 5.0))
pt *= 2.0
self.failUnless(feq(pt.x, 6.0))
self.failUnless(feq(pt.y, 8.0))
self.failUnless(feq(pt.z, 10.0))
pt /= 2
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt.z, 5.0))
self.failUnless(feq(pt.Length(), 7.0711))
self.failUnless(feq(pt.LengthSq(), 50.0))
pt.Normalize()
self.failUnless(feq(pt.Length(), 1.0))
pt1 = geom.Point3D(1.0, 0.0, 0.0)
pt2 = geom.Point3D(2.0*math.cos(math.pi/6), 2.0*math.sin(math.pi/6), 0.0)
ang = pt1.AngleTo(pt2)
self.failUnless(feq(ang, math.pi/6))
prod = pt1.DotProduct(pt2)
self.failUnless(feq(prod, 2.0*math.cos(math.pi/6)))
pt3 = pt1.CrossProduct(pt2)
self.failUnless(feq(pt3.x, 0.0))
self.failUnless(feq(pt3.y, 0.0))
self.failUnless(feq(pt3.z, 1.0))
def test1bPoint2D(self):
pt = geom.Point2D();
self.failUnless(feq(pt.x, 0.0))
self.failUnless(feq(pt.y, 0.0))
pt = geom.Point2D(3., 4.)
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt[0], 3.0))
self.failUnless(feq(pt[1], 4.0))
self.failUnless(feq(pt[-2], 3.0))
self.failUnless(feq(pt[-1], 4.0))
lst = list(pt)
self.failUnless(feq(lst[0], 3.0))
self.failUnless(feq(lst[1], 4.0))
pt2 = geom.Point2D(1., 1.)
pt3 = pt+pt2
self.failUnless(feq(pt3.x, 4.0))
self.failUnless(feq(pt3.y, 5.0))
pt += pt2
self.failUnless(feq(pt.x, 4.0))
self.failUnless(feq(pt.y, 5.0))
pt3 = pt-pt2
self.failUnless(feq(pt3.x, 3.0))
self.failUnless(feq(pt3.y, 4.0))
pt -= pt2
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
pt *= 2.0
self.failUnless(feq(pt.x, 6.0))
self.failUnless(feq(pt.y, 8.0))
pt /= 2
self.failUnless(feq(pt.x, 3.0))
self.failUnless(feq(pt.y, 4.0))
self.failUnless(feq(pt.Length(), 5.0))
self.failUnless(feq(pt.LengthSq(), 25.0))
pt.Normalize()
self.failUnless(feq(pt.Length(), 1.0))
pt1 = geom.Point2D(1.0, 0.0)
pt2 = geom.Point2D(2.0*math.cos(math.pi/6), 2.0*math.sin(math.pi/6))
ang = pt1.AngleTo(pt2)
self.failUnless(feq(ang, math.pi/6))
prod = pt1.DotProduct(pt2)
self.failUnless(feq(prod, 2.0*math.cos(math.pi/6)))
def test1cPointND(self):
dim=4
pt = geom.PointND(4);
for i in range(dim):
self.failUnless(feq(pt[i], 0.0))
pt[0]=3
pt[3]=4
self.failUnless(feq(pt[0], 3.0))
self.failUnless(feq(pt[3], 4.0))
self.failUnless(feq(pt[-4], 3.0))
self.failUnless(feq(pt[-1], 4.0))
lst = list(pt)
self.failUnless(feq(lst[0], 3.0))
self.failUnless(feq(lst[3], 4.0))
pt2 = geom.PointND(4)
pt2[0]=1.
pt2[2]=1.
pt3 = pt+pt2
self.failUnless(feq(pt3[0], 4.0))
self.failUnless(feq(pt3[2], 1.0))
self.failUnless(feq(pt3[3], 4.0))
pt += pt2
self.failUnless(feq(pt[0], 4.0))
self.failUnless(feq(pt[2], 1.0))
self.failUnless(feq(pt[3], 4.0))
pt3 = pt-pt2
self.failUnless(feq(pt3[0], 3.0))
self.failUnless(feq(pt3[2], 0.0))
self.failUnless(feq(pt3[3], 4.0))
pt -= pt2
self.failUnless(feq(pt[0], 3.0))
self.failUnless(feq(pt[2], 0.0))
self.failUnless(feq(pt[3], 4.0))
pt *= 2.0
self.failUnless(feq(pt[0], 6.0))
self.failUnless(feq(pt[1], 0.0))
self.failUnless(feq(pt[2], 0.0))
self.failUnless(feq(pt[3], 8.0))
pt /= 2
self.failUnless(feq(pt[0], 3.0))
self.failUnless(feq(pt[1], 0.0))
self.failUnless(feq(pt[2], 0.0))
self.failUnless(feq(pt[3], 4.0))
self.failUnless(feq(pt.Length(), 5.0))
self.failUnless(feq(pt.LengthSq(), 25.0))
pt.Normalize()
self.failUnless(feq(pt.Length(), 1.0))
pkl = cPickle.dumps(pt)
pt2 = cPickle.loads(pkl)
self.failUnless(len(pt)==len(pt2))
for i in range(len(pt)):
self.failUnless(feq(pt2[i],pt[i]))
def test3UniformGrid(self):
ugrid = geom.UniformGrid3D(20, 18, 15)
self.failUnless(ugrid.GetNumX() == 40)
self.failUnless(ugrid.GetNumY() == 36)
self.failUnless(ugrid.GetNumZ() == 30)
dvect = ugrid.GetOccupancyVect()
ugrid = geom.UniformGrid3D(20, 18, 15, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE)
dvect = ugrid.GetOccupancyVect()
self.failUnless(dvect.GetValueType() == DataStructs.DiscreteValueType.TWOBITVALUE)
grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)
geom.WriteGridToFile(grd, "junk.grd")
grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
dist = geom.TanimotoDistance(grd, grd2)
self.failUnless(dist == 0.25)
dist = geom.ProtrudeDistance(grd, grd2)
self.failUnless(dist == 0.25)
dist = geom.ProtrudeDistance(grd2, grd)
self.failUnless(dist==0.0)
grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5, DataStructs.DiscreteValueType.FOURBITVALUE)
grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25, 3)
grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25, 3)
grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25, 3)
self.failUnlessRaises(ValueError, lambda : geom.TanimotoDistance(grd, grd2))
grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 1.0)
self.failUnlessRaises(ValueError, lambda : geom.TanimotoDistance(grd, grd2))
grd2 = geom.UniformGrid3D(11.0, 10.0, 10.0, 1.0)
self.failUnlessRaises(ValueError, lambda : geom.TanimotoDistance(grd, grd2))
def testSymmetry(self):
grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
grd.SetSphereOccupancy(geom.Point3D(-2.2, -2.0, 0.0), 1.65, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.2, -2.0, 0.0), 1.65, 0.25)
bPt1 = geom.Point3D(-4.0, -2.0, -2.0)
bPt2 = geom.Point3D(4.0, -2.0, -2.0)
for k in range(8) :
bPt1 += geom.Point3D(0.0, 0.0, 0.5)
bPt2 += geom.Point3D(0.0, 0.0, 0.5)
for j in range(8):
bPt1 += geom.Point3D(0.0, 0.5, 0.0)
bPt2 += geom.Point3D(0.0, 0.5, 0.0)
for i in range(8) :
bPt1 += geom.Point3D(0.5, 0.0, 0.0)
bPt2 -= geom.Point3D(0.5, 0.0, 0.0)
self.failUnless(grd.GetValPoint(bPt1) == grd.GetValPoint(bPt2))
bPt1.x = -4.0
bPt2.x = 4.0
bPt1.y = -2.0
bPt2.y = -2.0
def testPointPickles(self):
pt = geom.Point3D(2.0,-3.0,1.0)
pt2 = cPickle.loads(cPickle.dumps(pt))
self.failUnless(feq(pt.x,pt2.x,1e-6))
self.failUnless(feq(pt.y,pt2.y,1e-6))
self.failUnless(feq(pt.z,pt2.z,1e-6))
pt = geom.Point2D(2.0,-4.0)
pt2 = cPickle.loads(cPickle.dumps(pt))
self.failUnless(feq(pt.x,pt2.x,1e-6))
self.failUnless(feq(pt.y,pt2.y,1e-6))
def test4GridPickles(self):
grd = geom.UniformGrid3D(10.0, 9.0, 8.0, 0.5)
self.failUnless(grd.GetNumX() == 20)
self.failUnless(grd.GetNumY() == 18)
self.failUnless(grd.GetNumZ() == 16)
grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)
self.failUnless(geom.TanimotoDistance(grd,grd)==0.0)
grd2 = cPickle.loads(cPickle.dumps(grd))
self.failUnless(grd2.GetNumX() == 20)
self.failUnless(grd2.GetNumY() == 18)
self.failUnless(grd2.GetNumZ() == 16)
self.failUnless(geom.TanimotoDistance(grd,grd2)==0.0)
def test5GridOps(self):
grd = geom.UniformGrid3D(10, 10, 10)
grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)
grd2 = geom.UniformGrid3D(10, 10, 10)
grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
grd2.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.0, 0.25)
self.failUnless(geom.TanimotoDistance(grd,grd)==0.0)
self.failUnless(geom.TanimotoDistance(grd,grd2)==1.0)
grd3 = copy.deepcopy(grd)
grd3 |= grd2
self.failUnless(geom.TanimotoDistance(grd3,grd)==.5)
self.failUnless(geom.TanimotoDistance(grd3,grd2)==.5)
grd3 = copy.deepcopy(grd)
grd3 += grd2
self.failUnless(geom.TanimotoDistance(grd3,grd)==.5)
self.failUnless(geom.TanimotoDistance(grd3,grd2)==.5)
grd3 -= grd
self.failUnless(geom.TanimotoDistance(grd3,grd)==1.0)
self.failUnless(geom.TanimotoDistance(grd3,grd2)==0)
grd4 = geom.UniformGrid3D(10, 10, 10)
grd4.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
grd4.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)
grd4.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
self.failUnless(feq(geom.TanimotoDistance(grd4,grd),.3333))
self.failUnless(feq(geom.TanimotoDistance(grd4,grd2),.75))
grd4&=grd2
self.failUnless(feq(geom.TanimotoDistance(grd4,grd),1.0))
self.failUnless(feq(geom.TanimotoDistance(grd4,grd2),.5))
if __name__=='__main__':
print "Testing Geometry wrapper"
unittest.main()
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