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 test1Shape(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'ShapeHelpers', 'test_data', '1oir.mol')
m = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m)
dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
m = Chem.MolFromMolFile(fileN)
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(),
trans=trans)
dims -= dims1
offset -= offset1
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd1, 0, trans)
ovect = grd1.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd2, 0)
fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'ShapeHelpers', 'test_data', '1oir_conf.mol')
m2 = Chem.MolFromMolFile(fileN2)
rmsd = rdMolAlign.AlignMol(m, m2)
self.failUnless(feq(rdshp.ShapeTanimotoDist(m, m2), 0.2813))
dist = rdshp.ShapeTanimotoDist(mol1=m,
mol2=m2,
confId1=0,
confId2=0,
gridSpacing=0.25,
stepSize=0.125)
self.failUnless(feq(dist, 0.3021))
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5,
DataStructs.DiscreteValueType.TWOBITVALUE,
offset)
dims -= geom.Point3D(13.927, 16.97, 9.775)
offset -= geom.Point3D(-4.353, 16.829, 2.782)
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9275)
geom.WriteGridToFile(grd, '1oir_shape.grd')
m = Chem.MolFromMolFile(fileN)
lc, uc = rdshp.ComputeConfBox(m.GetConformer())
rdmt.CanonicalizeMol(m)
lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
lc -= geom.Point3D(-4.353, 16.829, 2.782)
uc -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc.Length(), 0.0))
self.failUnless(feq(uc.Length(), 0.0))
lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123)
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
self.failUnless(feq(lc1.Length(), 0.0))
self.failUnless(feq(uc1.Length(), 0.0))
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc2.Length(), 0.0))
self.failUnless(feq(uc2.Length(), 0.0))
