def test7UniformGridIndices(self):
ugrid = geom.UniformGrid3D(20, 18, 15)
idx = ugrid.GetGridIndex(3, 2, 1)
xi, yi, zi = ugrid.GetGridIndices(idx)
self.assertEqual(xi, 3)
self.assertEqual(yi, 2)
self.assertEqual(zi, 1)
def ComputeMolShape(mol,
confId=-1,
boxDim=(20, 20, 20),
spacing=0.5,
**kwargs):
""" returns a grid representation of the molecule's shape
"""
res = rdGeometry.UniformGrid3D(boxDim[0],
boxDim[1],
boxDim[2],
spacing=spacing)
EncodeShape(mol, res, confId, **kwargs)
return res
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.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)
self.assertTrue(geom.TanimotoDistance(grd, grd2) == 1.0)
grd3 = copy.deepcopy(grd)
grd3 |= grd2
self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)
grd3 = copy.deepcopy(grd)
grd3 += grd2
self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)
grd3 -= grd
self.assertTrue(geom.TanimotoDistance(grd3, grd) == 1.0)
self.assertTrue(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.assertTrue(feq(geom.TanimotoDistance(grd4, grd), .3333))
self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .75))
grd4 &= grd2
self.assertTrue(feq(geom.TanimotoDistance(grd4, grd), 1.0))
self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .5))
def test4GridPickles(self):
grd = geom.UniformGrid3D(10.0, 9.0, 8.0, 0.5)
self.assertTrue(grd.GetNumX() == 20)
self.assertTrue(grd.GetNumY() == 18)
self.assertTrue(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.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)
grd2 = pickle.loads(pickle.dumps(grd))
self.assertTrue(grd2.GetNumX() == 20)
self.assertTrue(grd2.GetNumY() == 18)
self.assertTrue(grd2.GetNumZ() == 16)
self.assertTrue(geom.TanimotoDistance(grd, grd2) == 0.0)
def ComputeMolVolume(mol, confId=-1, gridSpacing=0.2, boxMargin=2.0):
""" Calculates the volume of a particular conformer of a molecule
based on a grid-encoding of the molecular shape.
"""
mol = rdchem.Mol(mol)
conf = mol.GetConformer(confId)
CanonicalizeConformer(conf)
box = ComputeConfBox(conf)
sideLen = (box[1].x - box[0].x + 2 * boxMargin, box[1].y - box[0].y + 2 * boxMargin,
box[1].z - box[0].z + 2 * boxMargin)
shape = rdGeometry.UniformGrid3D(sideLen[0], sideLen[1], sideLen[2], spacing=gridSpacing)
EncodeShape(mol, shape, confId, ignoreHs=False, vdwScale=1.0)
voxelVol = gridSpacing**3
occVect = shape.GetOccupancyVect()
voxels = [1 for x in occVect if x == 3]
vol = voxelVol * len(voxels)
return vol
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.assertTrue(grd.GetValPoint(bPt1) == grd.GetValPoint(bPt2))
bPt1.x = -4.0
bPt2.x = 4.0
bPt1.y = -2.0
bPt2.y = -2.0
def get_molec_shape(mol, conf, confId, vdwScale=1.0,
boxMargin=2.0, spacing=0.2):
"""
Get the shape of a conformer of a molecule as a grid
representation.
"""
box = Chem.ComputeConfBox(conf)
sideLen = (box[1].x-box[0].x + 2*boxMargin,
box[1].y-box[0].y + 2*boxMargin,
box[1].z-box[0].z + 2*boxMargin)
shape = rdGeometry.UniformGrid3D(2*sideLen[0],
2*sideLen[1],
2*sideLen[2],
spacing=spacing)
Chem.EncodeShape(
mol,
shape,
confId=confId,
ignoreHs=False,
vdwScale=vdwScale
)
return box, sideLen, shape
def ComputeMolVolume(mol, confId=-1, gridSpacing=0.2, boxMargin=2.0):
""" Calculates the volume of a particular conformer of a molecule
based on a grid-encoding of the molecular shape.
A bit of demo as well as a test of github #1883:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> mol = Chem.AddHs(Chem.MolFromSmiles('C'))
>>> AllChem.EmbedMolecule(mol)
0
>>> ComputeMolVolume(mol)
34...
>>> mol = Chem.AddHs(Chem.MolFromSmiles('O'))
>>> AllChem.EmbedMolecule(mol)
0
>>> ComputeMolVolume(mol)
23...
"""
mol = rdchem.Mol(mol)
conf = mol.GetConformer(confId)
CanonicalizeConformer(conf, ignoreHs=False)
box = ComputeConfBox(conf)
sideLen = (box[1].x - box[0].x + 2 * boxMargin,
box[1].y - box[0].y + 2 * boxMargin,
box[1].z - box[0].z + 2 * boxMargin)
shape = rdGeometry.UniformGrid3D(sideLen[0],
sideLen[1],
sideLen[2],
spacing=gridSpacing)
EncodeShape(mol, shape, confId, ignoreHs=False, vdwScale=1.0)
voxelVol = gridSpacing**3
occVect = shape.GetOccupancyVect()
voxels = [1 for x in occVect if x == 3]
vol = voxelVol * len(voxels)
return vol
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))
