def test5errorHandling(self):
refPts = (
Geometry.Point3D(0.0, 0.0, 0.0),
Geometry.Point3D(1.0, 0.0, 0.0),
Geometry.Point3D(0.0, 1.0, 0.0),
Geometry.Point3D(0.0, 0.0, 1.0),
)
prbPts = (
1,
2,
3,
4,
)
self.assertRaises(ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = ()
self.assertRaises(ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = 1
self.assertRaises(ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = (
Geometry.Point3D(2.0, 2.0, 3.0),
Geometry.Point3D(3.0, 2.0, 3.0),
Geometry.Point3D(2.0, 3.0, 3.0),
(2.0, 2.0, 5.0),
)
self.assertRaises(ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
def test2Weights(self):
refPts = np.array(
[[-math.cos(math.pi / 6), -math.sin(math.pi / 6), 0.0],
[math.cos(math.pi / 6), -math.sin(math.pi / 6), 0.0],
[0.0, 1.0, 0.0]], np.float)
prbPts = np.array([[
-2 * math.sin(math.pi / 6) + 3.0, 2 * math.cos(math.pi / 6), 4.0
], [-2 * math.sin(math.pi / 6) + 3.0, -2 * math.cos(math.pi / 6), 4.0],
[5.0, 0.0, 4.0]], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 3.0))
target = [[-1.732, -1., 0.], [1.732, -1., 0.], [0., 2., 0.]]
cnt = 0
for item in list(prbPts):
self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = np.array([1.0, 1.0, 2.0], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(feq(res[0], 3.75))
cnt = 0
target = [[-1.732, -1.25, 0.], [1.732, -1.25, 0.], [0., 1.75, 0.]]
for item in list(prbPts):
self.assertTrue(lstFeq(transformPoint(res[1], item), target[cnt]))
cnt += 1
weights = [1.0, 1.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(feq(res[0], 3.75))
weights = [1.0, 2.0, 2.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, weights)
self.assertTrue(feq(res[0], 4.8))
def test3tetra(self):
refPts = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]], np.float)
prbPts = np.array([[2.0, 2.0, 3.0], [3.0, 2.0, 3.0], [2.0, 3.0, 3.0]],
np.float)
self.assertRaises(ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts))
prbPts = np.array([[2.0, 2.0, 3.0], [3.0, 2.0, 3.0], [2.0, 3.0, 3.0],
[2.0, 2.0, 4.0]], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
wts = [1.0, 1.0, 1.0]
self.assertRaises(
ValueError,
lambda: rdAlg.GetAlignmentTransform(refPts, prbPts, wts))
wts = [1.0, 1.0, 1.0, 1.0]
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.assertTrue(feq(res[0], 0.0))
# test reflection
prbPts = np.array([[2.0, 2.0, 3.0], [3.0, 2.0, 3.0], [2.0, 2.0, 4.0],
[2.0, 3.0, 3.0]], np.float)
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts)
self.assertTrue(feq(res[0], 1.0))
res = rdAlg.GetAlignmentTransform(refPts, prbPts, wts, 1)
self.assertTrue(feq(res[0], 0.0))
cnt = 0
refLst = list(refPts)
for item in list(prbPts):
self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
cnt += 1
def test1Basic(self):
# passing two numeric arrays
refPts = np.zeros((2, 3), np.float)
prbPts = np.zeros((2, 3), np.float)
refPts[1, 0] = 1.0
prbPts[0, 0] = 2.0
prbPts[0, 1] = 2.0
prbPts[1, 0] = 2.0
prbPts[1, 1] = 3.0
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
refLst = list(refPts)
cnt = 0
for item in list(prbPts):
self.assertTrue(lstFeq(transformPoint(res[1], item), refLst[cnt]))
cnt += 1
# repeat with with lists or tuples
refPts = ((0.0, 0.0, 0.0), (1.0, 0.0, 0.0))
prbPts = ((2.0, 2.0, 0.0), (2.0, 3.0, 0.0))
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
refPts = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]
prbPts = [[2.0, 2.0, 0.0], [2.0, 3.0, 0.0]]
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
# mix it up
refPts = np.zeros((2, 3), np.float)
refPts[1, 0] = 1.0
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
def test4points(self):
refPts = (
Geometry.Point3D(0.0, 0.0, 0.0),
Geometry.Point3D(1.0, 0.0, 0.0),
Geometry.Point3D(0.0, 1.0, 0.0),
Geometry.Point3D(0.0, 0.0, 1.0),
)
prbPts = (
Geometry.Point3D(2.0, 2.0, 3.0),
Geometry.Point3D(3.0, 2.0, 3.0),
Geometry.Point3D(2.0, 3.0, 3.0),
Geometry.Point3D(2.0, 2.0, 4.0),
)
res = rdAlg.GetAlignmentTransform(refPts, prbPts)
self.assertTrue(feq(res[0], 0.0))
def check_mol(mol):
res = []
mol.RemoveAllConformers()
match, mList = EmbedLib.MatchPharmacophoreToMol(mol, feat_fact, pcophore)
#mList = [ m for m in Set( mList ) ]
if match:
num_match = len(mList)
for i in range(num_match):
num_feature = len(mList[i])
for j in range(num_feature):
print mList[i][j].GetAtomIds(), mList[i][j].GetFamily()
bounds = rdDistGeom.GetMoleculeBoundsMatrix(mol)
pList = EmbedLib.GetAllPharmacophoreMatches(mList, bounds, pcophore)
num_match = len(pList)
phMatches = []
for i in range(num_match):
num_feature = len(pList[i])
phMatch = []
for j in range(num_feature):
phMatch.append(pList[i][j].GetAtomIds())
phMatches.append(phMatch)
for phMatch in phMatches:
bm, embeds, nFail = EmbedLib.EmbedPharmacophore(mol,
phMatch,
pcophore,
count=5,
silent=1)
print "-----> embeds num:", len(embeds)
for embed in embeds:
AllChem.UFFOptimizeMolecule(embed)
feats = feat_fact.GetFeaturesForMol(embed)
feats_dict = GetFeatsPerAtoms(feats)
match_feats = [feats_dict[atomid] for atomid in phMatch]
pro_mat = [list(feat.GetPos()) for feat in match_feats]
align_data = rdAlignment.GetAlignmentTransform(
ref_mat, pro_mat, maxIterations=200)
AllChem.TransformMol(embed, align_data[1])
print align_data[0]
print align_data[1]
res.append(embed)
else:
print "no hits"
return res
def get_transform_matrix(align_ref, conf_embed, atom_match):
"""Get the transformation matrix for a conformer.
Parameters
----------
align_ref: list of rdkit.Geometry.Point3D
list of pharmacophore reference points for the alignment.
conf_embed: rdkit.Chem.Conformer
The conformer embedding.
atom_match: list of list
List of list of atoms ids that match the pharmacophore.
Returns
-------
a 2-tuple
ssd: float
SSD value for the alignment.
transform_matrix: numpy.ndarray; shape(4, 4)
The transform matrix.
"""
align_probe = [] # probe points to align to reference points
for match_ids in atom_match:
dummy_point = Geometry.Point3D(0.0, 0.0, 0.0)
for id in match_ids:
dummy_point += conf_embed.GetAtomPosition(id)
dummy_point /= len(match_ids)
align_probe.append(dummy_point)
ssd, transform_matrix = rdAlignment.GetAlignmentTransform(
align_ref, align_probe)
return ssd, transform_matrix