def test_similarity():
"""FP similarity"""
mols = list(
oddt.toolkit.readfile(
'sdf',
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
list(map(lambda x: x.addh(only_polar=True), mols))
receptor = next(
oddt.toolkit.readfile(
'pdb',
os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb')))
receptor.protein = True
receptor.addh(only_polar=True)
ref = SimpleInteractionFingerprint(mols[0], receptor)
outcome = [
dice(ref, SimpleInteractionFingerprint(mol, receptor))
for mol in mols[1:]
]
if oddt.toolkit.backend == 'ob':
target_outcome = np.array([
0.8, 0.625, 0.764706, 0.628571, 0.764706, 0.611111, 0.787879, 0.6,
0.62069, 0.6875, 0.555556, 0.727273, 0.642857, 0.685714, 0.736842,
0.666667, 0.484848, 0.533333, 0.588235
])
else:
target_outcome = np.array([
0.810811, 0.625, 0.777778, 0.611111, 0.777778, 0.648649, 0.787879,
0.6, 0.6, 0.666667, 0.578947, 0.742857, 0.62069, 0.628571,
0.736842, 0.645161, 0.571429, 0.580645, 0.628571
])
assert_array_almost_equal(outcome, target_outcome)
outcome = [
tanimoto(ref, SimpleInteractionFingerprint(mol, receptor))
for mol in mols[1:]
]
if oddt.toolkit.backend == 'ob':
target_outcome = np.array([
0.75, 0.5, 0.727273, 0.538462, 0.727273, 0.727273, 0.8, 0.636364,
0.545455, 0.636364, 0.636364, 0.636364, 0.7, 0.727273, 0.75,
0.636364, 0.454545, 0.454545, 0.416667
])
else:
target_outcome = np.array([
0.75, 0.416667, 0.727273, 0.538462, 0.727273, 0.727273, 0.7,
0.636364, 0.545455, 0.545455, 0.636364, 0.636364, 0.6, 0.636364,
0.75, 0.545455, 0.545455, 0.454545, 0.416667
])
assert_array_almost_equal(outcome, target_outcome)
def test_SimpleInteractionFingerprint():
"""Simple Interaction Fingerprint test """
if oddt.toolkit.backend == 'ob':
SIFP = np.array([
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 6, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0
])
else:
SIFP = np.array([
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 6, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0
])
assert_array_equal(SIFP, SimpleInteractionFingerprint(ligand, protein))
def test_SimpleInteractionFingerprint():
"""Simple Interaction Fingerprint test """
SIFP = [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0
]
assert_array_equal(SIFP, SimpleInteractionFingerprint(ligand, protein))
def test_similarity():
"""FP similarity"""
mols = list(
oddt.toolkit.readfile(
'sdf',
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
list(map(lambda x: x.addh(only_polar=True), mols))
receptor = next(
oddt.toolkit.readfile(
'pdb',
os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb')))
receptor.protein = True
receptor.addh(only_polar=True)
ref = SimpleInteractionFingerprint(mols[0], receptor)
outcome = [
dice(ref, SimpleInteractionFingerprint(mol, receptor))
for mol in mols[1:]
]
target_outcome = np.array([
0.742857, 0.645161, 0.727273, 0.571429, 0.727273, 0.588235, 0.75,
0.551724, 0.551724, 0.6875, 0.514286, 0.6875, 0.592593, 0.647059,
0.736842, 0.62069, 0.545455, 0.533333, 0.606061
])
assert_array_almost_equal(outcome, target_outcome)
outcome = [
tanimoto(ref, SimpleInteractionFingerprint(mol, receptor))
for mol in mols[1:]
]
target_outcome = np.array([
0.636364, 0.5, 0.666667, 0.384615, 0.666667, 0.545455, 0.666667, 0.5,
0.363636, 0.666667, 0.555556, 0.555556, 0.625, 0.6, 0.727273, 0.555556,
0.5, 0.4, 0.363636
])
assert_array_almost_equal(outcome, target_outcome)
def test_IFP_SIFP_Folding_cum_sum():
"""Checks, whether InteractionFingerprint and SimpleInteractionFingerprint outcomes matches"""
IFP = np.sum(InteractionFingerprint(ligand, protein), axis=0)
SIFP = np.sum(SimpleInteractionFingerprint(ligand, protein), axis=0)
assert_array_equal(IFP, SIFP)