def test_splif_similarity():
"""SPLIF 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 = SPLIF(mols[0], receptor)
splif_fps = [SPLIF(mol, receptor) for mol in mols]
outcome = [similarity_SPLIF(ref, fp) for fp in splif_fps]
target_outcome = np.array([
1.000, 0.779, 0.660, 0.805, 0.630, 0.802, 0.366, 0.817, 0.378, 0.553,
0.732, 0.705, 0.856, 0.797, 0.502, 0.418, 0.653, 0.436, 0.708, 0.688
])
assert_array_almost_equal(outcome, target_outcome, decimal=3)
# check if similarity is symmetric
for fp1, fp2 in combinations(splif_fps, 2):
assert similarity_SPLIF(fp1, fp2) == similarity_SPLIF(fp2, fp1)
def test_splif_similarity():
"""SPLIF 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)
# print(outcome)
ref = SPLIF(mols[0], receptor)
outcome = [similarity_SPLIF(ref, SPLIF(mol, receptor)) for mol in mols[1:]]
if oddt.toolkit.backend == 'ob':
target_outcome = np.array([
0.751, 0.705, 0.76, 0.674, 0.745, 0.45, 0.754, 0.477, 0.614, 0.737,
0.727, 0.772, 0.747, 0.585, 0.535, 0.681, 0.554, 0.736, 0.729
])
else:
target_outcome = np.array([
0.751, 0.705, 0.76, 0.674, 0.745, 0.467, 0.754, 0.485, 0.637,
0.737, 0.727, 0.772, 0.747, 0.585, 0.535, 0.681, 0.554, 0.736,
0.729
])
assert_array_almost_equal(outcome, target_outcome, decimal=3)
def SPLIF_Fingerprint(ref_input, Listoflig, proteinpath):
F_Scores = [0] * len(Listoflig)
#protein = next(oddt.toolkit.readfile('pdb', proteinpath, removeHs=False, cleanupSubstructures=False, sanitize=False))
try:
protein = next(
oddt.toolkit.readfile('pdb', proteinpath, removeHs=False))
protein.protein = True
except Exception as e:
print(
"Input structure could not be split into protein and ligand. Please check ligand identifier."
)
f2 = open(os.path.join(os.path.basename(proteinpath), 'ErrorLog.txt'),
'w')
f2.write(str(e))
f2.close()
# Read in and define the reference ligand
#ref_ligand = next(oddt.toolkit.readfile('pdb', ref_input, removeHs=False, cleanupSubstructures=False, sanitize=False))
ref_ligand = next(oddt.toolkit.readfile('pdb', ref_input, removeHs=False))
ref = fp.SPLIF(ref_ligand, protein)
# Loop through each ligand in the list
count = 0
# print(Listoflig)
for ligandpath in Listoflig:
#ligand = next(oddt.toolkit.readfile('pdb', ligandpath, removeHs=False, cleanupSubstructures=False, sanitize=False))
ligand = next(oddt.toolkit.readfile('pdb', ligandpath, removeHs=False))
fp_query = fp.SPLIF(ligand, protein)
# similarity score for current query
F_Scores[count] = fp.similarity_SPLIF(ref, fp_query, rmsd_cutoff=3.)
count = count + 1
return F_Scores
def test_splif_similarity():
"""SPLIF 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 = SPLIF(mols[0], receptor)
outcome = [similarity_SPLIF(ref, SPLIF(mol, receptor)) for mol in mols]
if oddt.toolkit.backend == 'ob':
target_outcome = np.array([
1.000, 0.811, 0.690, 0.833, 0.654, 0.860, 0.373, 0.833, 0.389,
0.550, 0.790, 0.771, 0.915, 0.851, 0.525, 0.436, 0.701, 0.479,
0.743, 0.728
])
else:
target_outcome = np.array([
1.000, 0.811, 0.690, 0.833, 0.654, 0.860, 0.387, 0.833, 0.394,
0.572, 0.790, 0.771, 0.915, 0.851, 0.525, 0.436, 0.701, 0.479,
0.743, 0.728
])
assert_array_almost_equal(outcome, target_outcome, decimal=3)
def test_splif_similarity():
"""SPLIF 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)
# print(outcome)
ref = SPLIF(mols[0], receptor)
outcome = [similarity_SPLIF(ref, SPLIF(mol, receptor)) for mol in mols[1:]]
if oddt.toolkit.backend == 'ob':
target_outcome = np.array([0.694, 0.639, 0.707, 0.657, 0.690,
0.450, 0.702, 0.477, 0.576, 0.669,
0.658, 0.714, 0.683, 0.585, 0.535,
0.611, 0.554, 0.665, 0.697])
else:
target_outcome = np.array([0.694, 0.639, 0.707, 0.657, 0.690,
0.467, 0.702, 0.485, 0.599, 0.669,
0.658, 0.714, 0.683, 0.585, 0.535,
0.611, 0.554, 0.665, 0.697])
assert_array_almost_equal(outcome, target_outcome, decimal=3)
