def test_vs_similarity():
"""VS similarity filter (USRs, IFPs) tests"""
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
receptor = next(oddt.toolkit.readfile('pdb', xiap_protein))
# following toolkit differences is due to different Hs treatment
vs = virtualscreening(n_cpu=1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('usr', cutoff=0.4, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 11
else:
assert len(list(vs.fetch())) == 6
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('usr_cat', cutoff=0.3, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 16
else:
assert len(list(vs.fetch())) == 11
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('electroshape', cutoff=0.45, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 55
else:
assert len(list(vs.fetch())) == 95
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('ifp', cutoff=0.95, query=ref_mol, protein=receptor)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 3
else:
assert len(list(vs.fetch())) == 6
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('sifp', cutoff=0.9, query=ref_mol, protein=receptor)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 14
else:
assert len(list(vs.fetch())) == 21
# test wrong method error
with pytest.raises(ValueError):
vs.similarity('sift', query=ref_mol)
def test_vs_similarity():
"""VS similarity filter (USRs, IFPs) tests"""
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
receptor = next(oddt.toolkit.readfile('pdb', xiap_protein))
# following toolkit differences is due to different Hs treatment
vs = virtualscreening(n_cpu=1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('usr', cutoff=0.4, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 11
else:
assert len(list(vs.fetch())) == 6
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('usr_cat', cutoff=0.3, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 16
else:
assert len(list(vs.fetch())) == 11
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('electroshape', cutoff=0.45, query=ref_mol)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 55
else:
assert len(list(vs.fetch())) == 95
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('ifp', cutoff=0.95, query=ref_mol, protein=receptor)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 3
else:
assert len(list(vs.fetch())) == 6
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.similarity('sifp', cutoff=0.9, query=ref_mol, protein=receptor)
if oddt.toolkit.backend == 'ob':
assert len(list(vs.fetch())) == 14
else:
assert len(list(vs.fetch())) == 21
# test wrong method error
with pytest.raises(ValueError):
vs.similarity('sift', query=ref_mol)
def test_vs_pains():
"""VS PAINS filter tests"""
vs = virtualscreening(n_cpu=1)
# TODO: add some failing molecules
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('pains', soft_fail=0)
assert len(list(vs.fetch())) == 100
def test_vs_pains():
"""VS PAINS filter tests"""
vs = virtualscreening(n_cpu=1)
# TODO: add some failing molecules
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('pains', soft_fail=0)
assert len(list(vs.fetch())) == 100
def test_vs_pains():
"""VS PAINS filter tests"""
vs = virtualscreening(n_cpu=-1)
# TODO: add some failing molecules
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
vs.apply_filter('pains', soft_fail=0)
assert_equal(len(list(vs.fetch())), 100)
def test_vs_multithreading_fallback():
vs = virtualscreening(n_cpu=8)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
with pytest.warns(UserWarning, match='Falling back to sub-methods multithreading'):
method_caller(vs, 'fetch')
def test_vs_multithreading_fallback():
vs = virtualscreening(n_cpu=8)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
with pytest.warns(UserWarning, match='Falling back to sub-methods multithreading'):
method_caller(vs, 'fetch')
def test_vs_multithreading_fallback():
vs = virtualscreening(n_cpu=8)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
assert_warns_message(UserWarning,
'Falling back to sub-methods multithreading',
method_caller, vs, 'fetch')
def test_vs_filtering():
"""VS preset filtering tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('ro5', soft_fail=1)
assert len(list(vs.fetch())) == 49
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('ro3', soft_fail=2)
assert len(list(vs.fetch())) == 9
def test_vs_filtering():
"""VS preset filtering tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('ro5', soft_fail=1)
assert len(list(vs.fetch())) == 49
vs.load_ligands('sdf', xiap_actives_docked)
vs.apply_filter('ro3', soft_fail=2)
assert len(list(vs.fetch())) == 9
def test_vs_filtering():
"""VS preset filtering tests"""
vs = virtualscreening(n_cpu=-1)
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
vs.apply_filter('ro5', soft_fail=1)
assert_equal(len(list(vs.fetch())), 49)
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
vs.apply_filter('ro3', soft_fail=2)
assert_equal(len(list(vs.fetch())), 9)
def test_vs_docking_empty():
vs = virtualscreening(n_cpu=1)
vs.load_ligands('smi', os.path.join(dude_data_dir, 'actives_rdkit.smi'))
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=5,
num_modes=9,
size=(20, 20, 20),
seed=0)
assert_raises_regexp(ValueError, 'has no 3D coordinates', next, vs.fetch())
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=-1)
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/crystal_ligand.sdf'))
vs.dock(engine='autodock_vina',
protein=os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb'),
auto_ligand=os.path.join(test_data_dir, 'data/dude/xiap/crystal_ligand.sdf'),
exhaustiveness=1,
seed=0)
mols = list(vs.fetch())
assert_equal(len(mols), 3)
mol_data = mols[0].data
assert_in('vina_affinity', mol_data)
assert_in('vina_rmsd_lb', mol_data)
assert_in('vina_rmsd_ub', mol_data)
def test_vs_docking_empty():
vs = virtualscreening(n_cpu=1)
vs.load_ligands('smi', os.path.join(dude_data_dir, 'actives_rdkit.smi'))
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=5,
num_modes=9,
size=(20, 20, 20),
seed=0)
with pytest.raises(ValueError, match='has no 3D coordinates'):
next(vs.fetch())
def test_vs_scoring_vina():
"""VS scoring (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/crystal_ligand.sdf'))
vs.score(function='autodock_vina',
protein=os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb'))
mols = list(vs.fetch())
assert_equal(len(mols), 1)
mol_data = mols[0].data
assert_in('vina_affinity', mol_data)
assert_in('vina_gauss1', mol_data)
assert_in('vina_gauss2', mol_data)
assert_in('vina_hydrogen', mol_data)
assert_in('vina_hydrophobic', mol_data)
assert_in('vina_repulsion', mol_data)
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
# bad docking engine
with pytest.raises(ValueError):
vs.dock('srina', 'prot.pdb')
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=6,
num_modes=7,
size=(20, 20, 20),
seed=0)
mols = list(vs.fetch())
assert len(mols) == 7
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_rmsd_lb' in mol_data
assert 'vina_rmsd_ub' in mol_data
if oddt.toolkit.backend == 'ob':
vina_scores = [-5.3, -4.0, -3.8, -3.7, -3.4, -3.4, -3.0]
else:
vina_scores = [-6.3, -6.0, -5.8, -5.8, -3.9, -3.0, -1.1]
assert_array_equal([float(m.data['vina_affinity']) for m in mols],
vina_scores)
# verify the SMILES of molecules
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
if oddt.toolkit.backend == 'ob':
# OB 2.3.2 will fail the following, since Hs are removed, etc.
# OB 2.4 recognizes the smiles chirality wrong
pass
else:
vina_rmsd = [
8.153314, 5.32554, 8.514586, 8.510169, 9.060128, 8.995098, 8.626776
]
assert_array_equal([mol.smiles for mol in mols],
[ref_mol.smiles] * len(mols))
assert_array_almost_equal(
[rmsd(ref_mol, mol, method='min_symmetry') for mol in mols],
vina_rmsd)
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
# bad docking engine
with pytest.raises(ValueError):
vs.dock('srina', 'prot.pdb')
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=6,
num_modes=7,
size=(20, 20, 20),
seed=0)
mols = list(vs.fetch())
assert len(mols) == 7
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_rmsd_lb' in mol_data
assert 'vina_rmsd_ub' in mol_data
if oddt.toolkit.backend == 'ob':
vina_scores = [-5.3, -4.0, -3.8, -3.7, -3.4, -3.4, -3.0]
else:
vina_scores = [-6.3, -6.0, -5.8, -5.8, -3.9, -3.0, -1.1]
assert_array_equal([float(m.data['vina_affinity']) for m in mols], vina_scores)
# verify the SMILES of molecules
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
if oddt.toolkit.backend == 'ob':
# OB 2.3.2 will fail the following, since Hs are removed, etc.
# OB 2.4 recognizes the smiles chirality wrong
pass
else:
vina_rmsd = [8.153314, 5.32554, 8.514586, 8.510169, 9.060128, 8.995098,
8.626776]
assert_array_equal([mol.smiles for mol in mols],
[ref_mol.smiles] * len(mols))
assert_array_almost_equal([rmsd(ref_mol, mol, method='min_symmetry')
for mol in mols], vina_rmsd)
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', os.path.join(test_data_dir, 'data/dude/xiap/crystal_ligand.sdf'))
vs.dock(engine='autodock_vina',
protein=os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb'),
auto_ligand=os.path.join(test_data_dir, 'data/dude/xiap/crystal_ligand.sdf'),
exhaustiveness=1,
num_modes=9,
size=(20, 20, 20),
seed=0)
mols = list(vs.fetch())
assert_equal(len(mols), 9)
mol_data = mols[0].data
assert_in('vina_affinity', mol_data)
assert_in('vina_rmsd_lb', mol_data)
assert_in('vina_rmsd_ub', mol_data)
assert_array_equal([float(m.data['vina_affinity']) for m in mols],
[-6.3, -6., -6., -5.9, -5.9, -5.8, -5.2, -4.2, -3.9])
def test_vs_scoring_vina():
"""VS scoring (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
mols = list(vs.fetch())
assert_equal(len(mols), 1)
mol_data = mols[0].data
assert_in('vina_affinity', mol_data)
assert_in('vina_gauss1', mol_data)
assert_in('vina_gauss2', mol_data)
assert_in('vina_hydrogen', mol_data)
assert_in('vina_hydrophobic', mol_data)
assert_in('vina_repulsion', mol_data)
assert_equal(mol_data['vina_affinity'], '-3.57594')
assert_equal(mol_data['vina_gauss1'], '63.01213')
assert_equal(mol_data['vina_gauss2'], '999.07625')
assert_equal(mol_data['vina_hydrogen'], '0.0')
assert_equal(mol_data['vina_hydrophobic'], '26.12648')
assert_equal(mol_data['vina_repulsion'], '3.63178')
def test_vs_scoring_vina():
"""VS scoring (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
mols = list(vs.fetch())
assert len(mols) == 1
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_gauss1' in mol_data
assert 'vina_gauss2' in mol_data
assert 'vina_hydrogen' in mol_data
assert 'vina_hydrophobic' in mol_data
assert 'vina_repulsion' in mol_data
assert mol_data['vina_affinity'] == '-3.57594'
assert mol_data['vina_gauss1'] == '63.01213'
assert mol_data['vina_gauss2'] == '999.07625'
assert mol_data['vina_hydrogen'] == '0.0'
assert mol_data['vina_hydrophobic'] == '26.12648'
assert mol_data['vina_repulsion'] == '3.63178'
def test_vs_scoring_vina():
"""VS scoring (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
vs.score(function='autodock_vina', protein=xiap_protein)
mols = list(vs.fetch())
assert len(mols) == 1
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_gauss1' in mol_data
assert 'vina_gauss2' in mol_data
assert 'vina_hydrogen' in mol_data
assert 'vina_hydrophobic' in mol_data
assert 'vina_repulsion' in mol_data
assert mol_data['vina_affinity'] == '-3.57594'
assert mol_data['vina_gauss1'] == '63.01213'
assert mol_data['vina_gauss2'] == '999.07625'
assert mol_data['vina_hydrogen'] == '0.0'
assert mol_data['vina_hydrophobic'] == '26.12648'
assert mol_data['vina_repulsion'] == '3.63178'
def test_vs_scoring():
protein = next(oddt.toolkit.readfile('pdb', xiap_protein))
protein.protein = True
data_dir = os.path.join(test_data_dir, 'data')
home_dir = mkdtemp()
pdbbind_versions = (2007, 2013, 2016)
pdbbind_dir = os.path.join(data_dir, 'pdbbind')
for pdbbind_v in pdbbind_versions:
version_dir = os.path.join(data_dir, 'v%s' % pdbbind_v)
if not os.path.isdir(version_dir):
os.symlink(pdbbind_dir, version_dir)
filenames = []
# train mocked SFs
for model in [nnscore(n_jobs=1)
] + [rfscore(version=v, n_jobs=1) for v in [1, 2, 3]]:
model.gen_training_data(data_dir,
pdbbind_versions=pdbbind_versions,
home_dir=home_dir)
filenames.append(model.train(home_dir=home_dir))
vs = virtualscreening(n_cpu=-1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
# error if no protein is fed
with pytest.raises(ValueError):
vs.score('nnscore')
# bad sf name
with pytest.raises(ValueError):
vs.score('bad_sf', protein=protein)
vs.score('nnscore', protein=xiap_protein)
vs.score('nnscore_pdbbind2016', protein=protein)
vs.score('rfscore_v1', protein=protein)
vs.score('rfscore_v1_pdbbind2016', protein=protein)
vs.score('rfscore_v2', protein=protein)
vs.score('rfscore_v3', protein=protein)
# use pickle directly
vs.score(filenames[0], protein=protein)
# pass SF object directly
vs.score(scorer.load(filenames[0]), protein=protein)
# pass wrong object (sum is not an instance of scorer)
with pytest.raises(ValueError):
vs.score(sum, protein=protein)
mols = list(vs.fetch())
assert len(mols) == 100
mol_data = mols[0].data
assert 'nnscore' in mol_data
assert 'rfscore_v1' in mol_data
assert 'rfscore_v2' in mol_data
assert 'rfscore_v3' in mol_data
vs = virtualscreening(n_cpu=-1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
vs.score('nnscore', protein=protein)
vs.score('rfscore_v1', protein=protein)
vs.score('rfscore_v2', protein=protein)
vs.score('rfscore_v3', protein=protein)
with NamedTemporaryFile('w', suffix='.sdf') as molfile:
with NamedTemporaryFile('w', suffix='.csv') as csvfile:
vs.write('sdf', molfile.name, csv_filename=csvfile.name)
data = pd.read_csv(csvfile.name)
assert 'nnscore' in data.columns
assert 'rfscore_v1' in data.columns
assert 'rfscore_v2' in data.columns
assert 'rfscore_v3' in data.columns
mols = list(oddt.toolkit.readfile('sdf', molfile.name))
assert len(mols) == 100
vs.write_csv(
csvfile.name,
fields=['nnscore', 'rfscore_v1', 'rfscore_v2', 'rfscore_v3'])
data = pd.read_csv(csvfile.name)
assert len(data.columns) == 4
assert 'nnscore' in data.columns
assert 'rfscore_v1' in data.columns
assert 'rfscore_v2' in data.columns
assert 'rfscore_v3' in data.columns
# remove files
for f in filenames:
os.unlink(f)
# remove symlinks
for pdbbind_v in pdbbind_versions:
version_dir = os.path.join(data_dir, 'v%s' % pdbbind_v)
if os.path.islink(version_dir):
os.unlink(version_dir)
def test_vs_empty():
vs = virtualscreening(n_cpu=1)
with pytest.raises(StopIteration, match='no molecules loaded'):
vs.fetch()
def test_vs_scoring():
protein = next(oddt.toolkit.readfile('pdb', xiap_protein))
protein.protein = True
data_dir = os.path.join(test_data_dir, 'data')
home_dir = mkdtemp()
pdbbind_versions = (2007, 2013, 2016)
pdbbind_dir = os.path.join(data_dir, 'pdbbind')
for pdbbind_v in pdbbind_versions:
version_dir = os.path.join(data_dir, 'v%s' % pdbbind_v)
if not os.path.isdir(version_dir):
os.symlink(pdbbind_dir, version_dir)
filenames = []
# train mocked SFs
for model in [nnscore(n_jobs=1)] + [rfscore(version=v, n_jobs=1)
for v in [1, 2, 3]]:
model.gen_training_data(data_dir, pdbbind_versions=pdbbind_versions,
home_dir=home_dir)
filenames.append(model.train(home_dir=home_dir))
vs = virtualscreening(n_cpu=-1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
# error if no protein is fed
with pytest.raises(ValueError):
vs.score('nnscore')
# bad sf name
with pytest.raises(ValueError):
vs.score('bad_sf', protein=protein)
vs.score('nnscore', protein=xiap_protein)
vs.score('nnscore_pdbbind2016', protein=protein)
vs.score('rfscore_v1', protein=protein)
vs.score('rfscore_v1_pdbbind2016', protein=protein)
vs.score('rfscore_v2', protein=protein)
vs.score('rfscore_v3', protein=protein)
vs.score('pleclinear', protein=protein)
vs.score('pleclinear_p5_l1_s65536_pdbbind2016', protein=protein)
# use pickle directly
vs.score(filenames[0], protein=protein)
# pass SF object directly
vs.score(scorer.load(filenames[0]), protein=protein)
# pass wrong object (sum is not an instance of scorer)
with pytest.raises(ValueError):
vs.score(sum, protein=protein)
mols = list(vs.fetch())
assert len(mols) == 100
mol_data = mols[0].data
assert 'nnscore' in mol_data
assert 'rfscore_v1' in mol_data
assert 'rfscore_v2' in mol_data
assert 'rfscore_v3' in mol_data
assert 'PLEClinear_p5_l1_s65536' in mol_data
vs = virtualscreening(n_cpu=-1, chunksize=10)
vs.load_ligands('sdf', xiap_actives_docked)
vs.score('nnscore', protein=protein)
vs.score('rfscore_v1', protein=protein)
vs.score('rfscore_v2', protein=protein)
vs.score('rfscore_v3', protein=protein)
with NamedTemporaryFile('w', suffix='.sdf') as molfile:
with NamedTemporaryFile('w', suffix='.csv') as csvfile:
vs.write('sdf', molfile.name, csv_filename=csvfile.name)
data = pd.read_csv(csvfile.name)
assert 'nnscore' in data.columns
assert 'rfscore_v1' in data.columns
assert 'rfscore_v2' in data.columns
assert 'rfscore_v3' in data.columns
mols = list(oddt.toolkit.readfile('sdf', molfile.name))
assert len(mols) == 100
vs.write_csv(csvfile.name, fields=['nnscore', 'rfscore_v1',
'rfscore_v2', 'rfscore_v3'])
data = pd.read_csv(csvfile.name)
assert len(data.columns) == 4
assert 'nnscore' in data.columns
assert 'rfscore_v1' in data.columns
assert 'rfscore_v2' in data.columns
assert 'rfscore_v3' in data.columns
# remove files
for f in filenames:
os.unlink(f)
# remove symlinks
for pdbbind_v in pdbbind_versions:
version_dir = os.path.join(data_dir, 'v%s' % pdbbind_v)
if os.path.islink(version_dir):
os.unlink(version_dir)
def test_vs_empty():
vs = virtualscreening(n_cpu=1)
with pytest.raises(StopIteration, match='no molecules loaded'):
vs.fetch()