def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(),
"3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(),
"3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(), "3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(), "3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]
class TestBinana(unittest.TestCase):
"""
Test Binana Binding Pose Featurizer.
"""
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(),
"3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(),
"3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]
def test_compute_hydrophobic(self):
"""
TestBinana: Test that hydrophobic contacts are established.
"""
hydrophobics_dict = {}
for name, protein, ligand in self.test_cases:
hydrophobics_dict[name] = compute_hydrophobic_contacts(
ligand, protein)
for name, hydrophobics in hydrophobics_dict.iteritems():
print("Processing hydrohobics for %s" % name)
assert len(hydrophobics) == 6
assert "BACKBONE_ALPHA" in hydrophobics
assert "BACKBONE_BETA" in hydrophobics
assert "BACKBONE_OTHER" in hydrophobics
assert "SIDECHAIN_ALPHA" in hydrophobics
assert "SIDECHAIN_BETA" in hydrophobics
assert "SIDECHAIN_OTHER" in hydrophobics
def test_compute_electrostatics(self):
"""
TestBinana: Test that electrostatic energies are computed.
"""
electrostatics_dict = {}
for name, protein, ligand in self.test_cases:
electrostatics_dict[name] = compute_electrostatic_energy(
ligand, protein)
for name, electrostatics in electrostatics_dict.iteritems():
print("Processing electrostatics for %s" % name)
# The keys of these dicts are pairs of atomtypes, but the keys are
# sorted so that ("C", "O") is always written as "C_O". Thus, for N
# atom types, there are N*(N+1)/2 unique pairs.
num_atoms = len(Binana.atom_types)
assert len(electrostatics) == num_atoms * (num_atoms + 1) / 2
# TODO(rbharath): Charges are not computed correctly for certain
# ligands! (see 2y2h_ligand). Understand why this happens.
#assert np.count_nonzero(np.array(electrostatics.values())) > 0
def test_compute_flexibility(self):
"""
TestBinana: Gather statistics about active site protein atoms.
"""
active_site_dict = {}
for name, protein, ligand in self.test_cases:
active_site_dict[name] = compute_active_site_flexibility(
ligand, protein)
for name, active_site_flexibility in active_site_dict.iteritems():
print("Processing active site flexibility for %s" % name)
assert len(active_site_flexibility.keys()) == 6
assert "BACKBONE_ALPHA" in active_site_flexibility
assert "BACKBONE_BETA" in active_site_flexibility
assert "BACKBONE_OTHER" in active_site_flexibility
assert "SIDECHAIN_ALPHA" in active_site_flexibility
assert "SIDECHAIN_BETA" in active_site_flexibility
assert "SIDECHAIN_OTHER" in active_site_flexibility
def test_compute_hydrogen_bonds(self):
"""
TestBinana: Compute the number of hydrogen bonds.
TODO(rbharath): The hydrogen-bond angle cutoff seems like it's
incorrect to me. The hydrogens are placed by openbabel and aren't
optimized, so I'm pretty sure that this code will miss many hydrogen
bonds.
Here are some options:
-) Find a method to optimize the hydrogen placement.
-) Place a more permissive angle cutoff for hydrogens.
-) Allow for "buckets": angles 0-20, 20-40, 40-60, etc. and count the
number of hydrogen bonds in each bucket.
"""
hbonds_dict = {}
for name, protein, ligand in self.test_cases:
hbonds_dict[name] = compute_hydrogen_bonds(ligand, protein)
for name, hbonds in hbonds_dict.iteritems():
print("Processing hydrogen bonds for %s" % name)
assert len(hbonds) == 12
assert "HDONOR-LIGAND_BACKBONE_ALPHA" in hbonds
assert "HDONOR-LIGAND_BACKBONE_BETA" in hbonds
assert "HDONOR-LIGAND_BACKBONE_OTHER" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_ALPHA" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_BETA" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_OTHER" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_ALPHA" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_BETA" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_OTHER" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_ALPHA" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_BETA" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_OTHER" in hbonds
def test_compute_ligand_atom_counts(self):
"""
TestBinana: Compute the Number of Ligand Atom Counts.
"""
counts_dict = {}
for name, _, ligand in self.test_cases:
counts_dict[name] = compute_ligand_atom_counts(ligand)
for name, counts in counts_dict.iteritems():
print("Processing ligand atom counts for %s" % name)
#print counts
assert len(counts) == len(Binana.atom_types)
def test_compute_contacts(self):
"""
TestBinana: Compute contacts between Ligand and receptor.
"""
contacts_dict = {}
for name, protein, ligand in self.test_cases:
contacts_dict[name] = compute_contacts(ligand, protein)
num_atoms = len(Binana.atom_types)
for name, (close_contacts, contacts) in contacts_dict.iteritems():
print("Processing contacts for %s" % name)
print("close_contacts")
for key, val in close_contacts.iteritems():
if val != 0:
print(key, val)
print("len(close_contacts): " + str(len(close_contacts)))
print("contacts")
for key, val in contacts.iteritems():
if val != 0:
print(key, val)
print("len(contacts): " + str(len(contacts)))
print("Desired Number: " + str(num_atoms * (num_atoms + 1) / 2))
assert len(close_contacts) == num_atoms * (num_atoms + 1) / 2
assert len(contacts) == num_atoms * (num_atoms + 1) / 2
def test_compute_pi_pi_stacking(self):
"""
TestBinana: Compute Pi-Pi Stacking.
"""
# 1zea is the only example that has any pi-stacking.
pi_stacking_dict = {}
for name, protein, ligand in self.test_cases:
pi_stacking_dict[name] = compute_pi_pi_stacking(ligand, protein)
for name, pi_stacking in pi_stacking_dict.iteritems():
print("Processing pi-stacking for %s" % name)
assert len(pi_stacking) == 3
print(pi_stacking)
assert "STACKING_ALPHA" in pi_stacking
assert "STACKING_BETA" in pi_stacking
assert "STACKING_OTHER" in pi_stacking
def test_compute_pi_t(self):
"""
TestBinana: Compute Pi-T Interactions.
TODO(rbharath): I believe that the imatininb-cabl complex has a pi-T
interaction. This code has a bug since it reports that no such
interaction is found.
"""
pi_t_dict = {}
for name, protein, ligand in self.test_cases:
pi_t_dict[name] = compute_pi_t(ligand, protein)
for name, pi_t in pi_t_dict.iteritems():
print("Processing pi-T for %s" % name)
assert len(pi_t) == 3
assert "T-SHAPED_ALPHA" in pi_t
assert "T-SHAPED_BETA" in pi_t
assert "T-SHAPED_OTHER" in pi_t
def test_compute_pi_cation(self):
"""
TestBinana: Compute Pi-Cation Interactions.
"""
pi_cation_dict = {}
for name, protein, ligand in self.test_cases:
pi_cation_dict[name] = compute_pi_cation(ligand, protein)
for name, pi_cation in pi_cation_dict.iteritems():
print("Processing pi-cation for %s" % name)
assert len(pi_cation) == 6
assert 'PI-CATION_LIGAND-CHARGED_ALPHA' in pi_cation
assert 'PI-CATION_LIGAND-CHARGED_BETA' in pi_cation
assert 'PI-CATION_LIGAND-CHARGED_OTHER' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_ALPHA' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_BETA' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_OTHER' in pi_cation
def test_compute_salt_bridges(self):
"""
TestBinana: Compute Salt Bridges.
TODO(bramsundar): None of the examples contain salt-bridge interactions. Find a
complex with an actual salt-bridge interaction.
"""
salt_bridges_dict = {}
for name, protein, ligand in self.test_cases:
salt_bridges_dict[name] = compute_salt_bridges(ligand, protein)
for name, salt_bridges in salt_bridges_dict.iteritems():
print("Processing salt-bridges for %s" % name)
assert len(salt_bridges) == 3
print(salt_bridges)
assert 'SALT-BRIDGE_ALPHA' in salt_bridges
assert 'SALT-BRIDGE_BETA' in salt_bridges
assert 'SALT-BRIDGE_OTHER' in salt_bridges
def test_compute_input_vector(self):
"""
TestBinana: Compute Input Vector.
"""
features_dict = {}
for name, protein, ligand in self.test_cases:
features_dict[name] = self.binana.compute_input_vector(
ligand, protein)
num_atoms = len(Binana.atom_types)
# Lengths:
# ligand_receptor_close_contacts: N*(N+1)/2
# ligand_receptor_contacts: N*(N+1)/2
# ligand_receptor_electrostatics: N*(N+1)/2
# ligand_atom_counts: N
# hbonds: 12
# hydrophobics: 6
# stacking: 3
# pi_cation: 6
# t_shaped: 3
# active_site_flexibility: 6
# salt_bridges: 3
# rotatable_boonds_count: 1
total_len = (3 * num_atoms * (num_atoms + 1) / 2 + num_atoms + 12 + 6 +
3 + 6 + 3 + 6 + 3 + 1)
for name, input_vector in features_dict.iteritems():
print("Processing input-vector for %s" % name)
assert len(input_vector) == total_len
class TestBinana(unittest.TestCase):
"""
Test Binana Binding Pose Featurizer.
"""
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(), "3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(), "3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]
def test_compute_hydrophobic(self):
"""
TestBinana: Test that hydrophobic contacts are established.
"""
hydrophobics_dict = {}
for name, protein, ligand in self.test_cases:
hydrophobics_dict[name] = compute_hydrophobic_contacts(
ligand, protein)
for name, hydrophobics in hydrophobics_dict.iteritems():
print("Processing hydrohobics for %s" % name)
assert len(hydrophobics) == 6
assert "BACKBONE_ALPHA" in hydrophobics
assert "BACKBONE_BETA" in hydrophobics
assert "BACKBONE_OTHER" in hydrophobics
assert "SIDECHAIN_ALPHA" in hydrophobics
assert "SIDECHAIN_BETA" in hydrophobics
assert "SIDECHAIN_OTHER" in hydrophobics
def test_compute_electrostatics(self):
"""
TestBinana: Test that electrostatic energies are computed.
"""
electrostatics_dict = {}
for name, protein, ligand in self.test_cases:
electrostatics_dict[name] = compute_electrostatic_energy(
ligand, protein)
for name, electrostatics in electrostatics_dict.iteritems():
print("Processing electrostatics for %s" % name)
# The keys of these dicts are pairs of atomtypes, but the keys are
# sorted so that ("C", "O") is always written as "C_O". Thus, for N
# atom types, there are N*(N+1)/2 unique pairs.
num_atoms = len(Binana.atom_types)
assert len(electrostatics) == num_atoms*(num_atoms+1)/2
# TODO(rbharath): Charges are not computed correctly for certain
# ligands! (see 2y2h_ligand). Understand why this happens.
#assert np.count_nonzero(np.array(electrostatics.values())) > 0
def test_compute_flexibility(self):
"""
TestBinana: Gather statistics about active site protein atoms.
"""
active_site_dict = {}
for name, protein, ligand in self.test_cases:
active_site_dict[name] = compute_active_site_flexibility(
ligand, protein)
for name, active_site_flexibility in active_site_dict.iteritems():
print("Processing active site flexibility for %s" % name)
assert len(active_site_flexibility.keys()) == 6
assert "BACKBONE_ALPHA" in active_site_flexibility
assert "BACKBONE_BETA" in active_site_flexibility
assert "BACKBONE_OTHER" in active_site_flexibility
assert "SIDECHAIN_ALPHA" in active_site_flexibility
assert "SIDECHAIN_BETA" in active_site_flexibility
assert "SIDECHAIN_OTHER" in active_site_flexibility
def test_compute_hydrogen_bonds(self):
"""
TestBinana: Compute the number of hydrogen bonds.
TODO(rbharath): The hydrogen-bond angle cutoff seems like it's
incorrect to me. The hydrogens are placed by openbabel and aren't
optimized, so I'm pretty sure that this code will miss many hydrogen
bonds.
Here are some options:
-) Find a method to optimize the hydrogen placement.
-) Place a more permissive angle cutoff for hydrogens.
-) Allow for "buckets": angles 0-20, 20-40, 40-60, etc. and count the
number of hydrogen bonds in each bucket.
"""
hbonds_dict = {}
for name, protein, ligand in self.test_cases:
hbonds_dict[name] = compute_hydrogen_bonds(
ligand, protein)
for name, hbonds in hbonds_dict.iteritems():
print("Processing hydrogen bonds for %s" % name)
assert len(hbonds) == 12
assert "HDONOR-LIGAND_BACKBONE_ALPHA" in hbonds
assert "HDONOR-LIGAND_BACKBONE_BETA" in hbonds
assert "HDONOR-LIGAND_BACKBONE_OTHER" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_ALPHA" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_BETA" in hbonds
assert "HDONOR-LIGAND_SIDECHAIN_OTHER" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_ALPHA" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_BETA" in hbonds
assert "HDONOR-RECEPTOR_BACKBONE_OTHER" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_ALPHA" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_BETA" in hbonds
assert "HDONOR-RECEPTOR_SIDECHAIN_OTHER" in hbonds
def test_compute_ligand_atom_counts(self):
"""
TestBinana: Compute the Number of Ligand Atom Counts.
"""
counts_dict = {}
for name, _, ligand in self.test_cases:
counts_dict[name] = compute_ligand_atom_counts(
ligand)
for name, counts in counts_dict.iteritems():
print("Processing ligand atom counts for %s" % name)
#print counts
assert len(counts) == len(Binana.atom_types)
def test_compute_contacts(self):
"""
TestBinana: Compute contacts between Ligand and receptor.
"""
contacts_dict = {}
for name, protein, ligand in self.test_cases:
contacts_dict[name] = compute_contacts(
ligand, protein)
num_atoms = len(Binana.atom_types)
for name, (close_contacts, contacts) in contacts_dict.iteritems():
print("Processing contacts for %s" % name)
print("close_contacts")
for key, val in close_contacts.iteritems():
if val != 0:
print (key, val)
print("len(close_contacts): " + str(len(close_contacts)))
print("contacts")
for key, val in contacts.iteritems():
if val != 0:
print (key, val)
print("len(contacts): " + str(len(contacts)))
print("Desired Number: " + str(num_atoms*(num_atoms+1)/2))
assert len(close_contacts) == num_atoms*(num_atoms+1)/2
assert len(contacts) == num_atoms*(num_atoms+1)/2
def test_compute_pi_pi_stacking(self):
"""
TestBinana: Compute Pi-Pi Stacking.
"""
# 1zea is the only example that has any pi-stacking.
pi_stacking_dict = {}
for name, protein, ligand in self.test_cases:
pi_stacking_dict[name] = compute_pi_pi_stacking(
ligand, protein)
for name, pi_stacking in pi_stacking_dict.iteritems():
print("Processing pi-stacking for %s" % name)
assert len(pi_stacking) == 3
print(pi_stacking)
assert "STACKING_ALPHA" in pi_stacking
assert "STACKING_BETA" in pi_stacking
assert "STACKING_OTHER" in pi_stacking
def test_compute_pi_t(self):
"""
TestBinana: Compute Pi-T Interactions.
TODO(rbharath): I believe that the imatininb-cabl complex has a pi-T
interaction. This code has a bug since it reports that no such
interaction is found.
"""
pi_t_dict = {}
for name, protein, ligand in self.test_cases:
pi_t_dict[name] = compute_pi_t(
ligand, protein)
for name, pi_t in pi_t_dict.iteritems():
print("Processing pi-T for %s" % name)
assert len(pi_t) == 3
assert "T-SHAPED_ALPHA" in pi_t
assert "T-SHAPED_BETA" in pi_t
assert "T-SHAPED_OTHER" in pi_t
def test_compute_pi_cation(self):
"""
TestBinana: Compute Pi-Cation Interactions.
"""
pi_cation_dict = {}
for name, protein, ligand in self.test_cases:
pi_cation_dict[name] = compute_pi_cation(
ligand, protein)
for name, pi_cation in pi_cation_dict.iteritems():
print("Processing pi-cation for %s" % name)
assert len(pi_cation) == 6
assert 'PI-CATION_LIGAND-CHARGED_ALPHA' in pi_cation
assert 'PI-CATION_LIGAND-CHARGED_BETA' in pi_cation
assert 'PI-CATION_LIGAND-CHARGED_OTHER' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_ALPHA' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_BETA' in pi_cation
assert 'PI-CATION_RECEPTOR-CHARGED_OTHER' in pi_cation
def test_compute_salt_bridges(self):
"""
TestBinana: Compute Salt Bridges.
TODO(bramsundar): None of the examples contain salt-bridge interactions. Find a
complex with an actual salt-bridge interaction.
"""
salt_bridges_dict = {}
for name, protein, ligand in self.test_cases:
salt_bridges_dict[name] = compute_salt_bridges(
ligand, protein)
for name, salt_bridges in salt_bridges_dict.iteritems():
print("Processing salt-bridges for %s" % name)
assert len(salt_bridges) == 3
print(salt_bridges)
assert 'SALT-BRIDGE_ALPHA' in salt_bridges
assert 'SALT-BRIDGE_BETA' in salt_bridges
assert 'SALT-BRIDGE_OTHER' in salt_bridges
def test_compute_input_vector(self):
"""
TestBinana: Compute Input Vector.
"""
features_dict = {}
for name, protein, ligand in self.test_cases:
features_dict[name] = self.binana.compute_input_vector(
ligand, protein)
num_atoms = len(Binana.atom_types)
# Lengths:
# ligand_receptor_close_contacts: N*(N+1)/2
# ligand_receptor_contacts: N*(N+1)/2
# ligand_receptor_electrostatics: N*(N+1)/2
# ligand_atom_counts: N
# hbonds: 12
# hydrophobics: 6
# stacking: 3
# pi_cation: 6
# t_shaped: 3
# active_site_flexibility: 6
# salt_bridges: 3
# rotatable_boonds_count: 1
total_len = (3*num_atoms*(num_atoms+1)/2 + num_atoms
+ 12 + 6 + 3 + 6 + 3 + 6 + 3 + 1)
for name, input_vector in features_dict.iteritems():
print("Processing input-vector for %s" % name)
assert len(input_vector) == total_len
