def test_load_bonds_from_pdb(self):
"""
TestPDB: Verifies that bonds can be loaded from PDB.
"""
pdb = PDB()
# Test that we can load CO2
carbon_atom = Atom(element="C")
oxygen_atom_1 = Atom(element="O")
oxygen_atom_2 = Atom(element="O")
pdb.add_new_atom(carbon_atom)
pdb.add_new_atom(oxygen_atom_1)
pdb.add_new_atom(oxygen_atom_2)
lines = [
"CONECT 1 2 3 "
"CONECT 2 "
"CONECT 3 "
]
with tempfile.NamedTemporaryFile() as temp:
temp.write("\n".join(lines))
temp.flush()
pdb.load_bonds_from_pdb(temp.name)
assert len(carbon_atom.indices_of_atoms_connecting) == 2
assert len(oxygen_atom_1.indices_of_atoms_connecting) == 0
assert len(oxygen_atom_2.indices_of_atoms_connecting) == 0
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.0
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
class TestAtom(unittest.TestCase):
"""
Test atom class.
"""
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.0
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
def test_copy_of(self):
"""
TestAtom: Verify that copy_of preserves atom information.
"""
copy_atom = self.trial_atom.copy_of()
assert copy_atom.atomname == "C"
assert np.array_equal(copy_atom.coordinates.as_array(), np.array([1, 2, 3]))
assert copy_atom.charge == 0
assert copy_atom.element == "C"
assert copy_atom.residue == "CYS"
assert copy_atom.chain == "FF"
assert copy_atom.indices_of_atoms_connecting == [4, 5, 6]
def test_create_pdb_line(self):
"""
TestAtom: Verify that PDB Line is in correct format.
"""
# TODO(bramsundar): Add a more nontrivial test after looking into
# PDB standard.
line = self.trial_atom.create_pdb_line(1)
assert type(line) == str
def test_number_of_neighors(self):
"""
TestAtom: Verify that the number of neighbors is computed correctly.
"""
assert self.empty_atom.number_of_neighbors() == 0
assert self.trial_atom.number_of_neighbors() == 3
class TestAtom(unittest.TestCase):
"""
Test atom class.
"""
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
def test_copy_of(self):
"""
TestAtom: Verify that copy_of preserves atom information.
"""
copy_atom = self.trial_atom.copy_of()
assert copy_atom.atomname == "C"
assert np.array_equal(copy_atom.coordinates.as_array(),
np.array([1, 2, 3]))
assert copy_atom.charge == 0
assert copy_atom.element == "C"
assert copy_atom.residue == "CYS"
assert copy_atom.chain == "FF"
assert copy_atom.indices_of_atoms_connecting == [4, 5, 6]
def test_create_pdb_line(self):
"""
TestAtom: Verify that PDB Line is in correct format.
"""
# TODO(bramsundar): Add a more nontrivial test after looking into
# PDB standard.
line = self.trial_atom.create_pdb_line(1)
assert type(line) == str
def test_number_of_neighors(self):
"""
TestAtom: Verify that the number of neighbors is computed correctly.
"""
assert self.empty_atom.number_of_neighbors() == 0
assert self.trial_atom.number_of_neighbors() == 3
def test_add_new_atom(self):
"""
TestPDB: Verifies that new atoms can be added.
"""
# Verify that no atoms are present when we start.
assert len(self.pdb.all_atoms.keys()) == 0
empty_atom = Atom()
self.pdb.add_new_atom(empty_atom)
# Verify that we now have one atom
assert len(self.pdb.all_atoms.keys()) == 1
def test_metallic_charges(self):
"""
TestPDB: Verify that non-protein charges are assigned properly.
"""
# Test metallic ion charge.
magnesium_pdb = PDB()
magnesium_atom = Atom(element="MG",
coordinates=Point(coords=np.array([0, 0, 0])))
magnesium_pdb.add_new_non_protein_atom(magnesium_atom)
metallic_charges = magnesium_pdb.identify_metallic_charges()
assert len(metallic_charges) == 1
def test_connected_heavy_atoms(self):
"""
TestPDB: Verifies retrieval of connected heavy atoms.
"""
# Verify that no atoms are present when we start.
assert len(self.pdb.all_atoms.keys()) == 0
carbon_atom = Atom(element="C")
oxygen_atom = Atom(element="O")
hydrogen_atom = Atom(element="H")
self.pdb.add_new_atom(carbon_atom)
self.pdb.add_new_atom(oxygen_atom)
self.pdb.add_new_atom(hydrogen_atom)
# We want a carboxyl, so C connects O and H
carbon_atom.indices_of_atoms_connecting = [2, 3]
oxygen_atom.indices_of_atoms_connecting = [1]
hydrogen_atom.indices_of_atoms_connecting = [1]
connected_heavy_atoms = self.pdb.connected_heavy_atoms(1)
assert len(connected_heavy_atoms) == 1
assert connected_heavy_atoms[0] == 2
def test_connected_heavy_atoms(self):
"""
TestPDB: Verifies retrieval of connected heavy atoms.
"""
# Verify that no atoms are present when we start.
assert len(self.pdb.all_atoms.keys()) == 0
carbon_atom = Atom(element="C")
oxygen_atom = Atom(element="O")
hydrogen_atom = Atom(element="H")
self.pdb.add_new_atom(carbon_atom)
self.pdb.add_new_atom(oxygen_atom)
self.pdb.add_new_atom(hydrogen_atom)
# We want a carboxyl, so C connects O and H
carbon_atom.indices_of_atoms_connecting = [2, 3]
oxygen_atom.indices_of_atoms_connecting = [1]
hydrogen_atom.indices_of_atoms_connecting = [1]
connected_heavy_atoms = self.pdb.connected_heavy_atoms(1)
assert len(connected_heavy_atoms) == 1
assert connected_heavy_atoms[0] == 2