def setUp(self):
MoleculeTest.setUp(self)
self.molecule = Molecule(self.atom1, self.atom2, self.atom3)
other_atoms = [Mock(), Mock(), Mock(), Mock(), Mock(), Mock(), Mock()]
self.atom1.nearby_atoms.return_value = set(other_atoms[:3] +
self.atoms[1:])
self.atom2.nearby_atoms.return_value = set(other_atoms[2:5] +
self.atoms[::1])
self.atom3.nearby_atoms.return_value = set(other_atoms[4:] +
self.atoms[:2])
self.residues = [
Mock(), Mock(),
Mock(), Mock(),
Mock(), Mock(),
Mock()
]
self.waters = [Mock(), Mock(), Mock(), Mock()]
self.waters[0].name = "HOH"
other_atoms[0].residue = self.residues[0]
other_atoms[1].residue = self.residues[0]
other_atoms[2].residue = self.residues[1]
other_atoms[3].residue = self.residues[1]
other_atoms[4].residue = self.residues[2]
other_atoms[5].residue = self.residues[2]
other_atoms[4].name = "C"
other_atoms[5].name = "N"
other_atoms[3].element = "C"
other_atoms[4].element = "C"
other_atoms[5].element = "C"
other_atoms[2].element = "C"
other_atoms[6].residue = None
other_atoms[6].molecule = self.waters[0]
def test_can_create_molecule(self):
mol = Molecule(self.atom1, self.atom2, self.atom3)
self.assertIsInstance(mol, AtomicStructure)
self.mock_init.assert_called_with(mol, self.atom1, self.atom2,
self.atom3)
self.assertEqual(mol._id, None)
self.assertEqual(mol._name, None)
def test_can_get_no_model(self, mock_atoms):
mock_atoms.return_value = set(self.atoms)
self.atom1.model = None
self.atom2.model = None
self.atom3.model = None
mol = Molecule(self.atom1, self.atom2, self.atom3)
self.assertIs(mol.model, None)
def test_can_get_model(self, mock_atoms):
mock_atoms.return_value = set(self.atoms)
model = Mock()
self.atom1.model = model
self.atom2.model = model
self.atom3.model = model
mol = Molecule(self.atom1, self.atom2, self.atom3)
self.assertIs(mol.model, model)
def ligand_contacts_protein(ligand: Molecule, model: Model) -> bool:
"""Determines if molecule is in contact with protein
Args:
ligand: The molecule
model: Model containing protein chains
Returns:
True if in contact and false when not in contact
"""
dist = 999.0
for latom in ligand.atoms():
for chain in model.chains():
for patom in chain.atoms():
ndist = latom.distance_to(patom)
if ndist < dist:
dist = ndist
# Added 1 angstrom because ligand is not protonated
return dist < MAX_CONTACT_DISTANCE + 1
def site(self, radius=BINDING_SITE_RADIUS) -> Site:
"""Site of fragment
If part of residue is inside radius then it is included in site.
Args:
radius (float): Radius of ligand within residues are included in site
Returns:
atomium.structures.chains.Site: Site
"""
fragment_positions = self.atom_positions()
atoms_of_near_residues = set()
residues = self.parent.model().residues()
for residue in residues:
if is_residue_nearby(fragment_positions, residue, radius):
atoms_of_near_residues.update(residue.atoms())
name = 'fragment of ' + self.parent.name()
ligand = Molecule(*self.atoms(), name=name)
return Site(*atoms_of_near_residues, ligand=ligand)
def test_atoms_are_linked_to_molecule(self):
mol = Molecule(self.atom1, self.atom2, self.atom3)
self.assertIs(self.atom1._molecule, mol)
self.assertIs(self.atom2._molecule, mol)
self.assertIs(self.atom3._molecule, mol)
def test_molecule_name_must_be_str(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, name="VAL")
with self.assertRaises(TypeError):
mol.name = 10
def test_can_update_molecule_name(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, name="VAL")
mol.name = "HIS"
self.assertEqual(mol._name, "HIS")
def test_molecule_name_property(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, name="VAL")
self.assertIs(mol._name, mol.name)
def test_molecule_id_property(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, id="B10C")
self.assertIs(mol._id, mol.id)
def test_molecule_repr_id_and_name(self):
mol = Molecule(self.atom1, self.atom2, id="B10B", name="GLY")
self.assertEqual(str(mol), "<Molecule B10B (GLY, 2 atoms)>")
def test_molecule_repr_name_no_id(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, name="GLY")
self.assertEqual(str(mol), "<Molecule (GLY, 3 atoms)>")
def test_molecule_repr_id_no_name(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, id="B10A")
self.assertEqual(str(mol), "<Molecule B10A (3 atoms)>")
def test_molecule_repr_no_id_or_name(self):
mol = Molecule(self.atom1, self.atom2, self.atom3)
self.assertEqual(str(mol), "<Molecule (3 atoms)>")
def test_molecule_name_must_be_str(self):
with self.assertRaises(TypeError):
Molecule(self.atom1, self.atom2, self.atom3, name=1000)
def test_can_create_molecule_with_name(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, name="HIS")
self.assertEqual(mol._name, "HIS")
def test_can_create_molecule_with_id(self):
mol = Molecule(self.atom1, self.atom2, self.atom3, id="A100")
self.assertEqual(mol._id, "A100")
class MoleculeSiteTests(MoleculeTest):
def setUp(self):
MoleculeTest.setUp(self)
self.molecule = Molecule(self.atom1, self.atom2, self.atom3)
other_atoms = [Mock(), Mock(), Mock(), Mock(), Mock(), Mock(), Mock()]
self.atom1.nearby_atoms.return_value = set(other_atoms[:3] +
self.atoms[1:])
self.atom2.nearby_atoms.return_value = set(other_atoms[2:5] +
self.atoms[::1])
self.atom3.nearby_atoms.return_value = set(other_atoms[4:] +
self.atoms[:2])
self.residues = [
Mock(), Mock(),
Mock(), Mock(),
Mock(), Mock(),
Mock()
]
self.waters = [Mock(), Mock(), Mock(), Mock()]
self.waters[0].name = "HOH"
other_atoms[0].residue = self.residues[0]
other_atoms[1].residue = self.residues[0]
other_atoms[2].residue = self.residues[1]
other_atoms[3].residue = self.residues[1]
other_atoms[4].residue = self.residues[2]
other_atoms[5].residue = self.residues[2]
other_atoms[4].name = "C"
other_atoms[5].name = "N"
other_atoms[3].element = "C"
other_atoms[4].element = "C"
other_atoms[5].element = "C"
other_atoms[2].element = "C"
other_atoms[6].residue = None
other_atoms[6].molecule = self.waters[0]
@patch("atomium.structures.Molecule.atoms")
@patch("atomium.structures.chains.Site")
def test_can_get_site(self, mock_site, mock_atoms):
mock_atoms.return_value = set(self.atoms)
returned_site = self.molecule.site()
mock_atoms.assert_called_with(hydrogen=False)
self.atom1.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom2.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom3.nearby_atoms.assert_called_with(4, hydrogen=False)
residues_passed = mock_site.call_args_list[0][0]
self.assertEqual(set(residues_passed), set(self.residues[:2]))
kwargs = mock_site.call_args_list[0][1]
self.assertEqual(kwargs, {"ligand": self.molecule})
@patch("atomium.structures.Molecule.atoms")
@patch("atomium.structures.chains.Site")
def test_can_get_site_with_water(self, mock_site, mock_atoms):
mock_atoms.return_value = set(self.atoms)
returned_site = self.molecule.site(water=True)
mock_atoms.assert_called_with(hydrogen=False)
self.atom1.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom2.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom3.nearby_atoms.assert_called_with(4, hydrogen=False)
residues_passed = mock_site.call_args_list[0][0]
self.assertEqual(set(residues_passed),
set(self.residues[:2] + self.waters[:1]))
kwargs = mock_site.call_args_list[0][1]
self.assertEqual(kwargs, {"ligand": self.molecule})
@patch("atomium.structures.Molecule.atoms")
@patch("atomium.structures.chains.Site")
def test_can_get_site_with_main_chain(self, mock_site, mock_atoms):
mock_atoms.return_value = set(self.atoms)
returned_site = self.molecule.site(main_chain=True)
mock_atoms.assert_called_with(hydrogen=False)
self.atom1.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom2.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom3.nearby_atoms.assert_called_with(4, hydrogen=False)
residues_passed = mock_site.call_args_list[0][0]
self.assertEqual(set(residues_passed), set(self.residues[:3]))
kwargs = mock_site.call_args_list[0][1]
self.assertEqual(kwargs, {"ligand": self.molecule})
@patch("atomium.structures.Molecule.atoms")
@patch("atomium.structures.chains.Site")
def test_can_get_site_with_cutoff(self, mock_site, mock_atoms):
mock_atoms.return_value = set(self.atoms)
returned_site = self.molecule.site(cutoff=1)
mock_atoms.assert_called_with(hydrogen=False)
self.atom1.nearby_atoms.assert_called_with(1, hydrogen=False)
self.atom2.nearby_atoms.assert_called_with(1, hydrogen=False)
self.atom3.nearby_atoms.assert_called_with(1, hydrogen=False)
residues_passed = mock_site.call_args_list[0][0]
self.assertEqual(set(residues_passed), set(self.residues[:2]))
kwargs = mock_site.call_args_list[0][1]
self.assertEqual(kwargs, {"ligand": self.molecule})
@patch("atomium.structures.Molecule.atoms")
@patch("atomium.structures.chains.Site")
def test_can_get_site_without_carbon(self, mock_site, mock_atoms):
mock_atoms.return_value = set(self.atoms)
returned_site = self.molecule.site(carbon=False)
mock_atoms.assert_called_with(hydrogen=False)
self.atom1.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom2.nearby_atoms.assert_called_with(4, hydrogen=False)
self.atom3.nearby_atoms.assert_called_with(4, hydrogen=False)
residues_passed = mock_site.call_args_list[0][0]
self.assertEqual(set(residues_passed), set(self.residues[:1]))
kwargs = mock_site.call_args_list[0][1]
self.assertEqual(kwargs, {"ligand": self.molecule})