def to_pdb(self):
self._populate_molecule()
self.molecule.add_sequential_ids()
self.molecule.update_internal_state()
parameters = Parameters()
self.molecule.set_force_field_parameters(parameters)
self._rotate_to_default_position()
return self.molecule
def setUp(self):
self.molecule = Molecule(pdb_file_location='tests/data/ref01.pdb')
self.parameters = Parameters()
self.molecule.set_force_field_parameters(self.parameters)
self.optimization = GradientDescent(self.atom_energy_function)
self.optimization.dimensions_number = 3
self.optimization.iterations = 40
self.optimization.precision = 0.01
self.optimization.small_step = 0.00015
self.optimization.smallest_step = self.optimization.small_step / 128
self.force_field = ForceField(self.parameters)
self.atom_index = 0
def test_rotation(self):
parameters = Parameters()
self.generated.set_force_field_parameters(parameters)
topology = self.generated.get_topology()
phi = []
psi = []
for i in range(len(input_phi_psi)):
phi.append(input_phi_psi[i][1])
psi.append(input_phi_psi[i][2])
topology.rotate_backbone('PHI', phi)
topology.rotate_backbone('PSI', psi)
expected = Molecule(pdb_file_location='tests/data/rotated.pdb')
rmsd = self.generated.rmsd(expected)
self.assertLess(rmsd, 0.05)
class AmberTestCase(unittest.TestCase):
def setUp(self):
self.parameters = Parameters()
def test_read_amino_acids(self):
self.assertEqual(len(self.parameters.amino_acids), 94)
def test_read_angle_type(self):
self.assertTrue(self.parameters.get_angle_type('CT', 'S', 'S') is not None)
def test_bond_atom_type(self):
for amino_acid in self.parameters.amino_acids.values():
for bond in amino_acid.bonds:
self.assertTrue(bond.atom_01_type is not None)
self.assertTrue(bond.atom_02_type is not None)
def test_read_molecule(self):
molecule = Molecule(pdb_file_location='tests/data/1l2y-01.pdb')
self.assertEqual(len(molecule.amino_acids), 20)
def setUp(self):
self.parameters = Parameters()
self.ligand = Molecule(pdb_file_location='tests/data/ligand.pdb')
def setUp(self): self.parameters = Parameters()