def test_raises_invalid_protein_assertion(self):
prot = _load_test_protein(
'alphafold/relax/testdata/multiple_disulfides_target.pdb')
prot.atom_mask[4, :] = 0
with self.assertRaisesRegex(
ValueError,
'Amber minimization can only be performed on proteins with well-defined'
' residues. This protein contains at least one residue with no atoms.'
):
amber_minimize.run_pipeline(prot,
max_iterations=10,
stiffness=1.,
max_attempts=1)
def process(
self, *,
prot: protein.Protein) -> Tuple[str, Dict[str, Any], np.ndarray]:
"""Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
out = amber_minimize.run_pipeline(
prot=prot,
max_iterations=self._max_iterations,
tolerance=self._tolerance,
stiffness=self._stiffness,
exclude_residues=self._exclude_residues,
max_outer_iterations=self._max_outer_iterations)
min_pos = out['pos']
start_pos = out['posinit']
rmsd = np.sqrt(np.sum((start_pos - min_pos)**2) / start_pos.shape[0])
debug_data = {
'initial_energy': out['einit'],
'final_energy': out['efinal'],
'attempts': out['min_attempts'],
'rmsd': rmsd
}
pdb_str = amber_minimize.clean_protein(prot)
min_pdb = utils.overwrite_pdb_coordinates(pdb_str, min_pos)
min_pdb = utils.overwrite_b_factors(min_pdb, prot.b_factors)
utils.assert_equal_nonterminal_atom_types(
protein.from_pdb_string(min_pdb).atom_mask, prot.atom_mask)
violations = out['structural_violations'][
'total_per_residue_violations_mask']
return min_pdb, debug_data, violations
def test_multiple_disulfides_target(self):
prot = _load_test_protein(
'alphafold/relax/testdata/multiple_disulfides_target.pdb')
ret = amber_minimize.run_pipeline(prot,
max_iterations=10,
max_attempts=1,
stiffness=10.)
self.assertIn('opt_time', ret)
self.assertIn('min_attempts', ret)
def test_iterative_relax(self):
prot = _load_test_protein(
'alphafold/relax/testdata/with_violations.pdb')
violations = amber_minimize.get_violation_metrics(prot)
self.assertGreater(violations['num_residue_violations'], 0)
out = amber_minimize.run_pipeline(prot=prot,
max_outer_iterations=10,
stiffness=10.)
self.assertLess(out['efinal'], out['einit'])
self.assertEqual(0, out['num_residue_violations'])