def test_c_get_result(collapser, coll_molecule, coll_final_position_matrix):
original_pos_mat = coll_molecule.get_position_matrix()
subunits = coll_molecule.get_subunits(bond_pair_ids=((0, 3), ))
test_mol, results = collapser.get_result(
mol=coll_molecule,
bond_pair_ids=((0, 3), ),
subunits=subunits,
)
final_min_distance = min(
dist for dist in collapser._get_subunit_distances(test_mol, subunits))
# Give it some wiggle room.
assert np.isclose(1.4947505, final_min_distance, atol=1E-8)
# Check position matrix because this code is deterministic.
test_pos_mat = test_mol.get_position_matrix()
for i in range(len(coll_final_position_matrix)):
test = test_pos_mat[i]
given = coll_final_position_matrix[i]
assert np.all(np.isclose(test, given, atol=1E-8))
# Test all other bond lengths are equivalent.
for bond in coll_molecule.get_bonds():
if (bond.get_atom1_id(), bond.get_atom2_id()) != (0, 3):
test = get_atom_distance(
position_matrix=results.get_position_matrix(),
atom1_id=bond.get_atom1_id(),
atom2_id=bond.get_atom2_id(),
)
bond_length = get_atom_distance(
position_matrix=original_pos_mat,
atom1_id=bond.get_atom1_id(),
atom2_id=bond.get_atom2_id(),
)
assert np.isclose(test, bond_length, atol=1E-6)
def test_opt_get_result(optimizer, molecule):
original_pos_mat = molecule.get_position_matrix()
subunits = molecule.get_subunits(bond_pair_ids=((0, 3), ))
mol, results = optimizer.get_result(
mol=molecule,
bond_pair_ids=((0, 3), ),
subunits=subunits,
)
final_bond_length = np.linalg.norm(
optimizer._get_bond_vector(
position_matrix=results.get_position_matrix(),
bond_pair=(0, 3),
), )
# Give it some wiggle room.
assert 1.5 < final_bond_length
assert final_bond_length < 2.5
# Test all other bond lengths are equivalent.
for bond in molecule.get_bonds():
if (bond.get_atom1_id(), bond.get_atom2_id()) != (0, 3):
test = get_atom_distance(
position_matrix=results.get_position_matrix(),
atom1_id=bond.get_atom1_id(),
atom2_id=bond.get_atom2_id(),
)
bond_length = get_atom_distance(
position_matrix=original_pos_mat,
atom1_id=bond.get_atom1_id(),
atom2_id=bond.get_atom2_id(),
)
assert np.isclose(test, bond_length, atol=1E-6)
def test_get_atom_distance():
position_matrix = np.array([
[0, 0, 0],
[0, 1, 0],
[2, 0, 0],
])
assert get_atom_distance(position_matrix, 0, 1) == 1
assert get_atom_distance(position_matrix, 0, 2) == 2