def test_run_molecule():
ff = vermouth.forcefield.ForceField(name='test_ff')
meta_mol = MetaMolecule(name="test", force_field=ff)
meta_mol.add_monomer(0, "PEO", [])
meta_mol.add_monomer(1, "PEO", [(1, 0)])
meta_mol.add_monomer(2, "PEO", [(1, 2)])
meta_mol.volumes = {}
meta_mol.volumes["PEO"] = 0.5
RandomWalk().run_molecule(meta_mol)
for node in meta_mol.nodes:
assert "position" in meta_mol.nodes[node]
def test_update_positions():
ff = vermouth.forcefield.ForceField(name='test_ff')
meta_mol = MetaMolecule(name="test", force_field=ff)
meta_mol.add_monomer(0, "PEO", [])
meta_mol.add_monomer(1, "PEO", [(1, 0)])
meta_mol.add_monomer(2, "PEO", [(1, 2)])
meta_mol.nodes[0]["position"] = np.array([0, 0, 0])
meta_mol.nodes[1]["position"] = np.array([0, 0, 0.5])
meta_mol.volumes = {}
meta_mol.volumes["PEO"] = 0.5
vectors = polyply.src.linalg_functions.norm_sphere(50)
update_positions(vectors, meta_mol, 2, 1)
assert "position" in meta_mol.nodes[2]
def test__is_overlap(new_point, tol, fudge, reference):
ff = vermouth.forcefield.ForceField(name='test_ff')
meta_mol = MetaMolecule(name="test", force_field=ff)
meta_mol.add_monomer(0, "PEO", [])
meta_mol.add_monomer(1, "PEO", [(1, 0)])
meta_mol.add_monomer(2, "PEO", [(1, 2)])
meta_mol.nodes[0]["position"] = np.array([0, 0, 0])
meta_mol.nodes[1]["position"] = np.array([0, 0, 0.5])
result = _is_overlap(meta_mol,
new_point,
tol,
current_node=2,
fudge=fudge)
assert result == reference