Exemple #1
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 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]
Exemple #2
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 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]
Exemple #3
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 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