def example_system():
"""
Create a dummy test system with three types of molecules AA, BB and
NA. NA is the molecule to be used a ligand. AA and BB are composed
of different residues.
"""
# dummy vermouth force-field
force_field = vermouth.forcefield.ForceField(name='test_ff')
# monomers used in the meta-molecule
ALA = Monomer(resname="ALA", n_blocks=2)
GLU = Monomer(resname="GLU", n_blocks=1)
THR = Monomer(resname="THR", n_blocks=1)
# two meta-molecules
meta_mol_A = MetaMolecule.from_monomer_seq_linear(force_field,
[ALA, GLU, THR],
"AA")
meta_mol_B = MetaMolecule.from_monomer_seq_linear(force_field,
[GLU, ALA, THR],
"BB")
NA = MetaMolecule()
NA.add_monomer(current=0, resname="NA", connections=[])
molecules = [meta_mol_A, meta_mol_A.copy(),
meta_mol_B.copy(), NA, NA.copy(),
NA.copy(), NA.copy()]
top = Topology(force_field=force_field)
top.molecules = molecules
top.mol_idx_by_name = {"AA":[0, 1], "BB": [2], "NA":[3, 4, 5, 6]}
return top
def test_from_monomer_seq_linear(monomers, edges, nodes, attrs):
ff = vermouth.forcefield.ForceField(name='test_ff')
name = "test"
meta_mol = MetaMolecule.from_monomer_seq_linear(ff, monomers, name)
assert nx.get_node_attributes(meta_mol, "resname") == attrs
assert list(meta_mol.nodes) == nodes
assert list(meta_mol.edges) == edges
def test_molecule():
# dummy vermouth force-field
force_field = vermouth.forcefield.ForceField(name='test_ff')
# monomers used in the meta-molecule
ALA = Monomer(resname="ALA", n_blocks=4)
GLU = Monomer(resname="GLU", n_blocks=2)
THR = Monomer(resname="THR", n_blocks=3)
# two meta-molecules
mol = MetaMolecule.from_monomer_seq_linear(force_field, [ALA, GLU, THR],
"AA")
return mol
def test_get_links(lines, ref_ids):
lines = textwrap.dedent(lines).splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
vermouth.ffinput.read_ff(lines, force_field)
meta_mol = MetaMolecule.from_monomer_seq_linear(
force_field, [Monomer(resname="PEO", n_blocks=5)], "test")
polyply.src.map_to_molecule.MapToMolecule().run_molecule(meta_mol)
resids = []
for edge in meta_mol.edges:
_, ids = polyply.src.apply_links._get_links(meta_mol, edge)
resids += ids
assert len(resids) == len(ref_ids)
for resid in ids:
assert resid in ref_ids