def dummy_molecule():
"""
A virtually empty molecule.
"""
molecule = vermouth.Molecule()
molecule.add_nodes_from((
(0, {
'atype': 'A',
'resid': 1,
'resname': 'X',
'atomname': 'A',
'charge_group': 1,
'charge': 0,
'mass': 72
}),
(1, {
'atype': 'A',
'resid': 1,
'resname': 'X',
'atomname': 'A',
'charge_group': 1,
'charge': 0,
'mass': 72
}),
))
molecule.moltype = 'TEST'
molecule.nrexcl = 1
return molecule
def basic_molecule(node_data, edge_data=None):
"""
Construct a simple Molecule based with specified nodes and edges.
"""
if edge_data is None:
edge_data = {}
mol = vermouth.Molecule()
for idx, node in enumerate(node_data):
mol.add_node(idx, **node)
for (idx, jdx), data in edge_data.items():
mol.add_edge(idx, jdx, **data)
return mol