def make_cg_mol(aa_mol, mapping, bead_names, bead_types):
molname = aa_mol.graph['name']
cg_mol = Molecule(nrexcl=1, meta=dict(moltype=molname))
mapdict = defaultdict(list)
for bd_idx, at_idxs in enumerate(mapping):
name = bead_names[bd_idx]
for member in at_idxs:
mapdict[member].append(bd_idx)
subgraph = aa_mol.subgraph(at_idxs)
charge = sum(nx.get_node_attributes(subgraph, 'charge').values())
position = np.mean([
subgraph.nodes[idx].get('position', (np.nan, np.nan, np.nan))
for idx in subgraph
],
axis=0)
cg_mol.add_node(bd_idx,
atomname=name,
resname=molname,
resid=1,
atype=bead_types[bd_idx],
charge_group=bd_idx + 1,
graph=subgraph,
charge=charge,
position=position)
for aa_idx, aa_jdx in aa_mol.edges:
cg_idxs = mapdict[aa_idx]
cg_jdxs = mapdict[aa_jdx]
for cg_idx, cg_jdx in product(cg_idxs, cg_jdxs):
if cg_idx != cg_jdx:
cg_mol.add_edge(cg_idx, cg_jdx)
for idx, jdx in cg_mol.edges:
cg_mol.add_interaction('bonds', [idx, jdx], [])
return cg_mol
def test_apply_mod_mapping(modified_molecule, modifications):
"""
Test apply_mod_mapping
"""
graph_out = Molecule(force_field=FF_UNIVERSAL)
graph_out.add_nodes_from([
(0, {'atomname': 'A', 'resid': 1})
])
mol_to_out = {0: {0: 1}}
out_to_mol = {0: {0: 1}}
match = ({1: {'mA': 1}}, modifications['mA'], {})
out = apply_mod_mapping(match, modified_molecule, graph_out, mol_to_out, out_to_mol)
print(mol_to_out)
print(out_to_mol)
print(graph_out.nodes[1])
print(modifications['mA'].nodes['mA'])
for key in modifications['mA'].nodes['mA']:
assert graph_out.nodes[1][key] == modifications['mA'].nodes['mA'][key]
assert out == ({}, {})
assert mol_to_out == {0: {0: 1}, 1: {1: 1}}
assert out_to_mol == {0: {0: 1}, 1: {1: 1}}
graph_out.add_node(2, atomname='J', resid=2)
mol_to_out[16] = {2: 1}
out_to_mol[2] = {16: 1}
out = apply_mod_mapping((
{16: {'J': 1}, 17: {'mJ': 1}, 18: {'mJ2': 1}},
modifications['mJ', 'mJ2'], {}
), modified_molecule, graph_out, mol_to_out, out_to_mol)
print(mol_to_out)
print(out_to_mol)
assert out == ({}, {})
assert mol_to_out == {0: {0: 1}, 1: {1: 1}, 16: {2: 1}, 17: {3: 1}, 18: {4: 1}}
assert out_to_mol == {0: {0: 1}, 1: {1: 1}, 2: {16: 1}, 3: {17: 1}, 4: {18: 1}}