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_peptide():
"""
Test multiple cg beads in residue
"""
gly = {'C': {'BB': 1}, 'N': {'BB': 1}, 'O': {'BB': 1}, 'CA': {'BB': 1}}
ile = {'C': {'BB': 1}, 'N': {'BB': 1}, 'O': {'BB': 1}, 'CA': {'BB': 1},
'CB': {'SC1': 1}, 'CG1': {'SC1': 1}, 'CG2': {'SC1': 1}, 'CD': {'SC1': 1}}
leu = {'C': {'BB': 1}, 'N': {'BB': 1}, 'O': {'BB': 1}, 'CA': {'BB': 1},
'CB': {'SC1': 1}, 'CG': {'SC1': 1}, 'CD1': {'SC1': 1}, 'CD2': {'SC1': 1}}
extra = ()
mappings = {'universal': {'martini22': {}}}
mappings['universal']['martini22']['GLY'] = Mapping(FF_UNIVERSAL.blocks['GLY'],
FF_MARTINI.blocks['GLY'],
mapping=gly,
references={},
ff_from=FF_UNIVERSAL,
ff_to=FF_MARTINI,
names=('GLY',),
extra=extra)
mappings['universal']['martini22']['ILE'] = Mapping(FF_UNIVERSAL.blocks['ILE'],
FF_MARTINI.blocks['ILE'],
mapping=ile,
references={},
ff_from=FF_UNIVERSAL,
ff_to=FF_MARTINI,
names=('ILE',),
extra=extra)
mappings['universal']['martini22']['LEU'] = Mapping(FF_UNIVERSAL.blocks['LEU'],
FF_MARTINI.blocks['LEU'],
mapping=leu,
references={},
ff_from=FF_UNIVERSAL,
ff_to=FF_MARTINI,
names=('LEU',),
extra=extra)
peptide = Molecule(force_field=FF_UNIVERSAL)
aa = FF_UNIVERSAL.blocks['GLY'].to_molecule()
peptide.merge_molecule(aa)
aa = FF_UNIVERSAL.blocks['ILE'].to_molecule()
peptide.merge_molecule(aa)
aa = FF_UNIVERSAL.blocks['LEU'].to_molecule()
peptide.merge_molecule(aa)
peptide.add_edge(list(peptide.find_atoms(atomname='N', resid=1))[0],
list(peptide.find_atoms(atomname='C', resid=2))[0])
peptide.add_edge(list(peptide.find_atoms(atomname='N', resid=2))[0],
list(peptide.find_atoms(atomname='C', resid=3))[0])
for node in peptide:
peptide.nodes[node]['atomid'] = node + 1
peptide.nodes[node]['chain'] = ''
cg = do_mapping(peptide, mappings, FF_MARTINI, attribute_keep=('chain',))
expected = Molecule(force_field=FF_MARTINI)
expected.add_nodes_from({1: {'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 1,
'resid': 1,
'resname': 'GLY'},
2: {'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 2,
'resid': 2,
'resname': 'ILE'},
3: {'atomname': 'SC1',
'atype': 'AC1',
'chain': '',
'charge': 0.0,
'charge_group': 3,
'resid': 2,
'resname': 'ILE'},
4: {'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 4,
'resid': 3,
'resname': 'LEU'},
5: {'atomname': 'SC1',
'atype': 'AC1',
'chain': '',
'charge': 0.0,
'charge_group': 5,
'resid': 3,
'resname': 'LEU'}}.items()
)
expected.add_edges_from([(1, 2), (2, 3), (2, 4), (4, 5)])
for node in expected:
expected.nodes[node]['atomid'] = node + 1
print(cg.nodes(data=True))
print(cg.edges())
print('-'*80)
print(expected.nodes(data=True))
print(expected.edges())
assert equal_graphs(cg, expected)
def test_peptide():
"""
Test multiple cg beads in residue
"""
gly = {
(0, 'C'): [(0, 'BB')],
(0, 'N'): [(0, 'BB')],
(0, 'O'): [(0, 'BB')],
(0, 'CA'): [(0, 'BB')]
}
ile = {
(0, 'C'): [(0, 'BB')],
(0, 'N'): [(0, 'BB')],
(0, 'O'): [(0, 'BB')],
(0, 'CA'): [(0, 'BB')],
(0, 'CB'): [(0, 'SC1')],
(0, 'CG1'): [(0, 'SC1')],
(0, 'CG2'): [(0, 'SC1')],
(0, 'CD'): [(0, 'SC1')]
}
leu = {
(0, 'C'): [(0, 'BB')],
(0, 'N'): [(0, 'BB')],
(0, 'O'): [(0, 'BB')],
(0, 'CA'): [(0, 'BB')],
(0, 'CB'): [(0, 'SC1')],
(0, 'CG1'): [(0, 'SC1')],
(0, 'CD1'): [(0, 'SC1')],
(0, 'CD2'): [(0, 'SC1')]
}
extra = ()
mappings = {
'universal': {
'martini22': {
'GLY': (gly, _map_weights(gly), extra),
'ILE': (ile, _map_weights(ile), extra),
'LEU': (leu, _map_weights(leu), extra),
}
}
}
peptide = Molecule(force_field=FF_UNIVERSAL)
aa = FF_UNIVERSAL.blocks['GLY'].to_molecule()
peptide.merge_molecule(aa)
aa = FF_UNIVERSAL.blocks['ILE'].to_molecule()
peptide.merge_molecule(aa)
aa = FF_UNIVERSAL.blocks['LEU'].to_molecule()
peptide.merge_molecule(aa)
peptide.add_edge(
list(peptide.find_atoms(atomname='N', resid=1))[0],
list(peptide.find_atoms(atomname='C', resid=2))[0])
peptide.add_edge(
list(peptide.find_atoms(atomname='N', resid=2))[0],
list(peptide.find_atoms(atomname='C', resid=3))[0])
for node in peptide:
peptide.nodes[node]['atomid'] = node + 1
peptide.nodes[node]['chain'] = ''
cg = do_mapping(peptide, mappings, FF_MARTINI)
expected = Molecule(force_field=FF_MARTINI)
expected.add_nodes_from({
1: {
'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 1,
'resid': 1,
'resname': 'GLY'
},
2: {
'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 2,
'resid': 2,
'resname': 'ILE'
},
3: {
'atomname': 'SC1',
'atype': 'AC1',
'chain': '',
'charge': 0.0,
'charge_group': 2,
'resid': 2,
'resname': 'ILE'
},
4: {
'atomname': 'BB',
'atype': 'P5',
'chain': '',
'charge': 0.0,
'charge_group': 3,
'resid': 3,
'resname': 'LEU'
},
5: {
'atomname': 'SC1',
'atype': 'AC1',
'chain': '',
'charge': 0.0,
'charge_group': 3,
'resid': 3,
'resname': 'LEU'
}
}.items())
expected.add_edges_from([(1, 2), (2, 3), (2, 4), (4, 5)])
for node in expected:
expected.nodes[node]['atomid'] = node + 1
assert _equal_graphs(cg, expected)