def test_no_residue_crossing():
"""
Make sure we don't cross residue boundaries
"""
mapping = {'C1': {'B1': 1}, 'C2': {'B1': 1}, 'C3': {'B1': 1}}
extra = ()
mappings = {'universal': {'martini22': {'IPO': Mapping(FF_UNIVERSAL.blocks['IPO'],
FF_MARTINI.blocks['IPO'],
mapping=mapping,
references={},
ff_from=FF_UNIVERSAL,
ff_to=FF_MARTINI,
names=('IPO',),
extra=extra)}}}
cg = do_mapping(AA_MOL, mappings, FF_MARTINI, attribute_keep=['chain'])
expected = Molecule(force_field=FF_MARTINI)
expected.add_nodes_from((
(0, {'resid': 1, 'resname': 'IPO', 'atomname': 'B1', 'chain': 'A', 'charge_group': 1}),
(1, {'resid': 2, 'resname': 'IPO', 'atomname': 'B1', 'chain': 'A', 'charge_group': 2}),
(2, {'resid': 3, 'resname': 'IPO', 'atomname': 'B1', 'chain': 'A', 'charge_group': 3}),
))
expected.add_edges_from(([0, 1], [1, 2]))
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_no_residue_crossing():
"""
Make sure we don't cross residue boundaries
"""
mapping = {
(0, 'C1'): [(0, 'B1')],
(0, 'C2'): [(0, 'B1')],
(0, 'C3'): [(0, 'B1')]
}
weights = {
(0, 'B1'): {
(0, 'C1'): 1,
(0, 'C2'): 1,
(0, 'C3'): 1,
}
}
extra = ()
mappings = {'universal': {'martini22': {'IPO': (mapping, weights, extra)}}}
cg = do_mapping(AA_MOL, mappings, FF_MARTINI)
expected = Molecule(force_field=FF_MARTINI)
expected.add_nodes_from((
(0, {
'resid': 1,
'resname': 'IPO',
'atomname': 'B1',
'chain': 'A',
'charge_group': 1
}),
(1, {
'resid': 2,
'resname': 'IPO',
'atomname': 'B1',
'chain': 'A',
'charge_group': 2
}),
(2, {
'resid': 3,
'resname': 'IPO',
'atomname': 'B1',
'chain': 'A',
'charge_group': 3
}),
))
expected.add_edges_from(([0, 1], [1, 2]))
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_residue_crossing():
'''
Make sure we do cross residue boundaries and can rename residues
'''
mapping = {'C1': {'B1': 1}, 'C2': {'B1': 1}, 'C3': {'B1': 1},
'C4': {'B2': 1}, 'C5': {'B2': 1}, 'C6': {'B2': 1},
'C7': {'B3': 1}, 'C8': {'B3': 1}, 'C9': {'B3': 1},
}
extra = ()
mappings = {
'universal': {
'martini22': {
'IPO_large': Mapping(FF_UNIVERSAL.blocks['IPO_large'],
FF_MARTINI.blocks['IPO_large'],
mapping=mapping,
references={},
ff_from=FF_UNIVERSAL,
ff_to=FF_MARTINI,
names=('IPO', 'IPO', 'IPO'),
extra=extra)
}
}
}
cg = do_mapping(AA_MOL, mappings, FF_MARTINI, attribute_keep=('chain',))
expected = Molecule()
expected.add_nodes_from((
(0, {'resid': 1, 'resname': 'IPO_large', 'atomname': 'B1', 'chain': 'A', 'charge_group': 1}),
(1, {'resid': 2, 'resname': 'IPO_large', 'atomname': 'B1', 'chain': 'A', 'charge_group': 1}),
(2, {'resid': 3, 'resname': 'IPO_large', 'atomname': 'B1', 'chain': 'A', 'charge_group': 1}),
))
expected.add_edges_from(([0, 1], [1, 2]))
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 = {'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)