def force_fields():
"""
Read a bunch of force fields fit for testing
"""
ffs = {}
ffs['universal-test'] = ForceField(FF_UNIVERSAL_TEST)
ffs['pepplane'] = ForceField(FF_PEPPLANE)
ffs['martini-test'] = ForceField(FF_MARTINI_TEST)
assert set(ffs.keys()) == {'universal-test', 'pepplane', 'martini-test'}
assert set(ffs['universal-test'].modifications.keys()) >= {'C-ter', 'N-ter'}
assert set(ffs['universal-test'].blocks.keys()) >= {'ALA',}
return ffs
def compare_itp(filename1, filename2):
"""
Asserts that two itps are functionally identical
"""
dummy_ff = ForceField(name='dummy')
with open(filename1) as fn1:
vermouth.gmx.read_itp(fn1, dummy_ff)
dummy_ff2 = ForceField(name='dummy')
with open(filename2) as fn2:
vermouth.gmx.read_itp(fn2, dummy_ff2)
for block in dummy_ff2.blocks.values():
block._force_field = dummy_ff
assert set(dummy_ff.blocks.keys()) == set(dummy_ff2.blocks.keys())
for name in dummy_ff.blocks:
block1 = dummy_ff.blocks[name]
block2 = dummy_ff2.blocks[name]
assert_equal_blocks(block1, block2)
def force_fields():
"""
Creates a simple forcefield for tests
"""
ffa = ForceField(name='test_A')
block_a = Block(name='block_A', force_field=ffa)
block_a.add_nodes_from(['A1', 'A2', 'B1', 'B2'])
for node in block_a.nodes:
block_a.nodes[node]['atomname'] = node
block_a.nodes[node]['resname'] = 'block_A'
block_a.add_edges_from([('A1', 'A2'), ('B1', 'B2')])
ffa.blocks['block_A'] = block_a
ffa.modifications['block_A'] = Link(block_a)
block_b = Block(name='block_B', force_field=ffa)
block_b.add_node('A', atomname='A', resname='block_B', replace={'atomname': 'B'})
ffa.blocks['block_B'] = block_b
return {'test_A': ffa}
def test_raise_residue_error(top_lines):
lines = textwrap.dedent(top_lines)
lines = lines.splitlines()
force_field = ForceField("test")
topology = Topology(force_field)
read_topology(lines=lines, topology=topology, cwdir="./")
topology.preprocess()
topology.volumes = {"GLY": 0.53, "GLU": 0.67, "ASP": 0.43}
with pytest.raises(IOError):
polyply.src.check_residue_equivalence.check_residue_equivalence(
topology)
def example_mol():
mol = Molecule(force_field=ForceField(FF_UNIVERSAL_TEST))
nodes = [
{
'chain': 'A',
'resname': 'A',
'resid': 1
}, # 0, R1
{
'chain': 'A',
'resname': 'A',
'resid': 2
}, # 1, R2
{
'chain': 'A',
'resname': 'A',
'resid': 2
}, # 2, R2
{
'chain': 'A',
'resname': 'B',
'resid': 2
}, # 3, R3
{
'chain': 'B',
'resname': 'A',
'resid': 1
}, # 4, R4
{
'chain': 'B',
'resname': 'A',
'resid': 2
}, # 5, R5
{
'chain': 'B',
'resname': 'A',
'resid': 2
}, # 6, R5
{
'chain': 'B',
'resname': 'B',
'resid': 2
}, # 7, R6
{
'chain': 'A',
'resname': 'C',
'resid': 3
}, # 8, R7
]
mol.add_nodes_from(enumerate(nodes))
mol.add_edges_from([(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (4, 7),
(3, 8)])
return mol
def test_single_residue_mol():
mol = Molecule(force_field=ForceField(FF_UNIVERSAL_TEST))
nodes = [
{'chain': 'A', 'resname': 'A', 'resid': 2},
{'chain': 'A', 'resname': 'A', 'resid': 2},
]
mol.add_nodes_from(enumerate(nodes))
mol.add_edges_from([(0, 1)])
modification = [({'resname': 'A', 'resid': 2}, 'C-ter'),]
annotate_modifications(mol, modification, [])
assert mol.nodes[0] == {'modification': ['C-ter'], 'resname': 'A', 'resid': 2, 'chain': 'A'}
assert mol.nodes[1] == {'modification': ['C-ter'], 'resname': 'A', 'resid': 2, 'chain': 'A'}
def example_topology():
top_lines = """
[ defaults ]
1 1 no 1.0 1.0
[ atomtypes ]
N0 45.0 0.000 A 0.0 0.0
[ nonbond_params ]
N0 N0 1 4.700000e-01 3.700000e+00
[ moleculetype ]
testA 1
[ atoms ]
1 N0 1 GLY BB 1 0.00 45
2 N0 1 GLY SC1 1 0.00 45
3 N0 1 GLY SC2 1 0.00 45
4 N0 2 GLU BB 2 0.00 45
5 N0 2 GLU SC1 2 0.00 45
6 N0 2 GLU SC2 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
1 4 1 0.47 2000
4 5 1 0.47 2000
4 6 1 0.47 2000
[ moleculetype ]
testB 1
[ atoms ]
1 N0 1 ASP BB 1 0.00
2 N0 1 ASP SC1 1 0.00
3 N0 1 ASP SC2 1 0.00
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
[ system ]
test system
[ molecules ]
testA 2
testB 1
"""
lines = textwrap.dedent(top_lines)
lines = lines.splitlines()
force_field = ForceField("test")
topology = Topology(force_field)
read_topology(lines=lines, topology=topology, cwdir="./")
topology.preprocess()
topology.volumes = {"GLY": 0.53, "GLU": 0.67, "ASP": 0.43}
return topology
def from_gmx_topfile(cls, path, name):
"""
Read a gromacs topology file and return an topology object.
Parameters
----------
path: str
The name of the topology file
name: str
The name of the system
"""
with open(path, 'r') as _file:
lines = _file.readlines()
cwdir = os.path.dirname(path)
force_field = ForceField(name)
topology = cls(force_field=force_field, name=name)
read_topology(lines=lines, topology=topology, cwdir=cwdir)
return topology
def test_nter_cter_modifications(node_data, edge_data, expected):
"""
Tests that 'nter' and 'cter' specifications only match protein N and C
termini
"""
mol = Molecule(force_field=ForceField(FF_UNIVERSAL_TEST))
mol.add_nodes_from(enumerate(node_data))
mol.add_edges_from(edge_data)
modification = [({'resname': 'cter'}, 'C-ter'), ({'resname': 'nter'}, 'N-ter')]
annotate_modifications(mol, modification, [])
found = {}
for node_idx in mol:
node = mol.nodes[node_idx]
if 'modification' in node:
found[node['resid']] = node['modification']
assert found == expected
def test_raise_residue_no_error():
"""
This test makes sure that we actually skip molecules that are defined
in the top file but not used in the actual system.
"""
top_lines = """
[ defaults ]
1 1 no 1.0 1.0
[ atomtypes ]
N0 72.0 0.000 A 0.0 0.0
N1 72.0 0.000 A 0.0 0.0
[ nonbond_params ]
N0 N0 1 4.700000e-01 3.700000e+00
N1 N1 1 4.700000e-01 3.700000e+00
[ moleculetype ]
testA 1
[ atoms ]
1 N0 1 GLY BB 1 0.00 45
2 N0 1 GLY SC1 1 0.00 45
3 N0 1 GLY SC2 1 0.00 45
4 N1 2 GLU BB 2 0.00 45
5 N1 2 GLU SC1 2 0.00 45
6 N1 2 GLU SC2 2 0.00 45
7 N1 2 GLU SC3 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
3 4 1 0.47 2000
4 5 1 0.47 2000
5 6 1 0.47 2000
6 7 1 0.47 2000
[ moleculetype ]
testB 1
[ atoms ]
1 N0 1 ASP BB 1 0.00 45
2 N0 1 ASP SC3 1 0.00 45
3 N0 1 ASP SC4 1 0.00 45
4 N1 2 GLU BB 2 0.00 45
5 N1 2 GLU SC1 2 0.00 45
6 N1 2 GLU SC2 2 0.00 45
7 N1 2 GLU SC3 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
3 4 1 0.47 2000
4 5 1 0.47 2000
5 6 1 0.47 2000
5 7 1 0.47 2000
[ system ]
test system
[ molecules ]
testA 1
"""
lines = textwrap.dedent(top_lines)
lines = lines.splitlines()
force_field = ForceField("test")
topology = Topology(force_field)
read_topology(lines=lines, topology=topology, cwdir="./")
topology.preprocess()
topology.volumes = {"GLY": 0.53, "GLU": 0.67, "ASP": 0.43}
polyply.src.check_residue_equivalence.check_residue_equivalence(topology)
def topology():
top_lines = """
[ defaults ]
1 1 no 1.0 1.0
[ atomtypes ]
N0 72.0 0.000 A 0.0 0.0
[ nonbond_params ]
N0 N0 1 4.700000e-01 3.700000e+00
[ moleculetype ]
testA 1
[ atoms ]
1 N0 1 GLY BB 1 0.00 45
2 N0 2 GLY SC1 1 0.00 45
3 N0 3 GLY SC2 1 0.00 45
4 N0 4 GLU BB 2 0.00 45
5 N0 5 GLU SC1 2 0.00 45
6 N0 6 GLU SC2 2 0.00 45
7 N0 7 GLU SC2 2 0.00 45
8 N0 8 GLU SC2 2 0.00 45
9 N0 9 GLU SC2 2 0.00 45
10 N0 10 GLU SC2 2 0.00 45
11 N0 11 GLU SC2 2 0.00 45
12 N0 12 GLU SC2 2 0.00 45
13 N0 13 GLU SC2 2 0.00 45
14 N0 14 GLU SC2 2 0.00 45
15 N0 15 GLU SC2 2 0.00 45
16 N0 16 GLU SC2 2 0.00 45
17 N0 17 GLU SC2 2 0.00 45
18 N0 18 GLU SC2 2 0.00 45
19 N0 19 GLU SC2 2 0.00 45
20 N0 20 GLU SC2 2 0.00 45
21 N0 21 GLU SC2 2 0.00 45
22 N0 22 GLU SC2 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
3 4 1 0.47 2000
4 5 1 0.47 2000
5 6 1 0.47 2000
6 7 1 0.47 2000
7 8 1 0.47 2000
8 9 1 0.47 2000
9 10 1 0.47 2000
10 11 1 0.47 2000
11 12 1 0.47 2000
12 13 1 0.47 2000
13 14 1 0.47 2000
14 15 1 0.47 2000
15 16 1 0.47 2000
16 17 1 0.47 2000
17 18 1 0.47 2000
18 19 1 0.47 2000
19 20 1 0.47 2000
20 21 1 0.47 2000
21 22 1 0.47 2000
[ moleculetype ]
testB 1
[ atoms ]
1 N0 1 ASP BB 1 0.00 45
2 N0 2 GLY SC1 1 0.00 45
3 N0 3 ASP SC2 1 0.00 45
4 N0 4 ASP BB 2 0.00 45
5 N0 5 GLY SC1 2 0.00 45
6 N0 6 ASP SC2 2 0.00 45
7 N0 7 ASP SC2 2 0.00 45
8 N0 8 GLU SC2 2 0.00 45
9 N0 9 GLU SC2 2 0.00 45
10 N0 10 GLY SC2 2 0.00 45
11 N0 11 ASP SC2 2 0.00 45
12 N0 12 GLU SC2 2 0.00 45
13 N0 13 ASP SC2 2 0.00 45
14 N0 14 ASP SC2 2 0.00 45
15 N0 15 GLU SC2 2 0.00 45
16 N0 16 ASP SC2 2 0.00 45
17 N0 17 ASP SC2 2 0.00 45
18 N0 18 GLY SC2 2 0.00 45
19 N0 19 ASP SC2 2 0.00 45
20 N0 20 ASP SC2 2 0.00 45
21 N0 21 GLY SC2 2 0.00 45
22 N0 22 ASP SC2 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
3 4 1 0.47 2000
4 5 1 0.47 2000
5 6 1 0.47 2000
6 7 1 0.47 2000
7 8 1 0.47 2000
8 9 1 0.47 2000
9 10 1 0.47 2000
10 11 1 0.47 2000
11 12 1 0.47 2000
12 13 1 0.47 2000
13 14 1 0.47 2000
14 15 1 0.47 2000
15 16 1 0.47 2000
16 17 1 0.47 2000
17 18 1 0.47 2000
18 19 1 0.47 2000
19 20 1 0.47 2000
20 21 1 0.47 2000
21 22 1 0.47 2000
[ moleculetype ]
testC 1
[ atoms ]
1 N0 1 GLY BB 1 0.00 45
2 N0 2 GLY SC1 1 0.00 45
3 N0 3 GLY SC2 1 0.00 45
4 N0 4 GLU BB 2 0.00 45
5 N0 5 GLU SC1 2 0.00 45
6 N0 6 GLU SC2 2 0.00 45
7 N0 7 GLU SC2 2 0.00 45
8 N0 8 GLU SC2 2 0.00 45
9 N0 9 GLU SC2 2 0.00 45
10 N0 10 GLU SC2 2 0.00 45
11 N0 11 GLU SC2 2 0.00 45
12 N0 12 GLU SC2 2 0.00 45
13 N0 13 GLU SC2 2 0.00 45
14 N0 14 GLU SC2 2 0.00 45
15 N0 15 GLU SC2 2 0.00 45
16 N0 16 GLU SC2 2 0.00 45
17 N0 17 GLU SC2 2 0.00 45
18 N0 18 GLU SC2 2 0.00 45
19 N0 19 GLU SC2 2 0.00 45
20 N0 20 GLU SC2 2 0.00 45
21 N0 21 GLU SC2 2 0.00 45
22 N0 22 GLU SC2 2 0.00 45
23 N0 23 GLU SC2 2 0.00 45
24 N0 24 GLU SC2 2 0.00 45
25 N0 25 GLU SC2 2 0.00 45
[ bonds ]
1 2 1 0.47 2000
2 3 1 0.47 2000
3 4 1 0.47 2000
4 5 1 0.47 2000
5 6 1 0.47 2000
6 7 1 0.47 2000
7 8 1 0.47 2000
8 9 1 0.47 2000
9 10 1 0.47 2000
10 11 1 0.47 2000
11 12 1 0.47 2000
12 13 1 0.47 2000
13 14 1 0.47 2000
14 15 1 0.47 2000
15 16 1 0.47 2000
16 17 1 0.47 2000
17 18 1 0.47 2000
18 19 1 0.47 2000
19 20 1 0.47 2000
20 21 1 0.47 2000
21 22 1 0.47 2000
3 23 1 0.47 2000
23 24 1 0.47 2000
3 25 1 0.47 2000
[ system ]
test system
[ molecules ]
testA 10
testB 10
testC 5
"""
lines = textwrap.dedent(top_lines)
lines = lines.splitlines()
force_field = ForceField("test")
topology = Topology(force_field)
read_topology(lines=lines, topology=topology, cwdir="./")
topology.preprocess()
topology.volumes = {"GLY": 0.53, "GLU": 0.67, "ASP": 0.43}
return topology