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_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 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