def test_replace_types_fail():
lines = """
[ defaults ]
1.0 1.0 yes 1.0 1.0
[ dihedraltypes ]
C Q Q Q 5 123.50 401.664 0.0 0.0
[ moleculetype ]
test 3
[ atoms ]
1 CT2 1 test C1 1 0.0 14.0
2 CE2 1 test C2 2 0.0 12.0
3 CE1 1 test C3 3 0.0 12.0
4 CT2 1 test C4 4 0.0 12.0
[ dihedrals ]
1 2 3 4 2
[ system ]
some title
[ molecules ]
test 1
"""
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
with pytest.raises(OSError):
top.gen_bonded_interactions()
def example_system():
"""
Create a dummy test system with three types of molecules AA, BB and
NA. NA is the molecule to be used a ligand. AA and BB are composed
of different residues.
"""
# dummy vermouth force-field
force_field = vermouth.forcefield.ForceField(name='test_ff')
# monomers used in the meta-molecule
ALA = Monomer(resname="ALA", n_blocks=2)
GLU = Monomer(resname="GLU", n_blocks=1)
THR = Monomer(resname="THR", n_blocks=1)
# two meta-molecules
meta_mol_A = MetaMolecule.from_monomer_seq_linear(force_field,
[ALA, GLU, THR],
"AA")
meta_mol_B = MetaMolecule.from_monomer_seq_linear(force_field,
[GLU, ALA, THR],
"BB")
NA = MetaMolecule()
NA.add_monomer(current=0, resname="NA", connections=[])
molecules = [meta_mol_A, meta_mol_A.copy(),
meta_mol_B.copy(), NA, NA.copy(),
NA.copy(), NA.copy()]
top = Topology(force_field=force_field)
top.molecules = molecules
top.mol_idx_by_name = {"AA":[0, 1], "BB": [2], "NA":[3, 4, 5, 6]}
return top
def test_replace_defines(lines, outcome):
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
top.replace_defines()
assert top.molecules[0].molecule.interactions["angles"][
0].parameters == outcome
def test_replace_types(lines, outcome):
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
top.gen_bonded_interactions()
for inter_type in outcome:
assert top.molecules[0].molecule.interactions[
inter_type] == outcome[inter_type]
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 test_gen_pairs(lines, outcome):
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
top.gen_pairs()
for atom_pair in outcome:
assert atom_pair in top.nonbond_params
nb1 = top.nonbond_params[atom_pair]["nb1"]
nb2 = top.nonbond_params[atom_pair]["nb2"]
nb1_ref = outcome[atom_pair]["nb1"]
nb2_ref = outcome[atom_pair]["nb2"]
assert math.isclose(nb1, nb1_ref)
assert math.isclose(nb2, nb2_ref)
def test_directives(lines, attr, value):
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert getattr(top, attr) == value
def nonbond_matrix():
toppath = TEST_DATA + "/struc_build/system.top"
topology = Topology.from_gmx_topfile(name="test", path=toppath)
topology.preprocess()
topology.volumes = {"PEO": 0.43}
return NonBondEngine.from_topology(topology.molecules,
topology,
box=np.array([10., 10., 10.]))
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_define(def_statements, result):
"""
test the handling of define statements in
"""
new_lines = textwrap.dedent(def_statements)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert top.defines == result
def test_convert_nonbond_to_sig_eps():
"""
Simply test if the conversion from C6 C12 to simga epsilon
is done properly.
"""
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
top.nonbond_params = {
frozenset(["EO", "EO"]): {
"nb1": 6.44779031E-02,
"nb2": 4.07588234E-04
}
}
top.convert_nonbond_to_sig_eps()
assert math.isclose(top.nonbond_params[frozenset(["EO", "EO"])]["nb1"],
0.43)
assert math.isclose(top.nonbond_params[frozenset(["EO", "EO"])]["nb2"],
3.4 * 0.75)
def test_def_fails(lines):
"""
test if incorrectly formatted ifdefs raise
appropiate error
"""
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
with pytest.raises(IOError):
polyply.src.top_parser.read_topology(new_lines, top)
def test_atom_type_fail():
lines = """
[ atomtypes ]
opls_001 C 6 12.01100 0.500 A 3.75000e-01 4.39320e-01 random; SIG
"""
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
with pytest.raises(IOError):
polyply.src.top_parser.read_topology(new_lines, top)
def test_persistence_parsers(test_system, lines, expected):
lines = textwrap.dedent(lines).splitlines()
ff = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(ff)
polyply.src.build_file_parser.read_build_file(lines, test_system.molecules,
top)
for ref, new in zip(expected, top.persistences):
print(ref, new)
for info_ref, info_new in zip(ref[:-1], new[:-1]):
assert info_ref == info_new
assert all(ref[-1] == new[-1])
def test_ifdefs_files(def_statements):
"""
test files in ifdef/ifndef statements are only
read if a define has been read before
"""
new_lines = textwrap.dedent(def_statements)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert True
def test_buckingham_fail():
lines = """
[ defaults ]
2 1 no 1.0 1.0
"""
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
with pytest.raises(IOError):
polyply.src.top_parser.read_topology(new_lines, top)
def test_parser(test_system, lines, tagged_mols, tagged_nodes):
lines = textwrap.dedent(lines).splitlines()
ff = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(ff)
polyply.src.build_file_parser.read_build_file(lines, test_system.molecules,
top)
for idx, mol in enumerate(test_system.molecules):
for node in mol.nodes:
if "restraints" in mol.nodes[node]:
assert node in tagged_nodes
assert idx in tagged_mols
def test_consistency():
"""
This test checks that all interaction formats defined
in TOPDirector.atom_idxs also have a corresponding
method in ITPDirector.METH_DICT.
"""
ff = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(ff, name="test")
top_director = polyply.src.top_parser.TOPDirector(top)
for inter_type in top_director.atom_idxs:
assert (tuple(['moleculetype', inter_type]) in top_director.METH_DICT or \
tuple([inter_type]) in top_director.METH_DICT)
def test_add_positions_from_pdb():
top = Topology.from_gmx_topfile(TEST_DATA + "/topology_test/pdb.top",
"test")
top.add_positions_from_file(TEST_DATA + "/topology_test/test.pdb")
for meta_mol in top.molecules:
for node in meta_mol.molecule.nodes:
assert "position" in meta_mol.molecule.nodes[node].keys()
for meta_mol in top.molecules:
for node in meta_mol.nodes:
assert "position" in meta_mol.nodes[node].keys()
assert meta_mol.nodes[node]["build"] == False
def test_add_positions_from_gro():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
top.add_positions_from_file(TEST_DATA + "/topology_test/test.gro")
for node in top.molecules[0].molecule.nodes:
if node < 14:
assert "position" in top.molecules[0].molecule.nodes[
node].keys()
for node in top.molecules[0].nodes:
if node != 2:
assert "position" in top.molecules[0].nodes[node].keys()
assert top.molecules[0].nodes[node]["build"] == False
else:
assert top.molecules[0].nodes[node]["build"] == True
def test_skip_directives(lines):
"""
Test that directives which currently cannot be read and
or interpreted are simply skipped and don't cause an
error when reading the topology file.
"""
new_lines = textwrap.dedent(lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert top.defaults == {"nbfunc":1.0,
"comb-rule":1.0,
"gen-pairs":'no',
"fudgeLJ":1.0,
"fudgeQQ":1.0}
def test_itp_handling():
"""
test if multiple itps are read correctly
"""
lines = """
[ defaults ]
1 1 no 1.0 1.0
[ moleculetype ]
GLY 1
[ atoms ]
1 P4 1 ALA BB 1
[ moleculetype ]
LYS 1
[ atoms ]
1 P4 1 ALA BB 1
[ molecules ]
LYS 2
"""
new_lines = textwrap.dedent(lines).splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert top.defaults == {"nbfunc": 1,
"comb-rule": 1,
"gen-pairs": "no",
"fudgeLJ": 1.0,
"fudgeQQ": 1.0}
# check that there are two LYS in topology
assert len(top.molecules) == 2
for mol in top.molecules:
assert mol.mol_name == "LYS"
# check that both are not the same instance of meta_molecule
assert top.molecules[0] is not top.molecules[1]
# also check that the high-res molecule is not the same
assert top.molecules[0].molecule is not top.molecules[1].molecule
# we also should have each molecule as block in the force
# field. Again we only check that it is there because
# the actual parsing is done elsewhere
assert len(force_field.blocks) == 2
def test_ifdefs(def_statements, bonds):
"""
test the handling if ifdefs and ifndefs at
different positions in itp-file
"""
lines = """
[ moleculetype ]
GLY 1
[ atoms ]
1 P4 1 ALA BB 1
2 P4 1 ALA SC1 1
3 P4 1 ALA SC2 1
4 P4 1 ALA SC3 1
"""
new_lines = lines + def_statements
new_lines = textwrap.dedent(new_lines)
new_lines = new_lines.splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
print(top.force_field.blocks["GLY"].interactions['bonds'])
assert top.force_field.blocks["GLY"].interactions['bonds'] == bonds
def test_itp_handling():
"""
test if multiple itps are read correctly
"""
lines = """
[ defaults ]
1 1 no 1.0 1.0
[ moleculetype ]
GLY 1
[ atoms ]
1 P4 1 ALA BB 1
[ moleculetype ]
LYS 1
[ atoms ]
1 P4 1 ALA BB 1
[ molecules ]
LYS 2
"""
new_lines = textwrap.dedent(lines).splitlines()
force_field = vermouth.forcefield.ForceField(name='test_ff')
top = Topology(force_field, name="test")
polyply.src.top_parser.read_topology(new_lines, top)
assert top.defaults == {
"nbfunc": 1,
"comb-rule": 1,
"gen-pairs": "no",
"fudgeLJ": 1.0,
"fudgeQQ": 1.0
}
# we just assert that one of the molecules is there
# because parsing is done via itp reader and thus covered
assert len(top.molecules[0]) == 1
# we also should have each molecule as block in the force
# field. Again we only check that it is there because
# the actual parsing is done elsewhere
assert len(force_field.blocks) == 2
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
def test_convert_to_vermouth_system():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
system = top.convert_to_vermouth_system()
assert isinstance(system, vermouth.system.System)
assert len(system.molecules) == 1
def test_from_gmx_topfile():
top = Topology.from_gmx_topfile(
TEST_DATA + "/topology_test/system.top", "test")
assert len(top.molecules) == 1
def molecule():
toppath = TEST_DATA + "/struc_build/system.top"
topology = Topology.from_gmx_topfile(name="test", path=toppath)
return topology.molecules[0]