def test_main_output(self, capsys):
"""Test main with user defined output name."""
args = self.args.copy()
args["out_file"] = "text.txt"
UI.main(**args)
captured = capsys.readouterr().out
assert "Results written to text.txt" in captured
def test_main_subdef(self, capsys):
"""Test main with partial def file."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "OP_def_HP_BergerPOPC.def")
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
def test_main_traj(self, capsys):
"""Test main with trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Dealing with frame 10 at 10000.0 ps." in captured
def test_fail_main_coord_def_mismatch(self):
"""Test when coord file and def file doesn't match."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "op_wrong1.def")
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert f"Atoms defined in {args['def_file']} are missing in the structure" in str(
err.value)
def test_fail_main_subdef_traj(self, ):
"""Test main with partial def file and a output trajectory. Must fail."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "OP_def_HP_BergerPOPC.def")
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["prefix_traj_ouput"] = "test"
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert "Error on the number of H's to rebuild" in str(err.value)
def test_main_traj_output(self, capsys):
"""Test main with trajectory and output trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["prefix_traj_ouput"] = "test"
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Writing new pdb with hydrogens." in captured
assert "Writing trajectory with hydrogens in xtc file." in captured
def test_main_traj_slice(self, capsys):
"""Test main with sliced trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["end"] = 3000
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Dealing with frame 3 at 3000.0 ps." in captured
# Make sure we stop at frame 3
assert "Dealing with frame 10 at 10000.0 ps." not in captured
def test_fail_main_coord_topology_mismatch(self):
"""Test when coord file and topology doesn't match."""
args = self.args.copy()
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "CHARMM36_POPC.json"])
dic_lipid = lipids_tops["CHARMM36_POPC"]
args["dic_lipid"] = dic_lipid
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert "The topology chosen does not match the structure provided" in str(
err.value)
def test_main_minimal(self, capsys):
"""Test main with minimal arguments."""
UI.main(**self.args)
captured = capsys.readouterr().out
assert self.stdout_output in captured