def univ_pbc(self, tmp_path, path_test_data, universe_class):
gro = path_test_data / 'spc2.gro'
traj = path_test_data / 'spc2-traj-pbc.xtc'
shutil.copy(gro, tmp_path)
shutil.copy(traj, tmp_path)
with cd(tmp_path):
_univ = universe_class(gro.name, traj.name, temp=205.)
return _univ
def reu(self, path_test_data):
from paratemp.re_universe import REUniverse
path = path_test_data / 'spc-and-methanol-run'
with cd(path):
reu = REUniverse('TOPO/nvt0.tpr',
base_folder='.',
traj_glob='PT-out*.trr')
return reu
def test_read_data(self, univ, univ_w_a, tmp_path, capsys):
"""
:type univ_w_a: paratemp.Universe
:type univ: paratemp.Universe
"""
with cd(tmp_path):
univ_w_a.save_data()
capsys.readouterr() # just so it doesn't print
univ.read_data()
assert (univ_w_a.data == univ.data).all().all()
def test_calculate_distances_read(self, univ_w_a, tmp_path, capsys):
"""
:type univ_w_a: paratemp.Universe
"""
with cd(tmp_path):
univ_w_a.save_data()
capsys.readouterr()
univ_w_a._data = univ_w_a._init_dataframe()
univ_w_a.calculate_distances(a='4 5')
out, err = capsys.readouterr()
assert out == 'Nothing (new) to calculate here.\n'
def test_save_data_add_new(self, univ, univ_w_a, tmp_path, capsys):
time = 'time_' + str(int(univ_w_a._last_time / 1000)) + 'ns'
f_name = univ_w_a.trajectory.filename.replace('xtc', 'h5')
with cd(tmp_path):
univ_w_a.save_data()
capsys.readouterr()
univ.calculate_distances(b='4 5', save_data=False)
univ.save_data()
out, err = capsys.readouterr()
assert out == 'Saved data to {f_name}[{time}]\n'.format(f_name=f_name,
time=time)
def test_save_data(self, univ_w_a, tmp_path, capsys):
time = 'time_' + str(int(univ_w_a._last_time / 1000)) + 'ns'
f_name = univ_w_a.trajectory.filename.replace('xtc', 'h5')
with cd(tmp_path):
univ_w_a.save_data()
out, err = capsys.readouterr()
assert (tmp_path / f_name).exists()
with pd.HDFStore(f_name) as store:
df = store[time]
assert out == 'Saved data to {f_name}[{time}]\n'.format(f_name=f_name,
time=time)
assert np.allclose(df, univ_w_a.data)
def test_read_data_no_data(self, univ, tmp_path, capsys):
"""
:type univ: paratemp.Universe
"""
time = 'time_' + str(int(univ._last_time / 1000)) + 'ns'
f_name = univ.trajectory.filename.replace('xtc', 'h5')
with cd(tmp_path):
with pytest.raises(IOError,
match=r'This data does not exist!\n'
r'{}\[{}\]'.format(f_name, time)):
univ.read_data()
univ.read_data(ignore_no_data=True)
out, err = capsys.readouterr()
assert out == 'No data to read in {}[{}]\n'.format(f_name, time)
def test_calculate_distances_save(self, univ, tmp_path, capsys):
"""
:type univ: paratemp.Universe
"""
time = 'time_' + str(int(univ._last_time / 1000)) + 'ns'
f_name = univ.trajectory.filename.replace('xtc', 'h5')
with cd(tmp_path):
univ.calculate_distances(a='4 5')
out, err = capsys.readouterr()
assert (tmp_path / f_name).exists()
with pd.HDFStore(f_name) as store:
df = store[time]
assert out == 'Saved data to {f_name}[{time}]\n'.format(f_name=f_name,
time=time)
assert np.allclose(df, univ.data)
def test_init(self, molecule_w_params, shift, box_length, include_gbsa,
n_args):
from paratemp.sim_setup import System
mol, tmp_path = molecule_w_params
with cd(tmp_path):
system = System(*([mol] * n_args),
shift=shift,
box_length=box_length,
include_gbsa=include_gbsa)
assert isinstance(system, System)
assert system.n_molecules == n_args
assert (hasattr(system, 'directory')
and isinstance(system.directory, pathlib.Path))
assert (hasattr(system, 'name') and isinstance(system.name, str))
assert repr(system) == ('<default System from {} '
'Molecules>'.format(n_args))
start_dir = os.getcwd()
temp_dir = "cctempdir"
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
edrs = glob('*.edr')
log_file = glob('*out*.log')[0]
colvar_files = glob('COLVAR*')
files_to_copy = edrs + [log_file] + colvar_files
for filename in files_to_copy:
copyfile(filename, temp_dir+'/'+filename)
with cd(temp_dir):
if len(colvar_files) == 0:
print('No COLVAR files; ignoring that part.')
with open(log_file, 'r') as f_log:
final_time = None
for line in f_log:
try:
final_time = regex_time.match(line).group(1)
final_time = '{:.0f}'.format(float(final_time)/1000)
except AttributeError:
continue
if final_time is None:
print("Couldn't find final time from log file.")
final_time = 'unk'
else:
colvars = dict()