def namd_tyr2ala():
dataset = alchemtest.namd.load_tyr2ala()
u_nk1 = namd.extract_u_nk(dataset['data']['forward'][0], T=300)
u_nk2 = namd.extract_u_nk(dataset['data']['backward'][0], T=300)
# combine dataframes of fwd and rev directions
u_nk1[u_nk1.isna()] = u_nk2
u_nk = u_nk1.sort_index(level=u_nk1.index.names[1:])
return u_nk
def test_u_nk_restarted_last_window_truncated(
restarted_dataset_last_window_truncated):
"""Test that when there is more than one lambda2 for a given lambda1, parsing throws an error."""
with pytest.raises(ValueError, match='Last window is truncated'):
u_nk = extract_u_nk(
restarted_dataset_last_window_truncated['data']['both'], T=300)
def test_u_nk_restarted_toomany_lambda2(restarted_dataset_toomany_lambda2):
"""Test that when there is more than one lambda2 for a given lambda1, parsing throws an error."""
with pytest.raises(
ValueError,
match='More than one lambda2 value for a particular lambda1'):
u_nk = extract_u_nk(restarted_dataset_toomany_lambda2['data']['both'],
T=300)
def test_u_nk_restarted_all_windows_truncated(
restarted_dataset_all_windows_truncated):
"""Test that when there is more than one lambda2 for a given lambda1, parsing throws an error."""
with pytest.raises(ValueError,
match='New window begun after truncated window'):
u_nk = extract_u_nk(
restarted_dataset_all_windows_truncated['data']['both'], T=300)
def test_u_nk(dataset, direction, shape):
"""Test that u_nk has the correct form when extracted from files.
"""
for filename in dataset['data'][direction]:
u_nk = extract_u_nk(filename, T=300)
assert u_nk.index.names == ['time', 'fep-lambda']
assert u_nk.shape == shape
def test_u_nk_idws():
"""Test that u_nk has the correct form when extracted from files.
"""
filenames = load_idws()['data']['forward']
u_nk = extract_u_nk(filenames, T=300)
assert u_nk.index.names == ['time', 'fep-lambda']
assert u_nk.shape == (29252, 11)
def test_u_nk_restarted():
"""Test that u_nk has the correct form when extracted from an IDWS
FEP run that includes terminations and restarts.
"""
filenames = load_restarted()['data']['both']
u_nk = extract_u_nk(filenames, T=300)
assert u_nk.index.names == ['time', 'fep-lambda']
assert u_nk.shape == (30061, 11)
def test_u_nk_restarted_inconsistent(restarted_dataset_inconsistent):
"""Test that when lambda values are inconsistent between start and end of a single window,
parsing throws an error.
"""
with pytest.raises(
ValueError,
match='Inconsistent lambda values within the same window'):
u_nk = extract_u_nk(restarted_dataset_inconsistent['data']['both'],
T=300)
def test_bar_namd():
"""Test BAR calculation on NAMD data.
"""
from alchemlyb.estimators import BAR
import numpy as np
# load data
dataset = load_tyr2ala()
u_nk1 = extract_u_nk(dataset['data']['forward'][0])
u_nk2 = extract_u_nk(dataset['data']['backward'][0])
# combine dataframes of fwd and rev directions
u_nk1.replace(0, np.nan, inplace=True)
u_nk1[u_nk1.isnull()] = u_nk2
u_nk1.replace(np.nan, 0, inplace=True)
u_nk = u_nk1.sort_index(level=u_nk1.index.names[1:])
# after loading BOTH fwd and rev data, do BAR calculation
bar = BAR()
bar.fit(u_nk)
dg = (bar.delta_f_.iloc[0].iloc[-1])
assert_almost_equal(dg, 6.03126982925, decimal=4)
def test_u_nk_restarted_reversed_missing_window_header(tmp_path):
"""Test that u_nk has the correct form when a #NEW line is missing from the restarted_reversed dataset
and the parser has to infer lambda_idws for that window."""
filenames = sorted(load_restarted_reversed()['data']['both'])
# Remove "#NEW" line
filenames[4] = _corrupt_fepout(filenames[4], [
('#NEW', lambda l: None),
], tmp_path)
u_nk = extract_u_nk(filenames, T=300)
assert u_nk.index.names == ['time', 'fep-lambda']
assert u_nk.shape == (30170, 11)
def test_u_nk():
"""Test that u_nk has the correct form when extracted from files.
"""
dataset = load_tyr2ala()
for direction in dataset['data']:
for filename in dataset['data'][direction]:
u_nk = extract_u_nk(filename)
assert u_nk.index.names == ['timestep', 'fep-lambda']
if direction == 'forward':
assert u_nk.shape == (21021, 21)
elif direction == 'backward':
assert u_nk.shape == (21021, 21)
def test_u_nk_restarted_idws_without_lambda_idws(
restarted_dataset_idws_without_lambda_idws):
"""Test that when the first window has IDWS data but no lambda_idws, parsing throws an error.
In this situation, the lambda_idws cannot be inferred, because there's no previous lambda
value available.
"""
with pytest.raises(
ValueError,
match=
'IDWS data present in first window but lambda_idws not included'):
u_nk = extract_u_nk(
restarted_dataset_idws_without_lambda_idws['data']['both'], T=300)
def namd_idws_restarted_reversed():
dataset = alchemtest.namd.load_restarted_reversed()
u_nk = namd.extract_u_nk(dataset['data']['both'], T=300)
return u_nk
def namd_idws():
dataset = alchemtest.namd.load_idws()
u_nk = namd.extract_u_nk(dataset['data']['forward'], T=300)
return u_nk
def test_u_nk_restarted_direction_changed(restarted_dataset_direction_changed):
"""Test that when lambda values change direction within a dataset, parsing throws an error."""
with pytest.raises(ValueError, match='Lambda values change direction'):
u_nk = extract_u_nk(
restarted_dataset_direction_changed['data']['both'], T=300)
def test_u_nk_restarted_reversed():
filenames = load_restarted_reversed()['data']['both']
u_nk = extract_u_nk(filenames, T=300)
assert u_nk.index.names == ['time', 'fep-lambda']
assert u_nk.shape == (30170, 11)
