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Added new function for calculating the occupation matrix

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This commit is contained in:
Sebastian Kloth
2023-12-08 17:20:06 +01:00
parent 5267f6abac
commit c40ea052b8
2 changed files with 74 additions and 23 deletions
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44
test/test_free_energy_landscape.py
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@ -9,39 +9,39 @@ from mdevaluate import free_energy_landscape as fel
@pytest.fixture
def trajectory(request):
return mdevaluate.open(os.path.join(os.path.dirname(__file__), 'data/pore'))
return mdevaluate.open(os.path.join(os.path.dirname(__file__), "data/pore"))
def test_get_fel(trajectory):
test_array = np.array(
[
0.0,
13.162354034697204,
5.327100985208421,
9.558746399158396,
4.116475238453127,
6.305715728953043,
3.231102391108276,
5.896478799115712,
8.381981206446293,
5.1191684352849816,
5.361112857237105,
8.053932845998895,
6.895396051256847,
7.588888886900885,
11.223429636542576,
3.779149304024221,
40.64319010769286,
93.1120609754045,
136.99287780099627,
171.4403749377496,
12.87438176,
4.95868203,
11.02055197,
5.44195534,
6.73933442,
3.30971789,
6.10424055,
8.56153733,
5.45777331,
5.64545817,
8.42100423,
6.28132121,
7.4777172,
11.64839354,
4.52566354,
40.84730838,
93.86241602,
140.3039937,
173.55970021,
]
)
oxygens_water = trajectory.subset(atom_name="OW", residue_name="SOL")
r, energy_differences = fel.get_fel(
oxygens_water,
os.path.join(os.path.dirname(__file__), 'data/pore'),
os.path.join(os.path.dirname(__file__), "data/pore"),
"cylindrical",
225,
edge=0.05,
@ -51,4 +51,4 @@ def test_get_fel(trajectory):
overwrite=True,
)
assert (energy_differences == test_array).all()
assert (np.round(energy_differences) == np.round(test_array)).all()