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added tests surf, H, K, with atoms out of bounds
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ojeda-e committed Jul 31, 2021
1 parent f950a5d commit bfe5f9e
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Showing 2 changed files with 189 additions and 4 deletions.
4 changes: 4 additions & 0 deletions membrane_curvature/surface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,10 @@ def get_z_surface(coordinates, n_x_bins=10, n_y_bins=10, x_range=(0, 100), y_ran
for l, m, z in zip(cell_x_floor, cell_y_floor, z_coords):

try:
if l < 0 or m < 0:
print("Atom outside grid boundaries. Skipping atom.")
continue

grid_z_coordinates[l, m] += z
grid_norm_unit[l, m] += 1

Expand Down
189 changes: 185 additions & 4 deletions membrane_curvature/tests/test_membrane_curvature.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
"""


from numpy.core.fromnumeric import mean
import pytest
from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
from membrane_curvature.curvature import mean_curvature, gaussian_curvature
Expand Down Expand Up @@ -236,6 +237,44 @@ def universe_dummy_full(self):

return u

@pytest.fixture()
def universe_dummy_wrap(self):
# +-----------+
# | | 7 | 8 | 9
# +-----------+
# 4 | 5 | 6 | |
# +-----------+
# | | 1 | 2 | 3
# +-----------+
a = np.array([[300., 0., 110.], [100., 0., 150.], [200., 0., 150.],
[0., 100., 150.], [100., 100., 150.], [-100., 100., 150.],
[300., 200., 110.], [100., 200., 150.], [200., 200., 150.]])

u = mda.Universe(a, n_atoms=9)
u.dimensions = [300, 300, 300, 90., 90., 90.]

return u

# Equivalent to universe_dummy_wrap when wrapping is applied.
# Atoms out of bounds in x and y
@pytest.fixture()
def universe_dummy_wrap_xy(self):
a = np.array([[300., 0., 110.], [100., 0., 150.], [200., 0., 150.],
[0., -200., 150.], [100., -200., 150.], [-100., 100., 150.],
[300., 200., 110.], [100., 200., 150.], [200., 200., 150.]])

u = mda.Universe(a, n_atoms=9)
u.dimensions = [300, 300, 300, 90., 90., 90.]

return u

@pytest.fixture()
def dummy_surface(self):
surface = np.array([[110., 150., 110.],
[150., 150., 150.],
[150., 150., 150.]])
return surface

def test_invalid_selection(self, universe):
with pytest.raises(ValueError, match=r'Invalid selection'):
MembraneCurvature(universe, select='name P')
Expand Down Expand Up @@ -299,7 +338,7 @@ def test_analysis_get_z_surface(self, universe, x_bin, y_bin, expected_surface):
avg_surface = mc.results.average_z_surface
assert_almost_equal(avg_surface, expected_surface)

# test using wrap=True
# test using wrap=True with test grofile
def test_analysis_mean_wrap(self, universe):
expected_mean = np.array([[7.50000000e+00, 1.33985392e-01, 2.77315457e-04],
[-2.77315457e-04, -3.53944270e-01, -7.50000000e+00],
Expand All @@ -311,7 +350,7 @@ def test_analysis_mean_wrap(self, universe):
avg_mean = mc.results.average_mean
assert_almost_equal(avg_mean, expected_mean)

# test using wrap=False
# test using wrap=False with test grofile
def test_analysis_mean_no_wrap(self, universe):
expected_mean = np.array([[7.50000000e+00, 1.33985392e-01, 2.77315457e-04],
[-2.77315457e-04, -3.53944270e-01, -7.50000000e+00],
Expand All @@ -324,7 +363,149 @@ def test_analysis_mean_no_wrap(self, universe):
avg_mean = mc.results.average_mean
assert_almost_equal(avg_mean, expected_mean)

# Expected values update after applying coordinates wrap
# test using dummy Universe with atoms out of boounds
# with wrap=True (default)
# +-----------+ +-----------+
# | | 7 | 8 | 9 | 9 | 7 | 8 |
# +-----------+ +-----------+
# 4 | 5 | 6 | | ---> | 5 | 6 | 4 |
# +-----------+ +-----------+
# | | 1 | 2 | 3 | 3 | 1 | 2 |
# +-----------+ +-----------+
#
# test surface in universe with atoms out of bounds in x
def test_analysis_get_z_surface_wrap(self, universe_dummy_wrap, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_surface = mc.results.average_z_surface
assert_almost_equal(avg_surface, dummy_surface)

# test surface in universe with atoms out of bounds in x and y
def test_analysis_get_z_surface_wrap_xy(self, universe_dummy_wrap_xy, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_surface = mc.results.average_z_surface
assert_almost_equal(avg_surface, dummy_surface)

# test mean curvature
def test_analysis_mean_wrap(self, universe_dummy_wrap, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_mean = mc.results.average_mean
expected_mean = mean_curvature(dummy_surface)
assert_almost_equal(avg_mean, expected_mean)

def test_analysis_mean_wrap_xy(self, universe_dummy_wrap_xy, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_mean = mc.results.average_mean
expected_mean = mean_curvature(dummy_surface)
assert_almost_equal(avg_mean, expected_mean)

# test gaussian
def test_analysis_gaussian_wrap(self, universe_dummy_wrap, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_gaussian = mc.results.average_gaussian
expected_gaussian = gaussian_curvature(dummy_surface)
assert_almost_equal(avg_gaussian, expected_gaussian)

def test_analysis_mean_gaussian_wrap_xy(self, universe_dummy_wrap_xy, dummy_surface):
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin).run()
avg_gaussian = mc.results.average_gaussian
expected_gaussian = gaussian_curvature(dummy_surface)
assert_almost_equal(avg_gaussian, expected_gaussian)

# test using dummy Universe with atoms out of boounds
# with wrap=False
# +-----------+
# | | 7 | 8 | 9
# +-----------+
# 4 | 5 | 6 | |
# +-----------+
# | | 1 | 2 | 3
# +-----------+
# test surface
# with wrap=False in universe with atoms out of bounds in x
def test_analysis_get_z_surface_no_wrap(self, universe_dummy_wrap):
expected_surface = [[np.nan, 150., np.nan],
[150., 150., 150.],
[150., np.nan, 150.]]
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_surface = mc.results.average_z_surface
assert_almost_equal(avg_surface, expected_surface)

# test surface in universe with atoms out of bounds in x and y
def test_analysis_get_z_surface_no_wrap_xy(self, universe_dummy_wrap_xy):
expected_surface = [[np.nan, np.nan, np.nan],
[150., np.nan, 150.],
[150., np.nan, 150.]]
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_surface = mc.results.average_z_surface
assert_almost_equal(avg_surface, expected_surface)

# test mean
def test_analysis_mean_no_wrap(self, universe_dummy_wrap):
expected_mean = np.array(np.full((3, 3), np.nan))
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_mean = mc.results.average_mean
assert_almost_equal(avg_mean, expected_mean)

def test_analysis_mean_no_wrap(self, universe_dummy_wrap_xy):
expected_mean = np.array(np.full((3, 3), np.nan))
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_mean = mc.results.average_mean
assert_almost_equal(avg_mean, expected_mean)

# test gaussian
def test_analysis_gaussian_no_wrap(self, universe_dummy_wrap):
expected_gaussian = np.array(np.full((3, 3), np.nan))
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_gaussian = mc.results.average_gaussian
assert_almost_equal(avg_gaussian, expected_gaussian)

def test_analysis_gaussian_no_wrap(self, universe_dummy_wrap_xy):
expected_gaussian = np.array(np.full((3, 3), np.nan))
x_bin = y_bin = 3
mc = MembraneCurvature(universe_dummy_wrap_xy,
n_x_bins=x_bin,
n_y_bins=y_bin,
wrap=False).run()
avg_gaussian = mc.results.average_gaussian
assert_almost_equal(avg_gaussian, expected_gaussian)

@pytest.mark.parametrize('x_bin, y_bin, expected_surface', [
(3, 3,
Expand Down Expand Up @@ -361,7 +542,7 @@ def test_analysis_mean(self, universe_dummy_full):
avg_mean = mc.results.average_mean
assert_almost_equal(avg_mean, expected_mean)

@ pytest.mark.parametrize('dummy_array, expected_surface', [
@pytest.mark.parametrize('dummy_array, expected_surface', [
# test with negative x coordinates
(np.array([[0., 0., 150.], [-100., 0., 150.], [- 200., 0., 150.],
[0., 100., 150.], [-100., 100., 120.], [-200., 100., 120.],
Expand Down

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