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Revert "changed comparisons of scalars to use pytest.approx function …
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…and comparison of arrays to use numpy.testing.assert_allclose function"

This reverts commit f894064.
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@yickysan
yickysan committed Apr 1, 2023
1 parent 1c49ead commit 7c98e9f
Showing 1 changed file with 36 additions and 49 deletions.
85 changes: 36 additions & 49 deletions testsuite/MDAnalysisTests/analysis/test_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ def test_subselection_alignto(self, universe, reference, subselection, expectati

with expectation:
rmsd = align.alignto(universe, reference, subselection=subselection)
assert rmsd[1] == pytest.approx(0.0, rel=1e-09)
assert_almost_equal(rmsd[1], 0.0, decimal=9)

def test_no_atom_masses(self, universe):
#if no masses are present
Expand Down Expand Up @@ -198,29 +198,25 @@ def test_rmsd(self, universe, reference):
first_frame = bb.positions
universe.trajectory[-1]
last_frame = bb.positions

# pytest.approx function is used here because the output of rmsd() is a scalar
# all comparisons of scalars have been changed from using the function assert_almost_equal to pytest.approx function
assert rms.rmsd(first_frame, first_frame) == pytest.approx(0.0), "error: rmsd(X,X) should be 0"

assert_almost_equal(rms.rmsd(first_frame, first_frame), 0.0, 5,
err_msg="error: rmsd(X,X) should be 0")
# rmsd(A,B) = rmsd(B,A) should be exact but spurious failures in the
# 9th decimal have been observed (see Issue 57 comment #1) so we relax
# the test to 6 decimals.
# by default pytest.approx has a relaive tolerance of 1e-06
rmsd = rms.rmsd(first_frame, last_frame, superposition=True)

assert rms.rmsd(last_frame, first_frame, superposition=True) == pytest.approx(rmsd), "error: rmsd() is not symmetric"

assert rmsd == pytest.approx(6.820321761927005, rel=1e-05), "RMSD calculation between 1st and last AdK frame gave wrong answer"

assert_almost_equal(
rms.rmsd(last_frame, first_frame, superposition=True), rmsd, 6,
err_msg="error: rmsd() is not symmetric")
assert_almost_equal(rmsd, 6.820321761927005, 5,
err_msg="RMSD calculation between 1st and last AdK frame gave wrong answer")
# test masses as weights
last_atoms_weight = universe.atoms.masses
A = universe.trajectory[0]
B = reference.trajectory[-1]
rmsd = align.alignto(universe, reference, weights='mass')
rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True,
superposition=True)
assert rmsd[1] == pytest.approx(rmsd_sup_weight), "Not equal to tolerance rel=1e-06"
assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)

def test_rmsd_custom_mass_weights(self, universe, reference):
last_atoms_weight = universe.atoms.masses
Expand All @@ -230,15 +226,15 @@ def test_rmsd_custom_mass_weights(self, universe, reference):
weights=reference.atoms.masses)
rmsd_sup_weight = rms.rmsd(A, B, weights=last_atoms_weight, center=True,
superposition=True)
assert rmsd[1] == pytest.approx(rmsd_sup_weight), "Not equal to tolerance rel=1e-06"
assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)

def test_rmsd_custom_weights(self, universe, reference):
weights = np.zeros(universe.atoms.n_atoms)
ca = universe.select_atoms('name CA')
weights[ca.indices] = 1
rmsd = align.alignto(universe, reference, select='name CA')
rmsd_weights = align.alignto(universe, reference, weights=weights)
assert rmsd[1] == pytest.approx(rmsd_weights[1]), "Not equal to tolerance rel=1e-06"
assert_almost_equal(rmsd[1], rmsd_weights[1], 6)

def test_AlignTraj_outfile_default(self, universe, reference, tmpdir):
with tmpdir.as_cwd():
Expand Down Expand Up @@ -288,9 +284,8 @@ def test_AlignTraj(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference, filename=outfile).run()
fitted = mda.Universe(PSF, outfile)


assert x.results.rmsd[0] == pytest.approx(6.9290, rel=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(5.2797e-07, rel=1e-03), "Not equal to tolerance rel=1e-03"
assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3)

# RMSD against the reference frame
# calculated on Mac OS X x86 with MDA 0.7.2 r689
Expand All @@ -303,10 +298,8 @@ def test_AlignTraj_weighted(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference,
filename=outfile, weights='mass').run()
fitted = mda.Universe(PSF, outfile)

assert x.results.rmsd[0] == pytest.approx(0, rel=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(6.9033, rel=1e-03), "Not equal to tolerance rel=1e-03"

assert_almost_equal(x.results.rmsd[0], 0, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3)

self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
Expand All @@ -325,19 +318,16 @@ def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
x_weights = align.AlignTraj(universe, reference,
filename=outfile, weights=weights).run()

# changed fucnion from assert_array_almost_equal to assert_allclose
assert_allclose(x.results.rmsd, x_weights.results.rmsd)
assert_array_almost_equal(x.results.rmsd, x_weights.results.rmsd)

def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
outfile = str(tmpdir.join('align_test.dcd'))
x = align.AlignTraj(universe, reference,
filename=outfile,
weights=reference.atoms.masses).run()
fitted = mda.Universe(PSF, outfile)

assert x.results.rmsd[0] == pytest.approx(0, rel=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(6.9033, rel=1e-03), "Not equal to tolerance rel=1e-03"

assert_almost_equal(x.results.rmsd[0], 0, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 6.9033, decimal=3)

self._assert_rmsd(reference, fitted, 0, 0.0,
weights=universe.atoms.masses)
Expand All @@ -357,9 +347,8 @@ def test_AlignTraj_in_memory(self, universe, reference, tmpdir):
x = align.AlignTraj(universe, reference, filename=outfile,
in_memory=True).run()
assert x.filename is None
assert x.results.rmsd[0] == pytest.approx(6.9290, rel=1e-03), "Not equal to tolerance rel=1e-03"
assert x.results.rmsd[-1] == pytest.approx(5.2797e-07, rel=1e-03), "Not equal to tolerance rel=1e-03"

assert_almost_equal(x.results.rmsd[0], 6.9290, decimal=3)
assert_almost_equal(x.results.rmsd[-1], 5.2797e-07, decimal=3)

# check in memory trajectory
self._assert_rmsd(reference, universe, 0, 6.929083044751061)
Expand Down Expand Up @@ -404,9 +393,8 @@ def test_alignto_partial_universe(self, universe, reference):
segB_free.translate(segB_bound.centroid() - segB_free.centroid())

align.alignto(u_free, u_bound, select=selection)
# changed function from assert_array_almost_equal to assert_allclose
assert_allclose(segB_bound.positions, segB_free.positions,
rtol=1e-03)
assert_array_almost_equal(segB_bound.positions, segB_free.positions,
decimal=3)


def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):
Expand Down Expand Up @@ -456,24 +444,24 @@ def test_average_structure(self, universe, reference):
def test_average_structure_mass_weighted(self, universe, reference):
ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, weights='mass')
avg = align.AverageStructure(universe, reference, weights='mass').run()
assert_allclose(avg.results.universe.atoms.positions, ref,
rtol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)

def test_average_structure_select(self, universe, reference):
select = 'protein and name CA and resid 3-5'
ref, rmsd = _get_aligned_average_positions(self.ref_files, reference, select=select)
avg = align.AverageStructure(universe, reference, select=select).run()
assert_allclose(avg.results.universe.atoms.positions, ref,
rtol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)

def test_average_structure_no_ref(self, universe):
ref, rmsd = _get_aligned_average_positions(self.ref_files, universe)
avg = align.AverageStructure(universe).run()
assert_allclose(avg.results.universe.atoms.positions, ref,
rtol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)

def test_average_structure_no_msf(self, universe):
avg = align.AverageStructure(universe).run()
Expand All @@ -496,16 +484,15 @@ def test_average_structure_ref_frame(self, universe):
universe.trajectory[0]
ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
avg = align.AverageStructure(universe, ref_frame=ref_frame).run()

assert_allclose(avg.results.universe.atoms.positions, ref,
rtol=1e-04)
assert avg.results.rmsd == pytest.approx(rmsd)
assert_almost_equal(avg.results.universe.atoms.positions, ref,
decimal=4)
assert_almost_equal(avg.results.rmsd, rmsd)

def test_average_structure_in_memory(self, universe):
avg = align.AverageStructure(universe, in_memory=True).run()
reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
assert_allclose(avg.results.universe.atoms.positions,
reference_coordinates, rtol=1e-044)
assert_almost_equal(avg.results.universe.atoms.positions,
reference_coordinates, decimal=4)
assert avg.filename is None


Expand Down

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