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BUG: Fixes #1795 sphzone selection regression #1818

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BUG: Fixes #1795 sphzone selection regression #1818

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2dcbf5c
BUG: Fixes #1795
tylerjereddy Mar 9, 2018
f14b7e7
TST: test_spherical_zone() now redefined in test subclasses to proper…
tylerjereddy Mar 13, 2018
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2 changes: 1 addition & 1 deletion package/MDAnalysis/core/selection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -388,7 +388,7 @@ def _apply_distmat(self, group):
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
periodic = box is not None
ref = sel.center_of_geometry(pbc=periodic).reshape(1, 3).\
ref = sel.center_of_geometry().reshape(1, 3).\
astype(np.float32)
d = distances.distance_array(ref,
group.positions,
Expand Down
42 changes: 27 additions & 15 deletions testsuite/MDAnalysisTests/core/test_atomselections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
#
from __future__ import division, absolute_import

from six.moves import range
from six.moves import range, zip

import itertools
import numpy as np
Expand Down Expand Up @@ -542,20 +542,6 @@ def test_spherical_layer(self, u, meth, periodic):

assert ref == set(result.indices)

@pytest.mark.parametrize('meth, periodic', methods)
def test_spherical_zone(self, u, meth, periodic):
sel = Parser.parse('sphzone 5.0 resid 1', u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(u.atoms)

r1 = u.select_atoms('resid 1')
box = u.dimensions if periodic else None
cog = r1.center_of_geometry(pbc=periodic).reshape(1, 3)
d = distance_array(u.atoms.positions, cog, box=box)
ref = set(np.where(d < 5.0)[0])

assert ref == set(result.indices)

@pytest.mark.parametrize('meth, periodic', methods)
def test_point(self, u, meth, periodic):
sel = Parser.parse('point 5.0 5.0 5.0 3.0', u.atoms)
Expand Down Expand Up @@ -602,12 +588,38 @@ def test_cyzone(self, u, meth, periodic):

assert ref == set(result.indices)

@pytest.mark.parametrize('input_val, expected',
zip(BaseDistanceSelection.methods,
[25, 31, 33, 25]))
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So this means that kdtree and non-kdtree are returning a different result for periodic=True

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Does that mean more changes are needed or we need to think about this a bit more?

def test_spherical_zone(self, u, input_val, expected):
# NOTE: this has been modified to regression test
# only for resolution of Issue #1795
# pending proper pbc & wrapping implementations
# in the future
sel = Parser.parse('sphzone 5.0 resid 1', u.atoms)
sel = self.choosemeth(sel, input_val[0], input_val[1])
result = len(sel.apply(u.atoms))
assert result == expected


class TestTriclinicDistanceSelections(BaseDistanceSelection):
@pytest.fixture()
def u(self):
return mda.Universe(GRO)

@pytest.mark.parametrize('input_val, expected',
zip(BaseDistanceSelection.methods,
[55, 55, 55, 55]))
def test_spherical_zone(self, u, input_val, expected):
# NOTE: this has been modified to regression test
# only for resolution of Issue #1795
# pending proper pbc & wrapping implementations
# in the future
sel = Parser.parse('sphzone 5.0 resid 1', u.atoms)
sel = self.choosemeth(sel, input_val[0], input_val[1])
result = len(sel.apply(u.atoms))
assert result == expected


class TestTriclinicSelections(object):
"""Non-KDTree based selections
Expand Down