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fixes #1795 #2074

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richardjgowers merged 2 commits into from
Sep 21, 2018
Merged

fixes #1795 #2074

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f810507
fixes #1795
richardjgowers Sep 14, 2018
e8a7863
additional tests for sphzone
richardjgowers Sep 14, 2018
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3 changes: 3 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,9 @@ Fixes
* Modifying coordinates by assignation is consistently persistent when using
the memory reader (Issue #2018)
* Allow import of WaterBridgeAnalysis from analysis.hbonds (#2064)
* Fixed SphericalLayer and SphericalZone selections with pbc=True. Previously
these shifted all atoms to inside the primary unit cell when calculating the
center of the reference group (Issue #1795)

Changes
* TopologyAttrs are now statically typed (Issue #1876)
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6 changes: 2 additions & 4 deletions package/MDAnalysis/core/selection.py
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Expand Up @@ -288,8 +288,7 @@ def apply(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).astype(
np.float32)
ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
pairs = distances.capped_distance(ref, group.positions, self.exRadius,
min_cutoff=self.inRadius,
box=box,
Expand All @@ -314,8 +313,7 @@ def apply(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).astype(
np.float32)
ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
pairs = distances.capped_distance(ref, group.positions, self.cutoff,
box=box,
return_distances=False)
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10 changes: 8 additions & 2 deletions testsuite/MDAnalysisTests/core/test_atomselections.py
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Expand Up @@ -530,7 +530,7 @@ def test_spherical_layer(self, u, periodic):

r1 = u.select_atoms('resid 1')
box = u.dimensions if periodic else None
cog = r1.center_of_geometry(pbc=periodic).reshape(1, 3)
cog = r1.center_of_geometry().reshape(1, 3)
d = distance_array(u.atoms.positions, cog, box=box)
ref = set(np.where((d > 2.4) & (d < 6.0))[0])

Expand All @@ -548,7 +548,7 @@ def test_spherical_zone(self, u, periodic):

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

Expand Down Expand Up @@ -603,6 +603,12 @@ def test_cyzone(self, u, meth, periodic):

assert ref == set(result.indices)

@pytest.mark.parametrize('periodic,expected', ([True, 33], [False, 25]))
def test_sphzone(self, u, periodic, expected):
sel = u.select_atoms('sphzone 5.0 resid 1', periodic=periodic)

assert len(sel) == expected


class TestTriclinicDistanceSelections(BaseDistanceSelection):
@pytest.fixture()
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