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Add pbc kwarg to Contacts #2646

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merged 8 commits into from Apr 22, 2020
Merged

Add pbc kwarg to Contacts #2646

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921eb56
Fixes #2368: added option to calculate distances using PBC
ss62171 Mar 25, 2020
d796742
Added test to check distance calculated using PBC
ss62171 Mar 25, 2020
856344c
test added
ss62171 Mar 29, 2020
05a442c
documented changes
ss62171 Mar 29, 2020
c97cacc
added box_dim and test modified
ss62171 Mar 31, 2020
8b204d2
added lambda func to get dimension of box
ss62171 Mar 31, 2020
ee62918
edit changelog and docstring of class
ss62171 Apr 8, 2020
043819b
fixed typo
ss62171 Apr 9, 2020
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -73,6 +73,7 @@ Fixes
* Fixed HydrogenBondAnalysis to return atom indices rather than atom ids (PR #2572).
Fixed the check for bond information in the _get_dh_pairs method (Issue #2396).
* Added missing selection module to leaflet.py (Issue #2612)
* Contact Analysis class respects PBC (Issue #2368)

Enhancements
* Added new density.DensityAnalysis (Issue #2502)
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2 changes: 2 additions & 0 deletions package/MDAnalysis/analysis/contacts.py
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Expand Up @@ -373,6 +373,8 @@ class Contacts(AnalysisBase):
.. versionchanged:: 1.0.0
``save()`` method has been removed. Use ``np.savetxt()`` on
:attr:`Contacts.timeseries` instead.
.. versionchanged:: 2.0.0
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Thanks @ss62171, just one final thing -- this should be for version 1.0.0 which hasn't been released yet.

added ``pbc`` attribute to calculate distances using PBC.

"""
def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
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17 changes: 7 additions & 10 deletions testsuite/MDAnalysisTests/analysis/test_contacts.py
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Expand Up @@ -303,8 +303,13 @@ def test_non_callable_method(self, universe):
with pytest.raises(ValueError):
self._run_Contacts(universe, method=2, stop=2)

@pytest.mark.parametrize("pbc", (True, False))
def test_distance_box(self, pbc):
@pytest.mark.parametrize("pbc,expected", [
(True, [1., 0.43138152, 0.3989021, 0.43824337, 0.41948765,
0.42223239, 0.41354071, 0.43641354, 0.41216834, 0.38334858]),
(False, [1., 0.42327791, 0.39192399, 0.40950119, 0.40902613,
0.42470309, 0.41140143, 0.42897862, 0.41472684, 0.38574822])
])
def test_distance_box(self, pbc, expected):
u = mda.Universe(TPR, XTC)
sel_basic = "(resname ARG LYS)"
sel_acidic = "(resname ASP GLU)"
Expand All @@ -314,14 +319,6 @@ def test_distance_box(self, pbc):
r = contacts.Contacts(u, select=(sel_acidic, sel_basic),
refgroup=(acidic, basic), radius=6.0, pbc=pbc)
r.run()
if pbc:
expected = [1., 0.43138152, 0.3989021, 0.43824337, 0.41948765,
0.42223239, 0.41354071, 0.43641354, 0.41216834, 0.38334858]

else:
expected = [1., 0.42327791, 0.39192399, 0.40950119, 0.40902613,
0.42470309, 0.41140143, 0.42897862, 0.41472684, 0.38574822]

assert_array_almost_equal(r.timeseries[:, 1], expected)

def test_q1q2():
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