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Adds test to make sure small box issue is now fixed #2670 #3163

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Mar 14, 2021
Merged

Adds test to make sure small box issue is now fixed #2670 #3163

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dc90869
Adds test for issue 2670
IAlibay Mar 14, 2021
9fd5e05
update changelog
IAlibay Mar 14, 2021
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -18,6 +18,7 @@ The rules for this file:
* 1.0.2

Fixes
* Adds test for crashes caused by small box NSGrid searches (Issue #2670)
* Replaces decreated NumPy type aliases and fixes NEP 34 explicit ragged
array warnings (PR #3139, backports PRs #2845 and #2834)
* Fixed several issues with NSGrid and triclinic boxes not finding some pairs.
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16 changes: 16 additions & 0 deletions testsuite/MDAnalysisTests/lib/test_nsgrid.py
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Expand Up @@ -352,3 +352,19 @@ def test_issue_2345():
c = Counter(len(v) for v in cn.values())

assert c == {9: 50, 12: 50}


def test_issue_2670():
# Tests that NSGrid no longer crashes when using small box sizes
u = mda.Universe(PDB)
u.dimensions = [1e-3, 1e-3, 1e-3, 90, 90, 90]

ag1 = u.select_atoms('resid 2 3')
# should return nothing as nothing except resid 3 is within 0.0 or resid 3
assert len(ag1.select_atoms('around 0.0 resid 3')) == 0

# force atom 0 of resid 1 to overlap with atom 0 of resid 3
u.residues[0].atoms[0].position = u.residues[2].atoms[0].position
ag2 = u.select_atoms('resid 1 3')
# should return the one atom overlap
assert len(ag2.select_atoms('around 0.0 resid 3')) == 1