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Update indexing in Charges and Masses get_residues #2991

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Merged
orbeckst merged 3 commits into from
Oct 16, 2020
Merged

Update indexing in Charges and Masses get_residues #2991

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664281e
Turn warnings into errors to avoid regression over #2990
jbarnoud Oct 15, 2020
ddc0274
Update indexing in Charges and Masses get_residues
jbarnoud Oct 15, 2020
3b8fbd8
Update CHANGELOG
jbarnoud Oct 15, 2020
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@ The rules for this file:
* 2.0.0

Fixes
* Avoid using deprecated array indexing in topology attributes
(Issue #2990, PR #2991)
* ParmedParser no longer guesses elements if they are not recognised, instead
empty strings are assigned (Issue #2933)
* Instead of using ATOM for both ATOM and HETATM, HETATM record type
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4 changes: 2 additions & 2 deletions package/MDAnalysis/core/topologyattrs.py
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Expand Up @@ -1116,7 +1116,7 @@ def get_residues(self, rg):

if isinstance(rg._ix, numbers.Integral):
# for a single residue
masses = self.values[resatoms].sum()
masses = self.values[tuple(resatoms)].sum()
else:
# for a residuegroup
masses = np.empty(len(rg))
Expand Down Expand Up @@ -1537,7 +1537,7 @@ def get_residues(self, rg):
resatoms = self.top.tt.residues2atoms_2d(rg.ix)

if isinstance(rg._ix, numbers.Integral):
charges = self.values[resatoms].sum()
charges = self.values[tuple(resatoms)].sum()
else:
charges = np.empty(len(rg))
for i, row in enumerate(resatoms):
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10 changes: 10 additions & 0 deletions testsuite/MDAnalysisTests/core/test_accumulate.py
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Expand Up @@ -116,6 +116,11 @@ def test_total_charge_compounds(self, group, name, compound):
ref = [sum(a.charges) for a in group.atoms.groupby(name).values()]
assert_almost_equal(group.total_charge(compound=compound), ref)

@pytest.mark.filterwarnings( # Prevents regression of issue #2990
"error:"
"Using a non-tuple sequence for multidimensional indexing is deprecated:"
"FutureWarning"
)
def test_total_charge_duplicates(self, group):
group2 = group + group[0]
ref = group.total_charge() + group[0].charge
Expand All @@ -133,6 +138,11 @@ def test_total_mass_compounds(self, group, name, compound):
ref = [sum(a.masses) for a in group.atoms.groupby(name).values()]
assert_almost_equal(group.total_mass(compound=compound), ref)

@pytest.mark.filterwarnings( # Prevents regression of issue #2990
"error:"
"Using a non-tuple sequence for multidimensional indexing is deprecated:"
"FutureWarning"
)
def test_total_mass_duplicates(self, group):
group2 = group + group[0]
ref = group.total_mass() + group2[0].mass
Expand Down