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Adds unwrap keyword to principal_axes #2295

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2052a80
Merge pull request #2 from MDAnalysis/develop
NinadBhat Mar 30, 2019
0c5ebc3
Merge pull request #3 from MDAnalysis/develop
NinadBhat May 8, 2019
4ac9ab0
Merge pull request #4 from MDAnalysis/develop
NinadBhat May 27, 2019
4819464
Adds unwrap to center
NinadBhat Jun 17, 2019
300c955
Adds tests
NinadBhat Jun 18, 2019
6f21b31
Review changes
NinadBhat Jun 19, 2019
55d0a84
add unwrap to 'cog'
NinadBhat Jun 19, 2019
76876d4
Merge develop
NinadBhat Jul 3, 2019
6ae780b
check for pbc and unwrap
NinadBhat Jul 3, 2019
6d33fe9
Removes unnecessary lines
NinadBhat Jul 3, 2019
71f5dc9
:Merge remote-tracking branch 'upstream/develop' into develop
NinadBhat Jul 5, 2019
cc6dae2
Merge remote-tracking branch 'upstream/develop' into develop
NinadBhat Jul 7, 2019
38478f8
Merge upstream-develop
NinadBhat Jul 9, 2019
33e609c
Merge upstream/develop
NinadBhat Jul 9, 2019
a6bdacd
adds unwrap to principal_axes
NinadBhat Jul 9, 2019
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14 changes: 11 additions & 3 deletions package/MDAnalysis/core/topologyattrs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -880,6 +880,10 @@ def moment_of_inertia(group, **kwargs):
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their centers.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional
Which type of component to keep together during unwrapping.

Note
----
Expand Down Expand Up @@ -1089,7 +1093,8 @@ def asphericity(group, pbc=None):
('asphericity', asphericity))

@warn_if_not_unique
def principal_axes(group, pbc=None):
@check_pbc_and_unwrap
def principal_axes(group, pbc=None, unwrap=False, compound='group'):
"""Calculate the principal axes from the moment of inertia.

e1,e2,e3 = AtomGroup.principal_axes()
Expand All @@ -1103,6 +1108,10 @@ def principal_axes(group, pbc=None):
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. If ``None`` use value defined in setup flags.
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their centers.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional
Which type of component to keep together during unwrapping.

Returns
-------
Expand All @@ -1119,10 +1128,9 @@ def principal_axes(group, pbc=None):
.. versionchanged:: 0.8 Added *pbc* keyword

"""
atomgroup = group.atoms
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@NinadBhat NinadBhat Jul 9, 2019

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@richardjgowers @jbarnoud Is there a reason for using atomgroup = group.atoms
in place of directly using group.moment_of_inertia?

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@richardjgowers richardjgowers Jul 10, 2019

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Here it should be fine since MOI is doing the conversion. In general these methods are attached to all groups, so ResidueGroup too, but they want to operate on atoms. So for a RG, atomgroup = group.atoms is converting to an AtomGroup within the method.

if pbc is None:
pbc = flags['use_pbc']
e_val, e_vec = np.linalg.eig(atomgroup.moment_of_inertia(pbc=pbc))
e_val, e_vec = np.linalg.eig(group.moment_of_inertia(pbc=pbc, unwrap=unwrap, compound=compound))

# Sort
indices = np.argsort(e_val)[::-1]
Expand Down
22 changes: 21 additions & 1 deletion testsuite/MDAnalysisTests/core/test_atomgroup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -858,6 +858,10 @@ def ref_noUnwrap_residues(self):
[7333.79167791, -211.8997285, -721.50785456],
[-211.8997285, 7059.07470427, -91.32156884],
[-721.50785456, -91.32156884, 6509.31735029]]),
'PAxes': np.array([
[-0.85911708, 0.19258726, 0.4741603],
[-0.07520116, -0.96394227, 0.25526473],
[-0.50622389, -0.18364489, -0.84262206]])

}

Expand All @@ -872,7 +876,11 @@ def ref_Unwrap_residues(self):
[2.045, 28.243, 54.127]], dtype=np.float32),
'MOI': np.array([[16747.486, -1330.489, 2938.243],
[-1330.489, 19315.253, 3306.212],
[ 2938.243, 3306.212, 8990.481]])
[ 2938.243, 3306.212, 8990.481]]),
'PAxes': np.array(
[[-0.15999399, 0.9581568, 0.23735515],
[-0.93680726, -0.0715994, -0.34244077],
[-0.31111746, -0.27714449, 0.90906372]]),
}

@pytest.fixture()
Expand All @@ -884,6 +892,10 @@ def ref_noUnwrap(self):
[0.0, 0.0, 0.0],
[0.0, 98.6542, 0.0],
[0.0, 0.0, 98.65421327]]),
'PAxes': np.array(
[[0., 0., 1.],
[0., 1., 0.],
[1., 0., 0.]]),
}

@pytest.fixture()
Expand All @@ -895,17 +907,23 @@ def ref_Unwrap(self):
[0.0, 0.0, 0.0],
[0.0, 132.673, 0.0],
[0.0, 0.0, 132.673]]),
'PAxes': np.array(
[[0., 0., 1.],
[0., 1., 0.],
[1., 0., 0.]]),
}

def test_default_residues(self, ag, ref_noUnwrap_residues):
assert_almost_equal(ag.center_of_geometry(compound='residues'), ref_noUnwrap_residues['COG'], self.prec)
assert_almost_equal(ag.center_of_mass(compound='residues'), ref_noUnwrap_residues['COM'], self.prec)
assert_almost_equal(ag.moment_of_inertia(compound='residues'), ref_noUnwrap_residues['MOI'], self.prec)
assert_almost_equal(ag.principal_axes(compound='residues'), ref_noUnwrap_residues['PAxes'], self.prec)

def test_UnWrapFlag_residues(self, ag, ref_Unwrap_residues):
assert_almost_equal(ag.center_of_geometry(unwrap=True, compound='residues'), ref_Unwrap_residues['COG'], self.prec)
assert_almost_equal(ag.center_of_mass(unwrap=True, compound='residues'), ref_Unwrap_residues['COM'], self.prec)
assert_almost_equal(ag.moment_of_inertia(unwrap=True, compound='residues'), ref_Unwrap_residues['MOI'], self.prec)
assert_almost_equal(ag.principal_axes(unwrap=True, compound='residues'), ref_Unwrap_residues['PAxes'], self.prec)

def test_default(self, ref_noUnwrap):
u = UnWrapUniverse(is_triclinic=False)
Expand All @@ -916,6 +934,7 @@ def test_default(self, ref_noUnwrap):
assert_almost_equal(group.center_of_geometry(), ref_noUnwrap['COG'], self.prec)
assert_almost_equal(group.center_of_mass(), ref_noUnwrap['COM'], self.prec)
assert_almost_equal(group.moment_of_inertia(), ref_noUnwrap['MOI'], self.prec)
assert_almost_equal(group.principal_axes(), ref_noUnwrap['PAxes'], self.prec)

def test_UnWrapFlag(self, ref_Unwrap):
u = UnWrapUniverse(is_triclinic=False)
Expand All @@ -925,6 +944,7 @@ def test_UnWrapFlag(self, ref_Unwrap):
assert_almost_equal(group.center_of_geometry(unwrap=True), ref_Unwrap['COG'], self.prec)
assert_almost_equal(group.center_of_mass(unwrap=True), ref_Unwrap['COM'], self.prec)
assert_almost_equal(group.moment_of_inertia(unwrap=True), ref_Unwrap['MOI'], self.prec)
assert_almost_equal(group.principal_axes(unwrap=True), ref_Unwrap['PAxes'], self.prec)

class TestPBCFlag(object):

Expand Down