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Merged
IAlibay merged 4 commits into from
May 7, 2021
Merged

Make align AnalysisBase classes use the Results class #3280

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0f1d0f4
Switch align AnalysisBase classes to use Results class
IAlibay May 7, 2021
649237b
Merge branch 'develop' into results-align
IAlibay May 7, 2021
d6c18af
fix pep8 issues
IAlibay May 7, 2021
3429bd0
Merge branch 'develop' into results-align
orbeckst May 7, 2021
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9 changes: 9 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,9 @@ Enhancements
checking if it can be used in parallel analysis. (Issue #2996, PR #2950)

Changes
* `analysis.align.AlignTraj` and `analysis.align.AverageStructure` now store
their result attributes using the `analysis.base.Results` class
(Issues #3278 and #3261)
* `analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalyis` now stores
`hbonds` data using the `analysis.base.Results class (Issues #3271, #3261)
* `analysis.rms.RMSD` and `analysis.rms.RMSF` classes now store `rmsd` and
Expand Down Expand Up @@ -238,6 +241,12 @@ Changes
* Added OpenMM coordinate and topology converters (Issue #2863, PR #2917)

Deprecations
* The `analysis.align.AlignTraj.rmsd` attribute is now deprecated in
favour of `analysis.align.AlignTraj.results.rmsd` (Issue #3278, #3261)
* The `universe`, `positions`, and `rmsd` attributes of
`analysis.align.AverageStructure` are now deprecated in favour of
`results.universe`, `results.positions`, and `results.rmsd`
(Issue #3278, #3261)
* The `hbonds` attribute of
`hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds` is now
deprecated in favour of `results.hbonds` (Issues #3271, #3261)
Expand Down
133 changes: 107 additions & 26 deletions package/MDAnalysis/analysis/align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -535,7 +535,7 @@ class AlignTraj(AnalysisBase):

.. versionchanged:: 1.0.0
``save()`` has now been removed, as an alternative use ``np.savetxt()``
on :attr:`rmsd`.
on :attr:`results.rmsd`.

"""

Expand Down Expand Up @@ -589,9 +589,19 @@ def __init__(self, mobile, reference, select='all', filename=None,
Atoms of the reference structure to be aligned against
mobile_atoms : AtomGroup
Atoms inside each trajectory frame to be rmsd_aligned
rmsd : Array
results.rmsd : :class:`numpy.ndarray`
Array of the rmsd values of the least rmsd between the mobile_atoms
and reference_atoms after superposition and minimimization of rmsd

.. versionadded:: 2.0.0

rmsd : :class:`numpy.ndarray`
Alias to the :attr:`results.rmsd` attribute.

.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use
:attr:`results.rmsd` instead.

filename : str
String reflecting the filename of the file where the aligned
positions will be written to upon running RMSD alignment
Expand Down Expand Up @@ -627,6 +637,10 @@ def __init__(self, mobile, reference, select='all', filename=None,
Support for the ``start``, ``stop``, and ``step`` keywords has been
removed. These should instead be passed to :meth:`AlignTraj.run`.

.. versionchanged:: 2.0.0
:attr:`rmsd` results are now stored in a
:class:`MDAnalysis.analysis.base.Results` instance.

"""
select = rms.process_selection(select)
self.ref_atoms = reference.select_atoms(*select['reference'])
Expand Down Expand Up @@ -677,17 +691,18 @@ def _prepare(self):
self._ref_com = self.ref_atoms.center(self._weights)
self._ref_coordinates = self.ref_atoms.positions - self._ref_com
# allocate the array for selection atom coords
self.rmsd = np.zeros((self.n_frames,))
self.results.rmsd = np.zeros((self.n_frames,))

def _single_frame(self):
index = self._frame_index
mobile_com = self.mobile_atoms.center(self._weights)
mobile_coordinates = self.mobile_atoms.positions - mobile_com
mobile_atoms, self.rmsd[index] = _fit_to(mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_com,
self._ref_com, self._weights)
mobile_atoms, self.results.rmsd[index] = _fit_to(
mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_com,
self._ref_com, self._weights)
# write whole aligned input trajectory system
self._writer.write(mobile_atoms)

Expand All @@ -696,6 +711,14 @@ def _conclude(self):
if not self._verbose:
logging.disable(logging.NOTSET)

@property
def rmsd(self):
wmsg = ("The `rmsd` attribute was deprecated in MDAnalysis 2.0.0 and "
"will be removed in MDAnalysis 3.0.0. Please use "
"`results.rmsd` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.rmsd


class AverageStructure(AnalysisBase):
"""RMS-align trajectory to a reference structure using a selection,
Expand All @@ -722,7 +745,7 @@ class AverageStructure(AnalysisBase):

# align to the third frame and average structure
av = align.AverageStructure(u, ref_frame=3).run()
averaged_universe = av.universe
averaged_universe = av.results.universe

"""

Expand Down Expand Up @@ -775,12 +798,42 @@ def __init__(self, mobile, reference=None, select='all', filename=None,
Atoms of the reference structure to be aligned against
mobile_atoms : AtomGroup
Atoms inside each trajectory frame to be rmsd_aligned
universe : mda.Universe
results.universe : :class:`MDAnalysis.Universe`
New Universe with average positions
positions : np.ndarray(dtype=float)

.. versionadded:: 2.0.0

universe : :class:`MDAnalysis.Universe`
Alias to the :attr:`results.universe` attribute.

.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use
:attr:`results.universe` instead.

results.positions : np.ndarray(dtype=float)
Average positions
rmsd : float

.. versionadded:: 2.0.0

positions : np.ndarray(dtype=float)
Alias to the :attr:`results.positions` attribute.

.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use
:attr:`results.positions` instead.

results.rmsd : float
Average RMSD per frame

.. versionadded:: 2.0.0

rmsd : float
Alias to the :attr:`results.rmsd` attribute.

.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use
:attr:`results.rmsd` instead.

filename : str
String reflecting the filename of the file where the average
structure is written
Expand All @@ -799,6 +852,9 @@ def __init__(self, mobile, reference=None, select='all', filename=None,


.. versionadded:: 1.0.0
.. versionchanged:: 2.0.0
:attr:`universe`, :attr:`positions`, and :attr:`rmsd` are now
stored in a :class:`MDAnalysis.analysis.base.Results` instance.
"""
if in_memory or isinstance(mobile.trajectory, MemoryReader):
mobile.transfer_to_memory()
Expand Down Expand Up @@ -832,9 +888,9 @@ def __init__(self, mobile, reference=None, select='all', filename=None,
self.ref_frame = ref_frame

self.filename = filename
self.universe = mda.Merge(self.mobile_atoms)
self.results.universe = mda.Merge(self.mobile_atoms)
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@orbeckst orbeckst May 7, 2021

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FYI @joaomcteixeira @PicoCentauri : mdacli will need to be able to deal with whole Universes in the results. This can be as simple as reporting that this result cannot be meaningfully saved. (Although, you can serialize a Universe nowadays — just the question if you want to).


natoms = len(self.universe.atoms)
natoms = len(self.results.universe.atoms)
self.ref_atoms, self.mobile_atoms = get_matching_atoms(
self.ref_atoms, self.mobile_atoms, tol_mass=tol_mass,
strict=strict, match_atoms=match_atoms)
Expand Down Expand Up @@ -863,28 +919,53 @@ def _prepare(self):
self.reference.universe.trajectory[current_frame]

# allocate the array for selection atom coords
self.positions = np.zeros((len(self.mobile_atoms), 3))
self.rmsd = 0
self.results.positions = np.zeros((len(self.mobile_atoms), 3))
self.results.rmsd = 0

def _single_frame(self):
mobile_com = self.mobile_atoms.center(self._weights)
mobile_coordinates = self.mobile_atoms.positions - mobile_com
self.rmsd += _fit_to(mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_com,
self._ref_com, self._weights)[1]
self.positions += self.mobile_atoms.positions
self.results.rmsd += _fit_to(mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_com,
self._ref_com, self._weights)[1]
self.results.positions += self.mobile_atoms.positions

def _conclude(self):
self.positions /= self.n_frames
self.rmsd /= self.n_frames
self.universe.load_new(self.positions.reshape((1, -1, 3)))
self._writer.write(self.universe.atoms)
self.results.positions /= self.n_frames
self.results.rmsd /= self.n_frames
self.results.universe.load_new(
self.results.positions.reshape((1, -1, 3)))
self._writer.write(self.results.universe.atoms)
self._writer.close()
if not self._verbose:
logging.disable(logging.NOTSET)

@property
def universe(self):
wmsg = ("The `universe` attribute was deprecated in MDAnalysis 2.0.0 "
"and will be removed in MDAnalysis 3.0.0. Please use "
"`results.universe` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.universe

@property
def positions(self):
wmsg = ("The `positions` attribute was deprecated in MDAnalysis 2.0.0 "
"and will be removed in MDAnalyssi 3.0.0. Please use "
"`results.positions` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.positions

@property
def rmsd(self):
wmsg = ("The `rmsd` attribute was deprecated in MDAnalysis 2.0.0 "
"and will be removed in MDAnalysis 3.0.0. Please use "
"`results.rmsd` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.rmsd


def sequence_alignment(mobile, reference, match_score=2, mismatch_penalty=-1,
gap_penalty=-2, gapextension_penalty=-0.1):
Expand Down
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