Source code for MDAnalysis.transformations.fit
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""\
Fitting transformations --- :mod:`MDAnalysis.transformations.fit`
=================================================================
Translate and/or rotates the coordinates of a given trajectory to align
a given AtomGroup to a reference structure.
.. autoclass:: fit_translation
.. autoclass:: fit_rot_trans
"""
import numpy as np
from ..analysis import align
from ..lib.transformations import euler_from_matrix, euler_matrix
from .base import TransformationBase
[docs]
class fit_translation(TransformationBase):
"""Translates a given AtomGroup so that its center of geometry/mass matches
the respective center of the given reference. A plane can be given by the
user using the option `plane`, and will result in the removal of
the translation motions of the AtomGroup over that particular plane.
Example
-------
Removing the translations of a given AtomGroup `ag` on the XY plane by
fitting its center of mass to the center of mass of a reference `ref`:
.. code-block:: python
ag = u.select_atoms("protein")
ref = mda.Universe("reference.pdb")
transform = mda.transformations.fit_translation(ag, ref, plane="xy",
weights="mass")
u.trajectory.add_transformations(transform)
Parameters
----------
ag : Universe or AtomGroup
structure to translate, a
:class:`~MDAnalysis.core.groups.AtomGroup` or a whole
:class:`~MDAnalysis.core.universe.Universe`
reference : Universe or AtomGroup
reference structure, a :class:`~MDAnalysis.core.groups.AtomGroup` or a
whole :class:`~MDAnalysis.core.universe.Universe`
plane: str, optional
used to define the plane on which the translations will be removed.
Defined as a string of the plane.
Suported planes are yz, xz and xy planes.
weights : {"mass", ``None``} or array_like, optional
choose weights. With ``"mass"`` uses masses as weights; with ``None``
weigh each atom equally. If a float array of the same length as
`ag` is provided, use each element of the `array_like` as a
weight for the corresponding atom in `ag`.
Returns
-------
MDAnalysis.coordinates.timestep.Timestep
.. versionchanged:: 2.0.0
The transformation was changed from a function/closure to a class
with ``__call__``.
.. versionchanged:: 2.0.0
The transformation was changed to inherit from the base class for
limiting threads and checking if it can be used in parallel analysis.
"""
def __init__(self, ag, reference, plane=None, weights=None,
max_threads=None, parallelizable=True):
super().__init__(max_threads=max_threads,
parallelizable=parallelizable)
self.ag = ag
self.reference = reference
self.plane = plane
self.weights = weights
if self.plane is not None:
axes = {'yz': 0, 'xz': 1, 'xy': 2}
try:
self.plane = axes[self.plane]
except (TypeError, KeyError):
raise ValueError(f'{self.plane} is not a valid plane') \
from None
try:
if self.ag.atoms.n_residues != self.reference.atoms.n_residues:
errmsg = (
f"{self.ag} and {self.reference} have mismatched"
f"number of residues"
)
raise ValueError(errmsg)
except AttributeError:
errmsg = (
f"{self.ag} or {self.reference} is not valid"
f"Universe/AtomGroup"
)
raise AttributeError(errmsg) from None
self.ref, self.mobile = align.get_matching_atoms(self.reference.atoms,
self.ag.atoms)
self.weights = align.get_weights(self.ref.atoms, weights=self.weights)
self.ref_com = self.ref.center(self.weights)
def _transform(self, ts):
mobile_com = np.asarray(self.mobile.atoms.center(self.weights),
np.float32)
vector = self.ref_com - mobile_com
if self.plane is not None:
vector[self.plane] = 0
ts.positions += vector
return ts
[docs]
class fit_rot_trans(TransformationBase):
"""Perform a spatial superposition by minimizing the RMSD.
Spatially align the group of atoms `ag` to `reference` by doing a RMSD
fit.
This fit works as a way to remove translations and rotations of a given
AtomGroup in a trajectory. A plane can be given using the flag `plane`
so that only translations and rotations in that particular plane are
removed. This is useful for protein-membrane systems to where the membrane
must remain in the same orientation.
Note
----
``max_threads`` is set to 1 for this transformation
with which it performs better.
Example
-------
Removing the translations and rotations of a given AtomGroup `ag` on the XY plane
by fitting it to a reference `ref`, using the masses as weights for the RMSD fit:
.. code-block:: python
ag = u.select_atoms("protein")
ref = mda.Universe("reference.pdb")
transform = mda.transformations.fit_rot_trans(ag, ref, plane="xy",
weights="mass")
u.trajectory.add_transformations(transform)
Parameters
----------
ag : Universe or AtomGroup
structure to translate and rotate, a
:class:`~MDAnalysis.core.groups.AtomGroup` or a whole
:class:`~MDAnalysis.core.universe.Universe`
reference : Universe or AtomGroup
reference structure, a :class:`~MDAnalysis.core.groups.AtomGroup` or a whole
:class:`~MDAnalysis.core.universe.Universe`
plane: str, optional
used to define the plane on which the rotations and translations will be removed.
Defined as a string of the plane. Supported planes are "yz", "xz" and "xy" planes.
weights : {"mass", ``None``} or array_like, optional
choose weights. With ``"mass"`` uses masses as weights; with ``None``
weigh each atom equally. If a float array of the same length as
`ag` is provided, use each element of the `array_like` as a
weight for the corresponding atom in `ag`.
Returns
-------
MDAnalysis.coordinates.timestep.Timestep
.. versionchanged:: 2.0.0
The transformation was changed from a function/closure to a class
with ``__call__``.
.. versionchanged:: 2.0.0
The transformation was changed to inherit from the base class for
limiting threads and checking if it can be used in parallel analysis.
"""
def __init__(self, ag, reference, plane=None, weights=None,
max_threads=1, parallelizable=True):
super().__init__(max_threads=max_threads,
parallelizable=parallelizable)
self.ag = ag
self.reference = reference
self.plane = plane
self.weights = weights
if self.plane is not None:
axes = {'yz': 0, 'xz': 1, 'xy': 2}
try:
self.plane = axes[self.plane]
except (TypeError, KeyError):
raise ValueError(f'{self.plane} is not a valid plane') \
from None
try:
if self.ag.atoms.n_residues != self.reference.atoms.n_residues:
errmsg = (
f"{self.ag} and {self.reference} have mismatched "
f"number of residues"
)
raise ValueError(errmsg)
except AttributeError:
errmsg = (
f"{self.ag} or {self.reference} is not valid "
f"Universe/AtomGroup"
)
raise AttributeError(errmsg) from None
self.ref, self.mobile = align.get_matching_atoms(self.reference.atoms,
self.ag.atoms)
self.weights = align.get_weights(self.ref.atoms, weights=self.weights)
self.ref_com = self.ref.center(self.weights)
self.ref_coordinates = self.ref.atoms.positions - self.ref_com
def _transform(self, ts):
mobile_com = self.mobile.atoms.center(self.weights)
mobile_coordinates = self.mobile.atoms.positions - mobile_com
rotation, dump = align.rotation_matrix(mobile_coordinates,
self.ref_coordinates,
weights=self.weights)
vector = self.ref_com
if self.plane is not None:
matrix = np.r_[rotation, np.zeros(3).reshape(1, 3)]
matrix = np.c_[matrix, np.zeros(4)]
euler_angs = np.asarray(euler_from_matrix(matrix, axes='sxyz'),
np.float32)
for i in range(0, euler_angs.size):
euler_angs[i] = (euler_angs[self.plane] if i == self.plane
else 0)
rotation = euler_matrix(euler_angs[0],
euler_angs[1],
euler_angs[2],
axes='sxyz')[:3, :3]
vector[self.plane] = mobile_com[self.plane]
ts.positions = ts.positions - mobile_com
ts.positions = np.dot(ts.positions, rotation.T)
ts.positions = ts.positions + vector
return ts