9.6.4. Fitting transformations — MDAnalysis.transformations.fit

Translate and/or rotates the coordinates of a given trajectory to align a given AtomGroup to a reference structure.

class MDAnalysis.transformations.fit.fit_translation(ag, reference, plane=None, weights=None, max_threads=None, parallelizable=True)[source]

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:

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 AtomGroup or a whole Universe

  • reference (Universe or AtomGroup) – reference structure, a AtomGroup or a whole 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.

Return type:

MDAnalysis.coordinates.timestep.Timestep

Changed in version 2.0.0: The transformation was changed from a function/closure to a class with __call__.

Changed in version 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.

Parameters:

  • max_threads (int, optional) – The maximum thread number can be used. Default is None, which means the default or the external setting.

  • parallelizable (bool, optional) – A check for if this can be used in split-apply-combine parallel analysis approach. Default is True.

class MDAnalysis.transformations.fit.fit_rot_trans(ag, reference, plane=None, weights=None, max_threads=1, parallelizable=True)[source]

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:

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 AtomGroup or a whole Universe

  • reference (Universe or AtomGroup) – reference structure, a AtomGroup or a whole 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.

Return type:

MDAnalysis.coordinates.timestep.Timestep

Changed in version 2.0.0: The transformation was changed from a function/closure to a class with __call__.

Changed in version 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.

Parameters:

  • max_threads (int, optional) – The maximum thread number can be used. Default is None, which means the default or the external setting.

  • parallelizable (bool, optional) – A check for if this can be used in split-apply-combine parallel analysis approach. Default is True.