9.6.5. Wrap/unwrap transformations — MDAnalysis.transformations.wrap

Wrap/unwrap the atoms of a given AtomGroup in the unit cell. wrap() translates the atoms back in the unit cell. unwrap() translates the atoms of each molecule so that bons don’t split over images.

class MDAnalysis.transformations.wrap.wrap(ag, compound='atoms', max_threads=None, parallelizable=True)[source]

Shift the contents of a given AtomGroup back into the unit cell.

+-----------+          +-----------+
|           |          |           |
|         3 | 6        | 6       3 |
|         ! | !        | !       ! |
|       1-2-|-5-8  ->  |-5-8   1-2-|
|         ! | !        | !       ! |
|         4 | 7        | 7       4 |
|           |          |           |
+-----------+          +-----------+

Example

ag = u.atoms
transform = mda.transformations.wrap(ag)
u.trajectory.add_transformations(transform)
Parameters:

  • ag (Atomgroup) – Atomgroup to be wrapped in the unit cell

  • compound ({'atoms', 'group', 'residues', 'segments', 'fragments'}, optional) – The group which will be kept together through the shifting process.

Notes

When specifying a compound, the translation is calculated based on each compound. The same translation is applied to all atoms within this compound, meaning it will not be broken by the shift. This might however mean that not all atoms from the compound are inside the unit cell, but rather the center of the compound is.

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.wrap.unwrap(ag, max_threads=None, parallelizable=True)[source]

Move all atoms in an AtomGroup so that bonds don’t split over images

Atom positions are modified in place.

This function is most useful when atoms have been packed into the primary unit cell, causing breaks mid molecule, with the molecule then appearing on either side of the unit cell. This is problematic for operations such as calculating the center of mass of the molecule.

+-----------+     +-----------+
|           |     |           |
| 6       3 |     |         3 | 6
| !       ! |     |         ! | !
|-5-8   1-2-| ->  |       1-2-|-5-8
| !       ! |     |         ! | !
| 7       4 |     |         4 | 7
|           |     |           |
+-----------+     +-----------+

Example

ag = u.atoms
transform = mda.transformations.unwrap(ag)
u.trajectory.add_transformations(transform)
Parameters:

atomgroup (AtomGroup) – The MDAnalysis.core.groups.AtomGroup to work with. The positions of this are modified in place.

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.