iZdZddlmZddlmZGddeZGddeZd S) aWrap/unwrap transformations --- :mod:`MDAnalysis.transformations.wrap` ====================================================================== Wrap/unwrap the atoms of a given AtomGroup in the unit cell. :func:`wrap` translates the atoms back in the unit cell. :func:`unwrap` translates the atoms of each molecule so that bons don't split over images. .. autoclass:: wrap .. autoclass:: unwrap ) make_whole)TransformationBasec,eZdZdZ dfd ZdZxZS)wrapav 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 ------- .. code-block:: python 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. 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. atomsNTcjt||||_||_dS)N max_threadsparallelizable)super__init__agcompound)selfrrr r __class__s i/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/transformations/wrap.pyrz wrap.__init__^s? #N      cF|j|j|S)N)r)rrr)rtss r _transformzwrap._transformhs  dm ,,, r)rNT__name__ __module__ __qualname____doc__rr __classcell__rs@rrr*s^11hFJ!!!!!!rrc*eZdZdZdfd ZdZxZS)unwrapa 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 ------- .. code-block:: python ag = u.atoms transform = mda.transformations.unwrap(ag) u.trajectory.add_transformations(transform) Parameters ---------- atomgroup : AtomGroup The :class:`MDAnalysis.core.groups.AtomGroup` to work with. The positions of this are modified in place. 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. NTct||||_ |jjdS#t$r(t d|jwxYw)Nr z{} has no fragments)r rr fragmentsAttributeErrorformat)rrr r rs rrzunwrap.__init__s #N     H G     H H H !6!=!=dg!F!FGG G Hs ;2A-cB|jjD]}t||S)N)rr"r)rrfrags rrzunwrap._transforms,G%  D t     r)NTrrs@rr r ms]..` H H H H H Hrr N)r lib._cutilrbaserrr rrr*s.  $#####$$$$$$@@@@@ @@@F@@@@@ @@@@@r