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mdtools.structure.com(ag, pbc=False, compound='group', make_whole=False, debug=False)[source]

Calculate the center of mass of (compounds of) a MDAnalysis AtomGroup.

Parameters

  • ag (MDAnalysis.core.groups.AtomGroup) – The MDAnalysis AtomGroup for which to calculate the center of mass.

  • pbc (bool, optional) – If True and compound is 'group', move all Atoms to the primary unit cell before calculating the center of mass. If True and compound is not 'group', the center of mass of each compound will be calculated without moving any Atoms to keep the compounds intact (if they were intact before). Instead, the resulting position vectors will be moved to the primary unit cell after calculating the center of mass.

  • compound ({‘group’, ‘segments’, ‘residues’, ‘molecules’, ‘fragments’}, optional) – The compounds of ag for which to calculate the center of mass. If 'group', the center of mass of all Atoms in ag will be returned as a single position vector. Else, the centers of mass of each Segment, Residue, molecule, or fragment contained in ag will be returned as an array of position vectors, i.e. a 2d array. Refer to the MDAnalysis’ user guide for an explanation of these terms. Note that in any case, even if compound is e.g. 'residues', only the Atoms belonging to ag are taken into account, even if the compound might comprise additional Atoms that are not contained in ag.

  • make_whole (bool, optional) – If True, first all Atoms in ag are wrapped back into the primary unit cell, to make sure that the algorithm is working properly. Then compounds whose bonds are broken across the box edges are made whole again. This means that making compounds whole in an unwrapped trajectory while keeping the trajectory unwrapped is not possible with this function.

  • debug (bool, optional) – If True, run in debug mode.

Returns

center – Center of mass positions of the compounds in ag. If compound was set to 'group', the output will be a single position vector. Else, the output will be a 2d array of shape (n, 3) where n is the number of compounds in ag.

Return type

numpy.ndarray

See also

MDAnalysis.core.groups.AtomGroup.center_of_mass()

Center of mass of (compounds of) the group

MDAnalysis.core.groups.AtomGroup.center()

Weighted center of (compounds of) the group

Notes

This function uses the center_of_mass() method of the input AtomGroup to calculate the center of mass.

If make_whole is True, all Atoms in ag are wrapped back into the primary unit cell using mdtools.box.wrap() before calling center_of_mass() with the option unwrap set to True. This is done to make sure that the unwrap algorithm (better called “make whole” algorithm) of center_of_mass() is working properly. This means that making compounds whole in an unwrapped trajectory while keeping the trajectory unwrapped is not possible with this function.

Todo

Check if it is really necessary to wrap all Atoms back into the primary unit cell before calling center_of_mass() with unwrap set to True. The currently done back-wrapping is a serious problem, because it implies an inplace change of the Atom coordinates.

If the no wrapping is necessary, we can mark this function as deprecated and instead recommend the direct use of center_of_mass().