com

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

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

Parameters:

ag (MDAnalysis.core.groups.AtomGroup) – The MDAnalysis AtomGroup for which to calculate the center of mass.
pbc (bool, optional) – See mdtools.structure.center().
compound ({'group', 'segments', 'residues', 'molecules', 'fragments', 'atoms'}, optional) – See mdtools.structure.center().
make_whole (bool, optional) – See mdtools.structure.center().
debug (bool, optional) – If True, run in debug mode.

Returns:

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

Raises:

RuntimeWarning : – If debug is True and the center of mass of any compound is nan.

See also

MDAnalysis.core.groups.AtomGroup.center(): Weighted center of (compounds of) the group
MDAnalysis.core.groups.AtomGroup.center_of_geometry(): Center of geometry of (compounds of) the group
MDAnalysis.core.groups.AtomGroup.center_of_mass(): Center of mass of (compounds of) the group
mdtools.structure.center(): Different types of centers of (compounds of) an MDAnalysis AtomGroup
mdtools.structure.wcenter(): Weighted center of (compounds of) an MDAnalysis AtomGroup
mdtools.structure.wcenter_pos(): Calculate the weighted center of a position array
mdtools.structure.coc(): Center of charge of (compounds of) an MDAnalysis AtomGroup
mdtools.structure.cog(): Center of geometry of (compounds of) an MDAnalysis AtomGroup

Notes

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

Important

MDAnalysis always guesses atom masses! If MDAnalysis cannot guess the mass from the atom type, it will assign this atom a zero mass. If the mass of a compound sum up to zero, the coordinates of that compound’s center of mass will be nan! If debug is set to True, a warning will be raised if any compound’s weighted center is nan. Also in the case if debug is false, a ValueError will be raised, if the mass of any atom in ag is less than or equal to zero.

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.