coc

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

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

Parameters:

ag (MDAnalysis.core.groups.AtomGroup) – The MDAnalysis AtomGroup for which to calculate the center of charge.
pbc (bool, optional) – See mdtools.structure.center().
cmp ({'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 charge position of each compound in ag. If cmp 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 charge 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.cog(): Center of geometry of (compounds of) an MDAnalysis AtomGroup
mdtools.structure.com(): Center of mass of (compounds of) an MDAnalysis AtomGroup

Notes

This function uses mdtools.structure.wcenter() which in turn relies on the center() method of the input AtomGroup to calculate the center of charge.

Important

If the charges of a compound sum up to zero, the coordinates of that compound’s center of charge will be nan! If debug is set to True, a warning will be raised if any compound’s center of charge is nan.