cog
- mdtools.structure.cog(ag, pbc=False, cmp='group', make_whole=False, debug=False)[source]
Calculate the center of geometry (a.k.a centroid) of (compounds of) an MDAnalysis
AtomGroup
.- Parameters:
ag (
MDAnalysis.core.groups.AtomGroup
) – The MDAnalysisAtomGroup
for which to calculate the center of geometry.pbc (
bool
, optional) – Seemdtools.structure.center()
.cmp (
{'group', 'segments', 'residues', 'molecules', 'fragments', 'atoms'}
, optional) – Seemdtools.structure.center()
.make_whole (
bool
, optional) – Seemdtools.structure.center()
.debug (
bool
, optional) – IfTrue
, run in debug mode.
- Returns:
center (
numpy.ndarray
) – Center of geometry 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)
wheren
is the number of compounds in ag.- Raises:
RuntimeWarning : – If debug is
True
and the center of geometry of any compound isnan
.
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.com()
Center of mass of (compounds of) an MDAnalysis
AtomGroup
Notes
This function uses the
center_of_geometry()
method of the inputAtomGroup
to calculate the center of geometry.Todo
Check if it is really necessary to wrap all
Atoms
back into the primary unit cell before callingcenter_of_geometry()
with unwrap set toTrue
. The currently done back-wrapping is a serious problem, because it implies an inplace change of theAtom
coordinates.