atoms_around_point

mdtools.select.atoms_around_point(ag, point, cutoff, **kwargs)

Select Atoms from an MDAnalysis AtomGroup instance that are within a cutoff of a point in space.

Parameters:

• ag (MDAnalysis.core.groups.AtomGroup) – MDAnalysis AtomGroup, UpdatingAtomGroup or Universe from which the Atoms will be selected.

• point (array_like) – Array of shape (3,) containing the coordinates in Angstrom of a point in space. All Atoms of ag that are within cutoff of that point will be selected.

• cutoff (scalar) – Select all Atoms that are within cutoff of point. Must be greater than zero.

• kwargs (dict, optional) – Additional keyword arguments to parse to MDAnalysis.core.groups.AtomGroup.select_atoms(). See there for possible choices. By default, warn_empty and verbose are set to False.

Returns:

selection (MDAnalysis.core.groups.AtomGroup) – An MDAnalysis AtomGroup containing the selected Atoms.

See also

mdtools.select.atoms()

Select

class:Atoms <MDAnalysis.core.groups.Atom> from an

MDAnalysis

class:~MDAnalysis.core.groups.AtomGroup

Notes

This function uses the MDAnalysis selection syntax point x y z distance. It is just a convenient wrapper around mdtools.select.atoms() that allows you to simply parse an array like point and a cutoff without the need to assemble them to an MDAnalysis selection string yourself.