aquaduct.traj.barber module

Module implements AutoBarber generation of spheres.

class WhereToCut(spaths=None, inlets=None, expected_nr_of_spaths=None, selection=None, mincut=None, mincut_level=False, maxcut=None, maxcut_level=False, tovdw=False, forceempty=False)

Bases: aquaduct.traj.sandwich.ReaderAccess

Class implements method for creating (optimal) set of AutoBarber spheres for a collection of spaths; access to trajectory is also required to read VdW radii.

barber_with_spheres(coords, spheres)

param numpy.ndarray coords: Path’s coordinates subjected to barber procedure. param spheres: Spheres used to cut input coordinates. rtype: numpy.ndarray. return: List of indices to be kept.