aquaduct.traj.barber module

Module implements AutoBarber generation of spheres.

class Sphere[source]

Bases: aquaduct.traj.barber.Sphere

Simple sphere class.

is_point_within(point)[source]
is_sphere_within(sphere)[source]
is_sphere_cloud(sphere)[source]
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)[source]

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.

__init__(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)[source]
Parameters:
  • spaths (list) – List of aquaduct.traj.paths.SinglePath objects.
  • expected_nr_of_spaths (int) – Number of spaths passed. Requilred when length of spaths cannod be calculated, eg when it is a generator.
  • selection (str) – Selection string of molecular object used for spheres generation.
  • mincut (float) – Value of mincut parameter.
  • maxcut (float) – Value of maxcut parameter.
  • mincut_level (bool) – Flag of mincut_level.
  • maxcut_level (bool) – Flag of maxcut_level.
  • tovdw (bool) – Flag of to VdW radii correction parameter.
  • forceemtpy (bool) – If set True spheres of radius 0 are returned if no other sphere can be generated.
check_minmaxcuts()[source]
add_spheres_from_spaths(spaths)[source]
add_spheres_from_inlets(inlets)[source]
get_current_nr()[source]
inlet2sphere(inlet)[source]
spath2spheres(sp)[source]
_cut_thyself(spheres_passed, progress=False)[source]
cut_thyself()[source]
is_overlaping_with_cloud(sphere)[source]
cloud_groups(progress=False)[source]