binding_sites package

Submodules

binding_sites.absl module

Binding site location algorithm

General procedure is to:

  • use the most central point in the molecule to first place the guest
  • align the guest with nearby probability peaks
  • report the outcome as site + orientation sets
binding_sites.absl.calculate_binding_sites(guest, tp_point, cell)[source]

Return the sets of points in the maxima that identify binding sites. Each set minimally contains a tuple (index of first atom, position of second atom), plus tuples of the index and vectors to a second and third atom.

Parameters:

guest : Guest

The guest instance containing the TABASCO maxima.

tp_point : tuple

The identifier for the state point to calculate the binding sites for.

cell : Cell

The unit cell of the system.
Returns:

binding_sites : list

A list of lists, each containing: (index_0, position_0, magnitude_0), (index_1, vector_0_1), # [optional] (index_2, vector_0_2) # [optional]
binding_sites.absl.direction3d(source, target)[source]

Return the vector connecting two 3d points.

binding_sites.absl.min_vect(c_coa, f_coa, c_cob, f_cob_in, box)[source]

Calculate the closest distance assuming fractional, in-cell coords.

binding_sites.absl.vecdist3(coord1, coord2)[source]

Calculate vector between two 3d points.

Module contents