chemcoord.ric_functions.get_primitives_idx

chemcoord.ric_functions.get_primitives_idx(start, end, bonds=None, linearity_thrshld=5)[source]

Returns the set of primitive internal coordinates for a pair of start and end structures. Takes a union of the required sets for both, as start and end need to use the same coordinates. Takes care of linearities by adding linear bending coordinates.

Parameters:

start (Cartesian) – starting structure
end (Cartesian) – ending structure
bonds (Mapping[AtomIdx, Set[AtomIdx]] | None) – default None, optional specification of connectivity. If not specified, generated automatically
linearity_thrshld (float) – default 5, tolerance for linearity, in degrees

Returns:

tuple of regular redundant primitive internal coordinates and linear bending coordinates.

Return type:

SortedSet