`topostats.tracing.dnacurvature`#

Module for calculating curvature statistics.

Module Contents#

Classes#

Class for determining the curvature of molecules.

Attributes#

topostats.tracing.dnacurvature.LOGGER#

class topostats.tracing.dnacurvature.Curvature(molecule_coordinates: numpy.ndarray, circular: bool)#

Class for determining the curvature of molecules.

Parameters:

molecule_coordinates (np.ndarray) – Coordinates of the simplified splined trace of a molecule. These are returned by dnaTracing.
circular (bool) – Whether the image is circular or not.

calculate_derivatives(edge_order: int = 1) → None#

Find the curvature for an individual molecule.

Parameters:: edge_order (int) – Gradient is passed to numpy.gradient and Gradient is calculated using N-th order accurate differences at boundaries. Also used to expand the array by the necessary number of coordinates at either end to form a loop for the calculations.

_calculate_local_curvature() → float#: Calculate the local curvature between points.