topostats.tracing.dnacurvature#
Module for calculating curvature statistics.
Attributes#
Classes#
Class for determining the curvature of molecules. |
Module Contents#
- topostats.tracing.dnacurvature.LOGGER#
- class topostats.tracing.dnacurvature.Curvature(molecule_coordinates: numpy.ndarray, circular: bool)[source]#
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.
- molecule_coordinates#
- circular#
- n_points#
- first_derivative = None#
- second_derivative = None#
- local_curvature = None#
- calculate_derivatives(edge_order: int = 1) None[source]#
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.