topo_metrics.ring_geometry#
Classes#
Module Contents#
- class topo_metrics.ring_geometry.RingGeometry[source]#
- nodes: tuple[topo_metrics.topology.Node, Ellipsis][source]#
The nodes in the ring.
- property positions: numpy.typing.NDArray[numpy.floating][source]#
Cartesian positions of the nodes in the ring.
- property gyration_tensor: numpy.typing.NDArray[numpy.floating][source]#
Gyration tensor of the ring.
The gyration tensor describes the second moments of position of a set of points around their center of mass. It is a symmetric 3x3 matrix.
- property principal_moments: numpy.typing.NDArray[numpy.floating][source]#
Principal moments of the gyration tensor.
The principal moments are the eigenvalues of the gyration tensor, which describe the distribution of points along the principal axes.
- property geometric_centroid: numpy.typing.NDArray[numpy.floating][source]#
Geometric centroid of the ring.
- writhe_and_acn(method: str = '1a', closed=True) tuple[float, float] | float[source]#
Writhe of the ring using specified method from
- Parameters:
method – Method to compute writhe. Options are ‘1a’, ‘1b’, ‘2a’, ‘2b’. Default is ‘1a’. Each method corresponds to those introduced in
- Return type:
Writhe of the ring.
- linking_number(other: RingGeometry, *, cell: numpy.typing.ArrayLike, pbc: tuple[bool, bool, bool] = (True, True, True), n_images: int = 1, method: str = '1a', eps: float = 1e-12, check_top_k: int | None = None, disjoint_tol: float | None = 0.05, disjoint_rel: float = 0.001) tuple[float, tuple[int, int, int]][source]#
Linking number between this ring and another ring.
- is_linked_to(other: RingGeometry, *, cell: numpy.typing.ArrayLike, pbc: tuple[bool, bool, bool] = (True, True, True), n_images: int = 1, method: str = '1a', eps: float = 1e-12, tol: float = 1e-06, check_top_k: int | None = None, disjoint_tol: float | None = None, disjoint_rel: float = 0.001) bool[source]#
Determine if this ring is linked to another ring.