nanover.utilities.transforms module

class nanover.utilities.transforms.StructureAlignment(*, atoms: list[int], positions: NDArray)

Bases: object

calculate_transform_to_framedata(framedata: FrameData)

calculate_transform_to_positions(positions: NDArray)

calculate_transform_to_universe(universe: Universe)

classmethod from_atom_group(atom_group: AtomGroup)

classmethod from_atoms_and_framedata(atoms: list[int], framedata: FrameData)

class nanover.utilities.transforms.Transform(*, local_to_parent: NDArray, parent_to_local: NDArray)

Bases: object

Convenience wrapper around transformation matrix.

classmethod from_local_to_parent_matrix(local_to_parent: NDArray)

classmethod from_parent_to_local_matrix(parent_to_local: NDArray)

classmethod from_state_cursor(cursor)

classmethod from_state_transform(transform: Iterable[float])

classmethod from_translation(translation: Iterable[float])

classmethod identity()

inverted()

property local_to_parent_matrix

property parent_to_local_matrix

point_local_to_parent(point)

point_parent_to_local(point)

points_local_to_parent(points)

points_parent_to_local(points)

to_state_transform() → Sequence[float]

nanover.utilities.transforms.find_transformation_between_point_patterns(start_points: NDArray, final_points: NDArray): Return the 4x4 transformation matrix that best maps the start points to the final points.

nanover.utilities.transforms.matrix_from_state_transform(transform: Iterable[float])

nanover.utilities.transforms.state_transform_from_matrix(matrix: NDArray) → Sequence[float]

nanover.utilities.transforms.unpack_partial_state_transform(transform: Iterable[float]): Pad partial state transform iterable up to full length with components of identity state transform.