Structure.align_structures#

classmethod Structure.align_structures(structure1, structure2, origin=None, sampling_rate=None, weighted=False)[source]#

Align structure2 to structure1 using the Kabsch Algorithm. Both structures need to have the same number of atoms.

Parameters:

structure1, structure2Structure: Structure instances to align.
origintuple of floats, optional: Coordinate system origin. For computing RMSD on discretized grids.
sampling_ratetuple of floats, optional: Sampling rate in units of atom_coordinate. For computing RMSD on discretized grids.
weightedbool, optional: Whether atoms should be weighted by their atomic weight.

Returns:

Structure: structure2 aligned to structure1.
float: Alignment RMSD

Examples

>>> from importlib_resources import files
>>> from tme import Structure
>>> from tme.matching_utils import get_rotation_matrices
>>> fname = str(files("tests.data").joinpath("Structures/5khe.cif"))
>>> structure = Structure.from_file(filename=fname)
>>> transformed = structure.rigid_transform(
>>>     rotation_matrix = get_rotation_matrices(60)[2],
>>>     translation = (0, 1, -5)
>>> )
>>> aligned, rmsd = Structure.align_structures(structure, transformed)
Initial RMSD: 31.07189 - Final RMSD: 0.00000