rmsd_calc

pyrosetta.numeric.alignment.rmsd_calc.superimpose_coordinate_array(src, onto, superimpose=None, rmsd_out=None, return_rmsd=False)

Calculate and apply superposition transform between src and onto coordinates.

src - array(shape=([a], n, 3), dtype=float) onto- array(shape=([a], n, 3), dtype=float) superimpose - array(shape=([a], m, 3), dtype=float) rmsd_out - array(shape=(a), dtype=float) return_rmsd - bool

src and onto must contain dimension n, the number of entries per coordinate set.

superimpose may contain a different number of coordinates per entry, and will be updated in-place with coordinates updated by src->onto transform.

returns:

superimposed_coordinates - array(shape=(a, m, 3), dtype=float) OR (superimposed_coordinates, pairwise_rmsd) if return_rmsd

pyrosetta.numeric.alignment.rmsd_calc.superimpose_structured_array(src, onto, superimpose=None)

Calculate and apply superposition transform between src and onto coordinates.

src - array(shape=([a], n), dtype=[(name, float, 3)…]) onto - array(shape=([a|1], n), dtype=[(name, float, 3)…]) superimpose - array(shape=([a], n_2), dtype=[(name, float, 3)…])

src and onto must contain dimension n and be of the same structured dtype.

returns superimposed - array(shape=([a], n_2), dtype=[(name, float, 3)…])

pyrosetta.numeric.alignment.rmsd_calc.coordinate_array_rmsd(coordinates_a, coordinates_b, out=None)

Calculate rmsd between entries in the given coordinate arrays.

coordinates_a - array(shape=([a], n, 3), dtype=float) coordinates_b - array(shape=([a], n, 3), dtype=float) out - array(shape=(a), dtype=float)

coordinates_a and coordinates_b must contain dimension n, the number of entries per coordinate set.

returns pairwise_rmsd - array(shape=(n), dtype=float) or shape () array-scalar if both inputs are 2-dim

pyrosetta.numeric.alignment.rmsd_calc.coordinate_array_broadcast_rmsd(coordinates_a, coordinates_b, out=None)

Calculate rmsd between entries in the given coordinate arrays.

coordinates_a - array(shape=([a], n, 3), dtype=float) coordinates_b - array(shape=([b], n, 3), dtype=float) out - array(shape=(a, b), dtype=float)

coordinates_a and coordinates_b must contain dimension n, the number of entries per coordinate set.

returns broadcast_rmsd - array(shape=(a,b), dtype=float)

Flattened to 1 dimension if a or b is dimension 2.

pyrosetta.numeric.alignment.rmsd_calc.structured_array_broadcast_rmsd(coordinates_a, coordinates_b)

Calculate rmsd between entries in the given structured coordinate arrays.

coordinates_a - array(shape=([a], n), dtype=[(name, float, 3)…]) coordinates_b - array(shape=([b], n), dtype=[(name, float, 3)…]) out - array(shape=(a, b), dtype=float)

coordinates_a and coordinates_b must contain dimension n and be of the same structured dtype.

returns broadcast_rmsd - array(shape=(a,b), dtype=float)

Flattened to 1 dimension if a or b is dimension 2.

pyrosetta.numeric.alignment.rmsd_calc.structured_array_unaligned_broadcast_rmsd(coordinates_a, coordinates_b)

Calculate rmsd between entries in the given structured coordinate arrays.

coordinates_a - array(shape=([a], n), dtype=[(name, float, 3)…]) coordinates_b - array(shape=([b], n), dtype=[(name, float, 3)…]) out - array(shape=(a, b), dtype=float)

coordinates_a and coordinates_b must contain dimension n and be of the same structured dtype.

returns broadcast_rmsd - array(shape=(a,b), dtype=float)

Flattened to 1 dimension if a or b is dimension 2.

pyrosetta.numeric.alignment.rmsd_calc.coordinate_array_unaligned_broadcast_rmsd(coordinates_a, coordinates_b, out=None)

Calculate rmsd between entries in the given coordinate arrays without performing superposition.

coordinates_a - array(shape=([a], n, 3), dtype=float) coordinates_b - array(shape=([b], n, 3), dtype=float) out - array(shape=(a, b), dtype=float)

coordinates_a and coordinates_b must contain dimension n, the number of entries per coordinate set.

returns broadcast_rmsd - array(shape=(a,b), dtype=float)

Flattened to 1 dimension if a or b is dimension 2.