pyrosetta.numeric.alignment.rmsd_calc Namespace Reference

Functions
def	superimpose_coordinate_array
def	superimpose_structured_array
def	coordinate_array_rmsd
def	coordinate_array_broadcast_rmsd
def	structured_array_broadcast_rmsd
def	structured_array_unaligned_broadcast_rmsd
def	coordinate_array_unaligned_broadcast_rmsd

Function Documentation

def 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.

Referenced by pyrosetta.numeric.alignment.rmsd_calc.structured_array_broadcast_rmsd().

def 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

References max().

def 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.

Referenced by pyrosetta.numeric.alignment.rmsd_calc.structured_array_unaligned_broadcast_rmsd().

def 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.

References pyrosetta.numeric.alignment.rmsd_calc.coordinate_array_broadcast_rmsd(), and pyrosetta.utility.array.structured_array_to_basic().

def 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.

References pyrosetta.numeric.alignment.rmsd_calc.coordinate_array_unaligned_broadcast_rmsd(), and pyrosetta.utility.array.structured_array_to_basic().

def 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

Referenced by pyrosetta.numeric.alignment.rmsd_calc.superimpose_structured_array().

def 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)...])

References pyrosetta.utility.array.basic_array_to_structured(), ObjexxFCL.len(), pyrosetta.utility.array.structured_array_to_basic(), and pyrosetta.numeric.alignment.rmsd_calc.superimpose_coordinate_array().