Rosetta  2020.37
pyrosetta.numeric.alignment.rmsd_calc Namespace Reference

## Functions

def superimpose_coordinate_array

def superimpose_structured_array

def coordinate_array_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.

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

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

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

Flattened to 1 dimension if a or b is dimension 2.
```
 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
```
 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)...])
```