spyrmsd.utils module

spyrmsd.utils.center(coordinates: ndarray) → ndarray

Center coordinates.

Parameters:

coordinates (np.ndarray) – Coordinates

Returns:

Centred coordinates

Return type:

np.ndarray

spyrmsd.utils.center_of_geometry(coordinates: ndarray) → ndarray

Center of geometry.

Parameters:

coordinates (np.ndarray) – Coordinates

Returns:

Center of geometry

Return type:

np.ndarray

spyrmsd.utils.deg_to_rad(angle: float) → float

Convert angle in degrees to angle in radians.

Parameters:

angle (float) – Angle (in degrees)

Returns:

Angle (in radians)

Return type:

float

spyrmsd.utils.format(fname: str) → str

Extract format extension from file name.

Parameters:

fname (str) – File name

Returns:

File extension

Return type:

str

Notes

The file extension is returned without the . character, i.e. for the file path/filename.ext the string ext is returned.

If a file is compressed, the .gz extension is ignored.

spyrmsd.utils.rotate(v: ndarray, angle: float, axis: ndarray, units: str = 'rad') → ndarray

Rotate vector.

Parameters:

• v (numpy.array) – 3D vector to be rotated

• angle (float) – Angle of rotation (in units)

• axis (numpy.array) – 3D axis of rotation

• units ({“rad”, “deg”}) – Units of angle (in radians rad or degrees deg)

Returns:

Rotated vector

Return type:

numpy.array

Raises:

• AssertionError – If the axis of rotation is not a 3D vector

• ValueError – If units is not rad or deg