spyrmsd.utils module
- spyrmsd.utils.center(coordinates: ndarray) ndarray[source]
Center coordinates.
- Parameters
coordinates (np.ndarray) – Coordinates
- Returns
Centred coordinates
- Return type
np.ndarray
- spyrmsd.utils.center_of_geometry(coordinates: ndarray) ndarray[source]
Center of geometry.
- Parameters
coordinates (np.ndarray) – Coordinates
- Returns
Center of geometry
- Return type
np.ndarray
- spyrmsd.utils.deg_to_rad(angle: float) float[source]
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[source]
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.molformat(fname: str) str[source]
Extract an OpenBabel-friendly format from file name.
- Parameters
fname (str) – File name
- Returns
File extension in an OpenBabel-friendly format
- Return type
str
Notes
File types in OpenBabel do not always correspond to the file extension. This function converts the file extension to an OpenBabel file type.
The following table shows the different conversions performed by this function:
Extension
File Type
xyz
XYZ
- spyrmsd.utils.rotate(v: ndarray, angle: float, axis: ndarray, units: str = 'rad') ndarray[source]
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