write_npz

macromol_voxelize.write_npz(path: str | Path, img: Image, grid: Grid, frame_xi: ndarray[Any, dtype[ScalarType]] | None = None)[source]

Write the given image to an *.npz file.

Parameters:

path – The path to write the image to. By convention, this path should have the .npz suffix.
img – The image to write. See image_from_atoms().
grid – The dimensions of the image. See ImageParams.
frame_xi –
A coordinate frame transformation that should be applied to the image when it’s being rendered in PyMOL. If no transformation is specified, the image will be centered at (0, 0, 0) and aligned with the x-, y-, and z-axes. The purpose of specifying a transformation is usually to align the image to the structure that it’s based on.

The frame should be given as a 4x4 matrix (i.e. a homogeneous transformation matrix). The matrix should transform from a coordinate frame “x” where the image is centered at the origin and aligned with all three axes, to the desired coordinate frame “i”, which is typically that of the input structure. The suffix “_xi” is meant to be a reminder of this.

The resulting file can be visualized using PyMOL. The physical dimensions of the image and its alignment are included in the file, so the image can be properly superimposed on a molecular structure.