visible-residues 0.3.0

Find residues with sidechains in a specific region

Visible Residues

This is an extension module implementing one performance-critical function used to create a machine learning dataset of 3D images of macromolecules with labeled amino acid identities. Specifically, the function accepts a dataframe of atoms in the image, then samples a fixed number of residues whose sidechains are likely to be mostly within the image. To avoid biasing the samples based on the specific sidechains involved (e.g. glycine has a smaller sidechain than arginine, so it might be sampled more often if the actual sidechain was considered), this "within the image" determination is based entirely on backbone coordinates.