rnaglib.transforms.BindingSiteAnnotator

class rnaglib.transforms.BindingSiteAnnotator(include_ions=False, cutoff=6.0)[source]

Annotation transform adding to each node of the dataset a binary node feature indicating whether it is part of a binding site

Parameters:

  • include_ions (bool) – if set to False, only small-molecule-binding RNA residues are considered part of a binding site. If set to True, ion-binding RNA residues are also considered part of a binding site

  • cutoff (float) – the maximal distance (in Angstroms) between an RNA residue and any small molecule or ion atom such that the RNA residue is considered part of a binding site (either 4.0, 6.0 or 8.0, default 6.0)

__init__(include_ions=False, cutoff=6.0)[source]

Methods

__init__([include_ions, cutoff])

forward(rna_dict)

Application of the transform to an RNA dictionary object