rnaglib.transforms.SmallMoleculeBindingTransform

class rnaglib.transforms.SmallMoleculeBindingTransform(structures_dir, cutoffs=[4.0, 6.0, 8.0], mass_lower_limit=160, mass_upper_limit=1000, verbose=False, additional_atoms=None, disallowed_atoms=None)[source]

Annotate RNAs with small molecule binding information.

Parameters:

  • structures_dir (Union[PathLike, str]) – path to directory containing the mmCIFs to annotate

  • cutoff – distance threshold (Angstroms) to use for including small molecule ligands (default= 6).

__init__(structures_dir, cutoffs=[4.0, 6.0, 8.0], mass_lower_limit=160, mass_upper_limit=1000, verbose=False, additional_atoms=None, disallowed_atoms=None)[source]

Methods

__init__(structures_dir[, cutoffs, ...])

forward(rna_dict)

Adds information at the graph level and on the small molecules partner of an RNA molecule