`rnaglib.utils`¶

General utilities for handling RNA structures and graphs.

Input/Output¶

Functions and writing and loading to/from disk.

`load_graph`(filename)	This is a utility function that supports loading from json or pickle.
`download_graphs`([redundancy, version, ...])	Based on the options, get the right data from the latest release and put it in download_dir.
`dump_json`(filename, graph)	Just a shortcut to dump a json graph more compactly.
`load_json`(filename)	Just a shortcut to load a json graph more compactly.
`graph_from_pdbid`(pdbid[, graph_dir, ...])	Fetch an annotated graph with a PDBID.

Wrappers for third-party executables.

Warning

Make sure the necessary executables are in your os PATH.

`cdhit_wrapper`(ids, sequences[, sim_thresh, ...])	Cluster sequences using CD-hit.
`rna_align_wrapper`(cif_path_1, cif_path_2[, ...])	Calls RNAalign on two mmCIF files and returns the output.
`locarna_wrapper`(seq_1, seq_2)	Calls LocaRNA on two RNA sequences to perform sequence-2d-structure aligment

cif_remove_residues(cif_path, keep_residues, ...)

Remove all residues from a cif file except for those in keep_residues list.