forgi

Forgi is a Python library for analyzing RNA tertiary structures, focusing on the elements comprising RNA secondary structures, including stems, bulges, and loops. This library adopts a unique approach by representing RNA molecules centered on these secondary structure elements, thereby facilitating a detailed examination of their tertiary structure. By fitting a cylinder to the helix axis, forgi can translate these secondary structure elements into a coarse-grained 3D structure representation, providing a simplified yet insightful view of the RNA's overall form.

Integration with Biopython enhances forgi's capabilities, enabling it to manage all-atom 3D information effectively. This feature allows for a seamless transition between detailed atomic models and the coarse-grained representations that forgi specializes in. The library supports many file formats, making it highly versatile in its applications. It can process dotbracket strings, PDB (Protein Data Bank), and MMCIF files. This flexibility is extended to accommodate various RNA structural complexities, such as modified residues, missing residues, and complex configurations like cofold and multifold structures. Moreover, forgi is adept at handling nucleotide sequences that begin at arbitrary numerical positions, ensuring that it can be applied to a broad spectrum of RNA molecules.