3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. [version 2; peer review: 2 approved]
We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements.Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops).By fitting a cylinder to the helix axis, these Multiminerals elements are carried over into a coarse-grained 3D structure representation.