rna-ss-params is both an executable binary that can be run, and a library that can be used in Rust programs.

Installing `generate_contrafold_scores` `generate_turner_scores` executables

Assuming you have Rust/Cargo installed, run this command in a terminal:

cargo install rna-ss-params

It will make generate_contrafold_scores generate_turner_scores commands available in your PATH if you've allowed the PATH to be modified when installing Rust. cargo uninstall rna-ss-params uninstalls.

Adding `rna_ss_params` library as a dependency

Run this command in a terminal, in your project's directory:

cargo add rna-ss-params

To add it manually, edit your project's Cargo.toml file and add to the [dependencies] section:

rna-ss-params = "0.1.24"

The rna_ss_params library will be automatically available globally. Read the rna_ss_params library documentation.

Back to the crate overview.

Readme

Library of RNA Secondary Structure Parameters

This library provides tuned computational parameters for RNA secondary structures. Available current parameters are from the Turner 2004 model or the CONTRAfold v2.02 model. The Turner 2004 model provides experimentally estimated structure parameters. (They are based on nearest-neighbor thermodynamics.) In contrast, the CONTRAfold v2.02 model provides secondary structure parameters computationally optimized by maximizing the log-likelihood of training secondary structures. My implementation of the CONTRAfold v2.02 model is just the copy of the CONTRAfold source code, pre-trained by CONTRAfold developers a decade ago. The comparison between the Turner 2004 model and the CONTRAfold v2.02 model is as below:

Model	Turner	CONTRAfold
Model simpleness	Complex	Simple
Parameter optimization	Wet & dry	Dry only
Are RNA loop structures captured?	Yes	Yes
Are noncanonical base-pairings allowed?	No	Yes (but they are disabled in this repository)

Author

Heartsh

Installing generate_contrafold_scores generate_turner_scores executables

Adding rna_ss_params library as a dependency

Installing `generate_contrafold_scores` `generate_turner_scores` executables

Adding `rna_ss_params` library as a dependency