librna-sys

This crate provides low-level Rust bindings to libRNA/RNAlib/viennaRNA.

Current State

librna-sys is highly experimental and provides unsafe low-level bindings. It's possible that building or linking does not work reliably. This crate was only tested on Linux but macOS might work as well.

Prerequisites

• Install Rust.
• Install ViennaRNA.

This crate requires the static library (libRNA.a on Linux and macOS) as well as the C header files.

Configuration

Using Environment Variables

librna-sys exposes two environment variables in case ViennaRNA is installed in a custom directory. Use them like this:

export LIBRNA_INCLUDE_DIR=/path/to/headerdirectory # default: /usr/include
export LIBRNA_LIB_DIR=/path/to/librarydirectory # default: /usr/lib

Afterwards the crate can be used as a dependency in cargo.toml:

[dependencies]
librna-sys = "0.1"

Using pkg-config

If pkg-config is available on your system and ViennaRNA was installed properly

[dependencies]
librna-sys = { version = "0.1" , features = ["auto"] }

may be used instead of setting environment variables.

Usage

Please refer to the original documentation of the C API. In most cases, you probably want to use the official Python bindings.

Use this crate only if some features of the C API are not exposed as Python bindings and you prefer writing unsafe Rust over C for some reason.

Example: Extending ViennaRNA

Note: This will probably at some point land in ViennaRNA.

examples/bpdist.rs extends the base pair distance of ViennaRNA to secondary structures with pseudoknots. Building this example by running

cargo build --release --example bpdist #--features auto

produces a dynamic library target/release/examples/libbpdist.so exposing Python bindings. Copy it whereever you want and import it like this:

from libbpdist import bp_distance_pk

structures = [".((..[[[..))..]]].", ".((.[.[[..))..]]]."]
print(bp_distance_pk(structures[0], structures[1]))