librna-sys 0.1.6

Low-level bindings for the ViennaRNA library.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89

# librna-sys

This crate provides low-level `Rust` bindings to [`libRNA/RNAlib/ViennaRNA`](https://www.tbi.univie.ac.at/RNA/).

## 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 should work as well.

## Prerequisites

- Install [`Rust`](https://rustup.rs/).
- Install [`ViennaRNA`](https://www.tbi.univie.ac.at/RNA/#download).

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:

```sh
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`:

```toml
[dependencies]
librna-sys = "0.1"
```

### Using `pkg-config`

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

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

may be used instead of setting environment variables.

## Usage

Please refer to the [original documentation](https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html) 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: As of version `2.5.0`, `ViennaRNA` contains support for the base pair distance with pseudoknots.*](https://github.com/ViennaRNA/ViennaRNA/pull/129)

This example is intended to illustrate how `librna-sys` could be used to build upon `ViennaRNA`.

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

```sh
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:

```python
from libbpdist import bp_distance_pk

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

I'm open to any ideas or advice.
At this point, it's not yet clear where this is going but here are a few thoughts:

- Providing complete *safe* bindings to `ViennaRNA` is probably as complex as a complete rewrite in `Rust`.
- Perhaps a separate crate could serve as a central collection of *safe* APIs extending `ViennaRNA`.

## Known Issues

If you encounter an error including `generated with LTO version X.0 instead of the expected Y.0`,
you could either recompile `ViennaRNA` yourself or [downgrade your `Rust` toolchain](https://doc.rust-lang.org/rustc/linker-plugin-lto.html#toolchain-compatibility).
Adjusting some [linker-related codegen options](https://doc.rust-lang.org/rustc/codegen-options/index.html#linker) might also help but was not thoroughly tested.