rdkit-rs

RDKit interface in safe Rust

Usage

Obtaining RDKit

I have not been able to get this to work with an RDKit installed with conda, so you must currently build RDKit yourself. To build from source, run this somewhere on your computer:

git clone --depth 1 https://github.com/rdkit/rdkit
cd rdkit
mkdir build
cd build
cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
make # optionally with -j and however many CPUs you want to give it

rdkit-sys, and thus rdkit-rs, includes InChi key support, so you must compile RDKit with InChi support enabled.

Running dependent crates

The rdkit-sys build script should take care of building the shared library and including the absolute path in the binary itself via rpath linker arguments. However, it does require the environment variable RDROOT to be set to locate the RDKit libraries and header files from the steps above. Probably the easiest way to do this is to add a Cargo config file in .cargo/config.toml in your project:

[env]
RDROOT = "/path/to/your/rdkit"

But you can also prefix your Cargo commands with RDROOT=/path/to/rdkit or however else you like to set environment variables.

Complete Example

Initialize a new Rust project and enter the directory:

cargo new rdkit-test
cd rdkit-test

Add rdkit-rs as a dependency:

cargo add --git=https://github.com/ntBre/rdkit-rs

Place the path to your cloned RDKit code in .cargo/config.toml:

[env]
RDROOT = "/home/brent/omsf/clone/rdkit"

Here I have used my actual path, but be sure to replace it with your own.

Update src/main.rs:

cat > src/main.rs <<INP
use rdkit_rs::ROMol;

fn main() {
    let mol = ROMol::from_smiles("CCO");
    let inchi = mol.to_inchi_key();
    println!("Hello inchi: {inchi}!")
}
INP

Run with cargo:

cargo run

Using Docker

Docker Hub

I've uploaded a Arch Linux-based image with RDKit and Rust to Docker Hub, which you can pull with the command:

docker pull ntbre/rdkit-rs

Then you can run the image

docker run -it rdkit-rs bash

And follow the rest of the steps in the example above. The Dockerfile copies RDKit to /opt/rdkit, so you can use RDROOT=/opt/rdkit in your .cargo/config.toml or at the command line.

Dockerfile

Alternatively, you can use the included Dockerfile to build this image on your machine:

docker build -t rdkit-rs - < Dockerfile

and then run with the same steps above.