rdkitcffi

This is an 🚧 experimental 🚧 rust wrapper for some functionality of the great RDKit cheminformatics library.

It makes use of its CFFI interface, see also this blog post.

Only a limited functionality is being exposed via cffi by RDKit and not all of this is available yet via this interface. Have a look at the examples below and the test functions.

The rust wrapper is linked against a pre-built RDKit shared library (MinimalLib), which is stored as an artifact created via github actions and is automatically downloaded from this location during build. Currently, only linux is supported.

Please note, that there is also a cargo crate providing low level wrapper to rdkit.

Examples

Basic usage:

use rdkitcffi::Molecule;

let smiles = "OCCC#CO";
let mol = Molecule::new(smiles).unwrap();

let natoms = mol.get_numatoms();

Additional arguments can be passed via json

use rdkitcffi::Molecule;

let json_args = "{\"removeHs\":false,\"canonical\":false}";
let mol = Molecule::new_with_args("c1cc(O[H])ccc1", json_args).unwrap();

Working with SD files and filtering invalid molecules:

use rdkitcffi::{Molecule,read_sdfile};

let mut mol_opt_list : Vec<Option<Molecule>>= read_sdfile("data/test.sdf");
let mut mol_list: Vec<Molecule> = mol_opt_list.into_iter().filter_map(|m| m).collect();
mol_list.iter_mut().for_each(|m| m.remove_all_hs());

Dealing with invalid molecules

use rdkitcffi::Molecule;

let result = Molecule::new("OCCO");
match result {
   Some(m) => println!("Molecule: {:?}", m),
   None => println!("Could not get molecule!"),
};

Getting a JSON represenation (via serde_json):

use rdkitcffi::Molecule;

let mol = Molecule::new("OCCO").unwrap();
println!("json: {:?}", mol.get_json(""));

Neutralizing a zwitterion

use rdkitcffi::Molecule;

let mut mol = Molecule::new("C(C(=O)[O-])[NH3+]").unwrap();
mol.neutralize("");
println!("{:?}", mol.get_smiles(""));

Computing RDKit descriptors

use rdkitcffi::Molecule;

let mol = Molecule::new("CCCN").unwrap();
let desc = mol.get_descriptors_as_dict();
let nrot = desc.get("NumRotatableBonds");
let logp = desc.get("CrippenClogP");

Generating 3D coordinates

use rdkitcffi::Molecule;

let mut mol = Molecule::new("CO").unwrap();
mol.add_hs();
mol.set_3d_coords("");
let coords: Vec<Vec<f32>> = mol.get_coords();

Creating a polars dataframe:

use rdkitcffi::Molecule;
use polars::prelude::*;
use polars::df;

let mut mol_list : Vec<Molecule> = rdkitcffi::read_smifile_unwrap("data/test.smi");
let a: Vec<_> = mol_list.iter().map(|m| m.get_smiles("")).collect();
let df = df!( "smiles" => a).unwrap();

Installation

Currently only linux is supported.

Download the repo:

git clone https://github.com/chrissly31415/rdkitcffi.git  

If you have a rust/cargo installation, just run

cd rdkitcffi
cargo build  
cargo test --lib  

After installation you may want to update your LD_LIBRARY_PATH in order to run binaries without cargo, e.g.:

export LD_LIBRARY_PATH=/home/username/rdkitcffi/lib/rdkitcffi_linux/linux-64/:$LD_LIBRARY_PATH

Using it in your project

Modify your Cargo.toml file:

[dependencies]
rdkitcffi = {path="/pathtorepo/rdkitcffi"}