oussama / rdkit-sys

Rust crate for linking against the RDKit C++ API

RDKit-Sys

Rust code that binds to the C++ rdkit library!

How does it work?

RDKit is a C++ mega-library, full of cheminformatics wisdom. We don't want to rewrite RDKit in Rust, we should instead meet somewhere in the middle and "bridge" Rust to C++ through some wrappers.

The goal is to do 1-1 bindings with the C++ library, exposing all the classes as we need them. The goal is not to create a high-level functionality like the MinimalLib (cffiwrapper). Our goal is to expose the building blocks. If you're looking for idiomatic Rust, check out the rdkit crate.

Static Linking

The build.rs script informs cargo how to find headers, library files, and finally how to link the final result. This crate currently links all RDKit libraries statically, meaning output binaries are portable and users of your software will not need to find their own RDKit.

Prerequisites

On Mac:

brew install rdkit

boost is a RDKit C++ dependency, cmake is how you create RDKit's Makefile, llvm is used by bind-gen to create the rust bindings.rs file with all the dylib definitions required to use RDKit from rust.

Testing

Or just run the test suite:

cargo test

TODO

• figure out how to cargo publish without --no-verify (otherwise it detects changes outside of OUTDIR)
• specify path to RDKit's cffiwrapper.h and all required search paths for other dependent headers
• use conditional rebuild logic to make the library build experience more reliable (for now, if you get stuck, try cargo clean and retry with cargo build -vv)

Related Documentation

• https://www.rdkit.org/docs/cppapi/index.html
• https://cxx.rs/

Prior art

• https://github.com/apahl/rdkit_cxx
• rdkafka's excellent librdkafka build.rs
• https://iwatobipen.wordpress.com/2022/01/29/use-rdkit-from-rust-rdkit-rdkitcffi-rust/
• an attempt at using rdkit in rust but without docs on how to build rdkit