RDKit-Rust Workspace

Welcome to the work-in-progress Rust rewrite of RDKit. The goal is to provide a fully native, idiomatic Rust implementation of RDKit’s core cheminformatics functionality – no C++ bindings involved.

⚠ Status: early prototyping phase (Stage 5 of the master plan). Only a subset of datastructures and UFF bond/angle energy terms are implemented so far.

Crate layout

crates/
  rdkit-core/        # common error types, invariant! macro, utilities
  datastructs/       # bit-vector containers, base64 helpers
  forcefield-uff/    # auto-generated UFF parameter table (build.rs)
  forcefield-core/   # generic force-field utilities – bond/angle energy so far
  geometry/          # (WIP) 3-D point / vector primitives
  … more crates will appear as the port grows …

Every crate is versioned together in this single workspace so a single cargo test --workspace builds everything.

Building & testing

# build all crates and run unit tests
cargo test --workspace

# run clippy on every target, denying warnings
cargo clippy --workspace --all-targets -- -D warnings

The first build downloads the nalgebra, bitvec, etc. dependencies; subsequent builds will be incremental.

Quick-start – computing a single UFF angle energy

use forcefield_core::angle_bend_energy;

fn main() {
    // Water H–O–H valence angle (~104.5°)
    let theta = 104.51_f64.to_radians();
    let e = angle_bend_energy("H_", "O_3", "H_", theta, 1.0, 1.0)
        .expect("energy");
    println!("Angle energy: {:.4} kcal/mol", e);
}

Compile and run with:

cargo run -q --example angle_energy

Code generation

crates/forcefield-uff/build.rs parses rdkit/Code/ForceField/UFF/Params.cpp at build time and emits a phf::Map containing one struct per atom label. This ensures parameter lookup is O(1) while keeping the table source-of-truth in sync with the original RDKit source.

Contributing

We follow the standard Rust style (rustfmt, clippy) and require that the workspace compiles and tests pass before every commit.