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RDKit

A high-level library for performing common RDKit tasks such as SMILES parsing, molecule normalization, etc. Uses the C++ API via bindings from rdkit-sys.

Notice: Requires rdkit 2023.09.1 or higher (like Ubuntu Noble 24.04)

This fork and branch contain the following deviations and / or new features compared to the original repo:

Comparison to Original Repo

  • RDKit changes
    • Exposed SMILES writing params, to allow generation of randomised SMILES (PR, issue).
    • Ensure that Mol -> SMILES is fallible (PR, issue)
  • Other
    • Added .pre-commit-config.yaml
    • Added rust-toolchain.toml, specifying nightly channel to appease clippy issues in benches/molecule_benchmark.rs

Conda rdkit compatability, for rdkit-rs 0.4.11, rdkit 2024.03.5 is incompatible (build will fail). 2024.03-1 -> 2024.03.4 seem to work.

Prerequisites

On a Mac:

brew install rdkit

On Linux you will need a custom build of rdkit with static libraries. At the moment, we have some pre-compiled tar balls available for AMD64 and ARM64 for the latest RKDit which get the job done for our CI (Note: these have been compiled on Ubuntu 22.04, not 14.04...):

https://rdkit-rs-debian.s3.eu-central-1.amazonaws.com/rdkit_2024_03_3_ubuntu_14_04_amd64.tar.gz https://rdkit-rs-debian.s3.eu-central-1.amazonaws.com/rdkit_2024_03_3_ubuntu_14_04_arm64.tar.gz

Release Both rdkit and rdkit-sys

The rdkit-sys crate is a member of the rdkit workspace. All crates in the workspace should move in lockstep versions for simplicity's sake, making it easy to tell which crates are compatible.

Managing multiple crates in a single repository:

rdkit % cargo workspaces version patch
rdkit % cargo publish
rdkit % cd rdkit-sys
rdkit-sys % cargo publish

Formatting

C++ formatting

Clang formatting should be automatically applied when saving files in VSCode if you have the clangd extension installed. If you don't have it installed, you can install it from the marketplace. Else by right-clicking on the file and selecting Format Document should do the work.

Rust formatting

Rust formatting should be automatically applied when saving files in VSCode if you have the rust-analyzer extension installed. Else by running cargo fmt in the root directory the entire project will be formatted.