Installation

Python

pip install omgkit

Wheels are published for macOS on Apple silicon. On other platforms pip falls back to the source distribution, which needs a Rust toolchain (1.75 or newer) to build — it is a normal pip install either way, just slower the first time.

To build from a clone instead, you need Rust and maturin:

git clone https://github.com/zbc0315/omgkit
cd omgkit

pip install maturin
maturin build --release -m crates/omgkit-py/Cargo.toml --out dist
pip install dist/omgkit-*.whl

Check it:

>>> import omgkit
>>> omgkit.parse_smiles("CCO").num_atoms
3

One wheel covers every supported Python. The extension is built against the stable ABI (abi3, Python 3.9+), so a wheel built on 3.9 runs on 3.13 as well. There are no system dependencies — nothing to apt install, no shared library to find at runtime.

Rust

Add the layers you need. Each depends only on the ones below it, so taking omgkit-io alone gets you SMILES parsing without pulling in the reaction engine.

[dependencies]
omgkit-core   = "0.0.7"   # data structures
omgkit-io     = "0.0.7"   # SMILES, SMARTS, .mol/.sdf
omgkit-chem   = "0.0.7"   # sanitization
omgkit-match  = "0.0.7"   # matching, reactions, byproducts
omgkit-conf   = "0.0.7"   # 3D structure generation
omgkit-depict = "0.0.7"   # 2D coordinates, 2D and 3D drawing

Or with cargo add:

cargo add omgkit-core omgkit-io omgkit-chem omgkit-match omgkit-conf omgkit-depict

Crate	Depends on	Gives you
omgkit-core	—	MolBuilder, MolBatch, MolView, the scalar types
omgkit-io	core	SMILES and SMARTS parsing and writing
omgkit-chem	core	the sanitization pipeline, valence, aromaticity
omgkit-match	core, io, chem	substructure matching, reaction templates, byproducts
omgkit-conf	core, io, chem	3D structure generation
omgkit-depict	core, io, chem, conf	2D coordinates, wedge assignment, 3D figures, SVG (PNG/JPEG behind raster)
omgkit-py	all of the above	the Python extension module (not a library)

Requirements

Rust	1.75 or newer (rust-version in the manifest)
Python	3.9 or newer
Platform	anything Rust and PyO3 support; no system libraries

Building from a clone

The gates below are what CI runs. They pass on a fresh clone — the smoke oracles for the differential tests are committed, so nothing has to be generated first.

cargo fmt --all --check
cargo clippy --workspace --all-targets -- -D warnings
cargo test --release
cargo test --workspace
cargo doc --workspace --no-deps --document-private-items

# the external judges for omgkit-conf, on the committed smoke baseline
cargo run -p omgkit-conf --release --example smooth_oracle -- harness/baseline/smoke.bounds.jsonl
cargo run -p omgkit-conf --release --example bounds_oracle -- harness/baseline/smoke.bounds.jsonl
cargo run -p omgkit-conf --release --example eigen_oracle  -- harness/baseline/smoke.bounds.jsonl harness/baseline/smoke.gram_eigs.jsonl

The large-corpus tier of the differential tests is marked #[ignore] and needs oracles you generate yourself. See Building and testing.