Rust API¶

The Rust API documentation is generated by rustdoc.

Crate	Documentation
`omgkit-core`	docs.rs/omgkit-core
`omgkit-io`	docs.rs/omgkit-io
`omgkit-chem`	docs.rs/omgkit-chem
`omgkit-match`	docs.rs/omgkit-match
`omgkit-conf`	docs.rs/omgkit-conf
`omgkit-depict`	docs.rs/omgkit-depict

Or build it from a clone, which also documents the Python binding crate:

git clone https://github.com/zbc0315/omgkit
cd omgkit
cargo doc --workspace --no-deps --open

The crates¶

Crate	Depends on	Contains
`omgkit-core`	—	`MolBuilder`, `MolBatch`, `MolView`, `MolBatchBuilder`, the scalar types (`BondOrder`, chirality, stereo, atom and bond flags)
`omgkit-io`	core	`smiles` — parsing and writing; `smarts` — query and reaction parsing and writing; `molblock` — V2000 and SDF, read and written; `canon` — canonical ranks; `stereo` — reading stereochemistry off coordinates
`omgkit-chem`	core	`sanitize` and the individual stages: valence, implicit hydrogens, rings, kekulization, aromaticity, conjugation, hybridization. Also two consumers of that output rather than stages of it: `gasteiger` — partial charges (PEOE); `descriptors` — the per-atom and per-bond values a graph model reads
`omgkit-match`	core, io, chem	substructure matching (VF2++-style ordering), `MolProps`, reaction application (`run_reactants`, `run_on_substrate`), byproduct reconstruction
`omgkit-conf`	core, io, chem	deterministic 3D structure generation: bounds matrix, triangle smoothing, metric-matrix embedding, L-BFGS refinement — see 3D structures
`omgkit-depict`	core, io, chem, conf	2D coordinate generation and structure drawing, plus 3D figures; SVG with no dependencies, PNG/JPEG behind the `raster` feature — see Drawing structures
`omgkit-py`	all	the Python extension module — a `cdylib`, not published to crates.io; its distribution channel is the wheel

Documentation gates¶

Two lints are set to deny across the workspace, so the API documentation cannot drift:

[workspace.lints.rust]
missing_docs = "warn"

[workspace.lints.rustdoc]
broken_intra_doc_links = "deny"
private_intra_doc_links = "deny"
redundant_explicit_links = "deny"

Every public item is documented — cargo doc reports zero missing_docs warnings. Broken links are a build failure, not a warning: without a gate they accumulate silently (one sweep found 16, all historical).

Equivalents of the Python calls¶

Python	Rust
`omgkit.parse_smiles`	`omgkit_io::smiles::parse`
`omgkit.parse_smarts`	`omgkit_io::smarts::parse`
`omgkit.parse_reaction`	`omgkit_io::smarts::parse_reaction`
`Mol.sanitize`	`omgkit_chem::sanitize`
`Mol.to_canonical_smiles`	`omgkit_io::canon::canonical_smiles`
`Query.match`	`omgkit_match` matching entry points
`Reaction.run`	`omgkit_match::run_reactants`
`Reaction.run_on_substrate`	`omgkit_match::run_on_substrate`
`Mol.atom_descriptors`	`omgkit_chem::atom_descriptors`
`Mol.bond_descriptors`	`omgkit_chem::bond_descriptors`

Names are indicative; see the generated documentation for exact signatures.

One difference worth knowing: Mol.sanitize() on the Python side runs two Rust calls — omgkit_chem::sanitize and then omgkit_io::stereo::perceive_bond_stereo, which turns the / and \ of the input into the double bond's own cis/trans property. Rust callers have to make that second call themselves. Skipping it does not raise; it leaves every double bond's geometry unset, so bond_descriptors reports BondStereo::None throughout and writing the molecule back out loses the geometry. The reason the two are separate is that stereo perception needs symmetry classes, which live in omgkit-io, a sibling of omgkit-chem rather than a dependency.