xenosite.forest
Metabolic Forest: enumerate explicit metabolite structures from reaction rules, and search pathways that connect a reactant to a putative product.
The product API is the Rust chematic engine (crates/xenosite-forest) exposed as xenosite.forest (PyO3 wrapper). New features go there — not in the pure-Python RDKit package xenosite.forest.native, which is a frozen reference/validation engine. See docs/forest/NATIVE.md.
Site-of-metabolism prediction models (epoxidation, quinonation, Phase I, reactivity, and others) are on the web at xenosite.org. This package is the structure-enumeration engine, not those neural-network models.
If you use this software, please cite the Metabolic Forest paper (DOI and BibTeX below).
Install
uv add xenosite-forest
or
pip install xenosite-forest
The default install is the Rust chematic door (no RDKit) — that is the supported surface for new work. For the frozen RDKit reference engine and the frozen 0.6.x archive (parity / historical only; not extended for new features):
uv add "xenosite-forest[rdkit]"
Optional NetworkX helpers for building a metabolite graph:
uv add "xenosite-forest[network]"
Optional xenosite-predict (site-of-metabolism models; Python ≥3.11). Not installed in this repo’s CI:
uv add "xenosite-forest[predict]"
Requires Python 3.11–3.14. RDKit 2022.03+ only with the [rdkit] extra.
A WASM-clean Rust crate (chematic + canonaut) lives in crates/xenosite-forest. See docs/forest/RUST.md and docs/forest/MIGRATING_0.8.md.
Quick start
from xenosite.forest import find_path, PhaseOne, Epoxidation
hits, counters = find_path("CC", "CCO", max_paths=1)
print(hits[0]["steps"], counters["billed"])
RDKit reference engine (requires [rdkit]; feature-frozen — prefer Rust above):
from rdkit import Chem
from xenosite.forest.native import bfs, rules, PhaseOneRS
smiles, steps, mols = next(bfs(["CCO", "CC=O"], ruleset="PhaseOneRS"))
print(smiles, steps)
for products, info in rules.Hydroxylation().metabolize(Chem.MolFromSmiles("CCC")):
print(info["site"], [p.xf.csmi for p in products])
A longer walkthrough is in examples/tutorial.ipynb. API notes are in docs/usage.md. Rulesets and their papers are in docs/rulesets.md.
Command line
Requires the [rdkit] extra (temporary native bridge until a Rust CLI ships):
xenosite-forest CCO CC=O --ruleset PhaseOneRS --depth 1
Useful flags: --all-paths, --depth N, --phase1 (Phase I site strings), --max N, --ruleset NAME.
Rulesets and papers
Pass these names to bfs(..., ruleset=...) or load_ruleset(...). Full rule lists, Rainbow colors/hex codes, aliases, and BibTeX are in docs/rulesets.md.
| Ruleset | What it enumerates | Matched paper |
|---|---|---|
PhaseOneRS |
Phase I: SO, UO, DH, HD, RD | Dang et al., Metabolic Rainbow, JCIM 2020. DOI 10.1021/acs.jcim.9b00836 |
SO / UO / DH / HD / RD |
One Rainbow color each (see hex table in docs) | Same Rainbow paper; Forest rule lists differ slightly for HD/RD/DH |
QuinoneFormationRS (QF) |
Quinone, quinone-imine, and quinone-methide structures | Hughes & Swamidass, Chem. Res. Toxicol. 2017. DOI 10.1021/acs.chemrestox.6b00385 |
Bioactivation (BA) |
Quinone, epoxidation, nitroaromatic reduction, thiophene S-oxidation | Hughes et al., Chem. Res. Toxicol. 2021. DOI 10.1021/acs.chemrestox.0c00417 |
Full |
Complete Metabolic Forest generator (Phase I, conjugations, quinone, tautomerization) | Hughes et al., Metabolic Forest, JCIM 2020. DOI 10.1021/acs.jcim.0c00360 |
Rainbow colorblind-safe hex (Wong / Okabe–Ito, closest to the paper figures): SO Stable Oxygenation red #D55E00, UO Unstable Oxygenation orange #E69F00, DH Dehydrogenation green #009E73, HD Hydrolysis blue #56B4E9, RD Reduction purple #CC79A7.
Related single-rule papers: epoxidation (10.1021/acscentsci.5b00131), N-dealkylation (10.1021/acs.chemrestox.7b00191), UGT glucuronidation (10.1093/bioinformatics/btw350), glutathione reactivity (10.1021/acs.chemrestox.5b00017).
Documentation
- Rulesets and papers — every built-in ruleset, Rainbow colors, and publication BibTeX
- Usage — public API and pathway search
- Migrating to 0.7.0 —
metabolizeyield shape and other breaking changes - Migrating to 0.8.0 — rust / native / legacy layout, optional RDKit
- Native freeze — RDKit Python engine is reference-only; new features go to Rust
- Legacy freeze — frozen 0.6.x archive notes
- xenosite-predict notes — RDKit 2026 valence caches and DNA/CN conjugation vs GSH (downstream adapters)
- Path-search performance — archive BFS/DFS vs live
find_pathhead-to-head - Heuristics / divergences / dropped — design notes (
HEURISTICS,DIVERGENCES,DROPPED,PAIR_ORBITS) - Tutorial notebook — interactive walkthrough
- xenosite.org — XenoSite models for sites of metabolism and reactivity
- Source repository — code, issues, and releases
Import the package as xenosite.forest (Rust public API). xenosite.forest.native
is the RDKit reference engine (no new features — NATIVE.md).
xenosite.forest.legacy is the frozen 0.6.x archive (LEGACY.md).
xenosite is a PEP 420 namespace, so other xenosite.* packages can be
installed alongside this one.
Citation
Please cite Metabolic Forest if you use this package:
Hughes, T. B.; Dang, N. L.; Kumar, A.; Flynn, N. R.; Swamidass, S. J. Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. J. Chem. Inf. Model. 2020, 60 (10), 4702–4716. DOI: 10.1021/acs.jcim.0c00360
BibTeX (copy and paste):
@article{Hughes2020MetabolicForest,
title = {Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites},
author = {Hughes, Tyler B. and Dang, Na Le and Kumar, Ayush and Flynn, Noah R. and Swamidass, S. Joshua},
journal = {Journal of Chemical Information and Modeling},
volume = {60},
number = {10},
pages = {4702--4716},
year = {2020},
doi = {10.1021/acs.jcim.0c00360},
url = {https://doi.org/10.1021/acs.jcim.0c00360},
publisher = {American Chemical Society}
}
A machine-readable citation is also in CITATION.cff.
Development
New features: implement in crates/xenosite-forest/ and expose via
src/xenosite/forest/ (this package’s public wrapper). Do not extend
src/xenosite/forest/native/ or legacy/ for product work — see
docs/forest/NATIVE.md.
git clone https://github.com/swamidasslab/xenosite-forest.git
cd xenosite-forest
uv sync --extra network --group dev # maturin builds the Rust extension
make check # CI non-test gates (fmt/clippy/WASM/ruff/pyright)
make test # Rust + Python (see Makefile)
make test-python # pytest tests/forest only
make test-rust # cargo test -p xenosite-forest
Versioning is the vX.Y.Z git tag. Release CI rewrites
crates/xenosite-forest/Cargo.toml from
the tag before building (maturin). Read it at runtime as
xenosite.forest.__version__. User-facing notes go in
changelog.d/; the tag workflow compiles them into
CHANGELOG.md and commits the Cargo/JS version bump. See
docs/release.md.
Pushing a v* tag runs .github/workflows/release.yml: tests must pass, then platform wheels (manylinux / musllinux / macOS / Windows, x86_64 + aarch64) and an sdist are published to GitHub Releases and PyPI. A red tag workflow means do not treat that tag as released.
License
Academic / non-commercial only. Free for educational and academic research use; commercial use requires a separate license. See LICENSE.
1 maintainer
Metadata
1 maintainer
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Transparency logRelease files / xenosite_forest-0.10.2-cp311-cp311-macosx_10_12_x86_64.whl
| Download URL | xenosite_forest-0.10.2-cp311-cp311-macosx_10_12_x86_64.whl |
|---|---|
| Size | 1.9 MB |
| Tags | CPython 3.11 macOS 10.12+ x86-64 |
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SHA-256 checksum How to use checksums |
2233267234f1d7c90d62d59e30fe937b18b6424eb89a93bf795468f7307422ec
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BLAKE2b-256 checksum How to use checksums |
5a8e05ebf929b304be6634f11025c18d1422f60ab0cf92b276c96b034b83a10d
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
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twine/7.0.0 CPython/3.13.14
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