SynEPD

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Electron Pushing database

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- - publish-package.yml
  - test-and-lint.yml
- dependabot.yml
- epdb.sqlite
- hierarchy.md
- polar.json
- release-manifest.json
- rxno.obo
- rxno_crosswalk.tsv
- rxno_mapping_overrides.tsv
- taxonomy_redirects.tsv
- - changelog.rst
  - conf.py
  - index.rst
  - modules.rst
  - querying_guide.rst
  - synepd.construct.rst
  - synepd.core.rst
  - synepd.database.rst
  - synepd.precheck.rst
  - synepd.query.rst
  - synepd.rst
  - synepd.web.rst
- Makefile
- requirements.txt
- demo_predictor.py
- query_demo.py
- build_rxno_mapping.py
- compare_taxonomy_rxno.py
- render_taxonomy.py
- - __init__.py
  - build_release_db.py
  - builder.py
  - checks.py
  - release_manifest.py
- - __init__.py
  - data.py
  - export.py
  - graph_codec.py
  - ingest.py
  - mechanism.py
  - query.py
  - representation.py
- - __init__.py
  - chem_db.py
  - core.py
  - managers.py
  - migrations.py
  - models.py
  - repository.py
  - sqlite.py
- - __init__.py
  - check_alpha_elimination_arrow_order.py
  - check_atom_map.py
  - check_balance.py
  - check_carbocation_shift_adjacency.py
  - check_entry_codes.py
  - check_epd_reaction_center.py
  - check_h_completion.py
  - check_unimolecular_arrow_order.py
  - epd_verification.py
  - report.py
- - __init__.py
  - filters.py
  - release.py
- - __init__.py
  - knowledge_graph.py
  - operations.py
  - server.py
- __init__.py
- io.py
- linkage.py
- models.py
- render_epd_pdf.py
- - test_build_release_db.py
  - test_builder.py
  - test_checks.py
  - test_release_manifest.py
- - test_data.py
  - test_export.py
  - test_graph_codec.py
  - test_ingest.py
  - test_mechanism.py
  - test_query.py
  - test_representation.py
- - test_chem_db.py
  - test_core.py
  - test_database.py
  - test_database_models.py
  - test_managers.py
  - test_migrations.py
  - test_repository.py
  - test_sqlite.py
  - test_verify_db.py
- - test_check_alpha_elimination_arrow_order.py
  - test_check_atom_map.py
  - test_check_balance.py
  - test_check_carbocation_shift_adjacency.py
  - test_check_entry_codes.py
  - test_check_epd_reaction_center.py
  - test_check_h_completion.py
  - test_check_unimolecular_arrow_order.py
  - test_report.py
- - test_filters.py
  - test_public_api.py
- - test_enhancements.py
  - test_error_redaction.py
  - test_operations.py
  - test_server.py
- __init__.py
- test_epd_verification.py
- test_import.py
- test_io.py
- test_models.py
- test_rxno_mapping.py
.gitattributes
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.readthedocs.yaml
env.yaml
LICENSE
lint.sh
pyproject.toml
pytest.sh
README.md
requirements.txt
run_server.sh

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SynEPD is a hierarchical database of polar organic reaction mechanisms. It
combines curated atom-mapped reactions, the POLAR taxonomy, reaction-center
(RC) and mechanistic-center (MC) templates, ITS graphs, and ordered
electron-pushing diagram (EPD) arrows in SQLite and a web explorer.

- [Web explorer](https://synepd.bioinf.uni-leipzig.de)
- [Zenodo releases](https://doi.org/10.5281/zenodo.21235891)
- [Documentation](docs/source/index.rst)

## Dataset

| Item | Count |
| --- | ---: |
| Reactions | 1,926 |
| Molecules | 2,277 |
| RC templates | 1,521 |
| MC templates | 1,540 |
| EPD arrows | 8,129 |
| Taxonomy classes | 939 |
| Accepted RXNO/MOP links | 218 |

An RC describes changed bonds. An MC extends its RC with the transition edges
required by the curated electron flow. In the current release, 284 MC
templates (18.44%) differ from their RC and 229 (14.87%) structurally extend
it.

The corpus covers closed-shell, paired-electron mechanisms. Concerted
reactions are included when their electron movement is expressible with
two-electron arrows. Radical and single-electron-transfer mechanisms are
excluded because the current vocabulary has no fishhook-arrow representation.

## Quick Start

Create the Conda environment and install the package:

```bash
conda env create -f env.yaml
conda activate synepd
python -m pip install -e ".[dev]"
```

Start the local explorer:

```bash
./run_server.sh
```

Then open <http://127.0.0.1:8000/>. Versioned API routes are available under
`/api/v1`; `/api` remains as a compatibility alias.

## Query from Python

```python
from synepd.query import SynEPDQuery

with SynEPDQuery("data/epdb.sqlite") as query:
    result = query.epd("CC[O-].[NH4+]>>CCO")
    for arrow in result.get("arrows", []):
        print(
            arrow["arrow_index"],
            arrow["arrow_type_code"],
            arrow["source_atoms"],
            "->",
            arrow["target_atoms"],
        )
```

The same interface supports molecule, taxonomy, arrow-sequence, RC-template,
ITS/RC/MC, and RXNO/MOP queries. `SynEPDQuery.from_release(...)` resolves a
tagged release through the `zenodo`, `github`, or `auto` sources.

## Build and Validate the Data

Build the release database:

```bash
PYTHONPATH=. python -m synepd.construct.build_release_db
```

Rebuild or check the external RXNO/MOP linkage:

```bash
python scripts/build_rxno_mapping.py --obo data/rxno.obo
python scripts/build_rxno_mapping.py --check --obo data/rxno.obo
```

Verify the checked-in release artifact:

```bash
python -m synepd.construct.release_manifest data/epdb.sqlite \
  --verify data/release-manifest.json
```

Core release files are:

| Path | Purpose |
| --- | --- |
| `data/polar.json` | Curated production reaction records |
| `data/hierarchy.md` | POLAR taxonomy source |
| `data/epdb.sqlite` | Built read-only release database |
| `data/rxno_crosswalk.tsv` | SynEPD-to-RXNO/MOP linkage |
| `data/release-manifest.json` | Version, counts, and checksums |
| `synepd/web/static/data_arch.tex` | Editable database diagram source |

SQLite contains the reaction, molecular, taxonomy, RC, MC, ITS, and EPD core.
RXNO/MOP mappings remain versioned TSV/RDF artifacts and are resolved on
demand instead of being duplicated in SQLite. Narrative curation notes and
internal named-reaction relations are not exposed through the public schema.

## Development Checks

```bash
python -m black --check --workers 1 synepd test
./lint.sh
./pytest.sh
python -m synepd.precheck.epd_verification --strict
```

The EPD command uses strict ordered electron-resource replay by default. It
checks every intermediate state, charge propagation, locality, and the mapped
product endpoint. Pass ``--legacy-editor`` only for compatibility comparisons
with the historical endpoint-only check.

For a multi-worker deployment, run `./run_server.sh run --no-reload --workers
4` behind a reverse proxy. The bundled SQLite release is opened read-only;
PostgreSQL is supported for horizontally scaled or write-heavy deployments.

## License and Acknowledgment

The software is licensed under Apache License 2.0. Curated release data is
distributed under CC BY 4.0 where stated in its metadata. See
[LICENSE](LICENSE).

This project received funding from the European Union's Horizon Europe
Doctoral Network programme under Marie Skłodowska-Curie grant agreement No.
101072930 ([TACsy](https://tacsy.eu/)).

SynEPD

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