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| # API Reference | ||
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| ## Functional API | ||
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| ::: rtemis.a3.create_a3 | ||
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| ::: rtemis.a3.a3_from_json | ||
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| ::: rtemis.a3.a3_to_json | ||
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| ::: rtemis.a3.residue_at | ||
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| ::: rtemis.a3.variants_at | ||
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| ## File I/O | ||
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| ::: rtemis.a3.read_a3json | ||
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| ::: rtemis.a3.write_a3json | ||
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| ## Types | ||
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| ::: rtemis.a3.A3 | ||
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| ::: rtemis.a3.VariantRecord | ||
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| ## Errors | ||
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| ::: rtemis.a3.A3ValidationError | ||
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| ::: rtemis.a3.A3ParseError |
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| # rtemis-a3 | ||
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| Python implementation of the **Amino Acid Annotation (A3)** format — | ||
| a structured JSON format for amino acid sequences with site, region, PTM, | ||
| processing, and variant annotations. | ||
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| Part of the [rtemis-org/a3](https://github.com/rtemis-org/a3) monorepo, | ||
| which provides A3 implementations in Python, TypeScript, R, Julia, and Rust. | ||
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| ## Installation | ||
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| ```bash | ||
| pip install rtemis-a3 | ||
| # or with uv | ||
| uv add rtemis-a3 | ||
| ``` | ||
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| ## Quick Start | ||
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| ```python | ||
| from rtemis.a3 import create_a3 | ||
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| a3 = create_a3( | ||
| "MKTAYIAKQR", | ||
| site={ | ||
| "Active site": {"index": [3, 5], "type": "activeSite"}, | ||
| }, | ||
| region={ | ||
| "Repeat 1": {"index": [[1, 4]], "type": ""}, | ||
| }, | ||
| ptm={ | ||
| "Phosphorylation": {"index": [7], "type": ""}, | ||
| }, | ||
| variant=[{"position": 3, "from": "K", "to": "R"}], | ||
| metadata={ | ||
| "uniprot_id": "P12345", | ||
| "description": "Example protein", | ||
| "organism": "Homo sapiens", | ||
| }, | ||
| ) | ||
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| len(a3.sequence) # 10 | ||
| ``` | ||
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| ## Parsing JSON | ||
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| ```python | ||
| from rtemis.a3 import a3_from_json, A3ValidationError, A3ParseError | ||
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| try: | ||
| a3 = a3_from_json(json_string) | ||
| except A3ValidationError as e: | ||
| print(e.errors) # list of Pydantic error dicts with field paths | ||
| except A3ParseError as e: | ||
| print(e) # malformed JSON | ||
| ``` | ||
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| ## File I/O | ||
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| ```python | ||
| from rtemis.a3 import read_a3json, write_a3json | ||
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| a3 = read_a3json("protein.json") | ||
| write_a3json(a3, "output.json", indent=2) | ||
| ``` | ||
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| ## Serialization | ||
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| ```python | ||
| from rtemis.a3 import a3_to_json | ||
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| json_string = a3_to_json(a3) # compact | ||
| json_string = a3_to_json(a3, indent=2) # pretty-printed | ||
| ``` | ||
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| ## Wire Format | ||
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| ```json | ||
| { | ||
| "sequence": "MKTAYIAKQR", | ||
| "annotations": { | ||
| "site": { "Active site": { "index": [3, 5], "type": "activeSite" } }, | ||
| "region": { "Repeat 1": { "index": [[1, 4]], "type": "" } }, | ||
| "ptm": { "Phospho": { "index": [7], "type": "" } }, | ||
| "processing": {}, | ||
| "variant": [{ "position": 3, "from": "K", "to": "R" }] | ||
| }, | ||
| "metadata": { | ||
| "uniprot_id": "P12345", | ||
| "description": "Example protein", | ||
| "reference": "", | ||
| "organism": "Homo sapiens" | ||
| } | ||
| } | ||
| ``` | ||
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| All five annotation families are always present in output. Each annotation | ||
| entry is `{ index, type }` — bare arrays are rejected. Positions are | ||
| 1-based, sorted, and deduplicated. Ranges are `[start, end]` pairs | ||
| (`start < end`), sorted by start; overlapping ranges are rejected. | ||
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| ## Canonical Schema | ||
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| See the [A3 specification](https://github.com/rtemis-org/a3/blob/main/specs/A3.md) | ||
| for the language-agnostic schema definition. | ||
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| site_name: rtemis_a3 | ||||||
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There was a problem hiding this comment. The site_name: rtemis-a3
site_description: Python implementation of the A3 amino acid annotation format.
site_author: E.D. Gennatas
nav:
- Home: index.md
- API Reference: api.md
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| plugins: | ||||||
| - mkdocstrings: | ||||||
| handlers: | ||||||
| python: | ||||||
| paths: [src] | ||||||
| inventories: | ||||||
| - https://docs.python.org/3/objects.inv | ||||||
| options: | ||||||
| docstring_style: numpy | ||||||
| inherited_members: true | ||||||
| show_source: false | ||||||
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There was a problem hiding this comment. The repo’s Python CI workflow currently runs lint/typecheck/tests but does not build the documentation site. Since this PR adds MkDocs/Zensical configuration and mkdocstrings directives, consider adding a CI step to at least run a docs build (or a mkdocstrings render check) so doc generation failures are caught early. |
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docs/index.mdappears to duplicate the existingREADME.mdcontent in this package (and alsopython/README.md). Keeping multiple copies of the same introductory text tends to drift over time; consider reusing a single source (e.g., include/redirect the README into MkDocs) so updates only need to be made in one place.