tacular 1.1.0

Includes lookups for modifications, amino acids, and other data types.

tacular

A Python library for looking up common MS-proteomics values. Includes the following modifications: UNIMOD, RESID, XLMOD, GNOme, PSIMOD, and UniProt-PTM. Also contains a lookup of elements, MS ion types, neutral deltas, proteases, and some reference molecules. Tacular is mainly a helper package for peptacular and paftacular.

Updating data from the latest ontologies

tacular ships with a snapshot of each ontology baked into the package. To refresh to the latest releases without reinstalling, use the tacular CLI. It downloads the current .obo sources, regenerates the data, and stores it in a per-user cache that the lookups prefer over the bundled snapshot on the next import.

tacular update                 # refresh all pullable ontologies (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme, UniProt-PTM)
tacular update unimod xlmod    # refresh a subset (GNOme is a large download; opt in explicitly)
tacular update --offline DIR   # regenerate from local .obo files in DIR (no network)
tacular status                 # show bundled vs cached versions
tacular clear                  # remove the cache and revert to the bundled data
tacular where                  # print the cache directory
tacular -vv update             # -v/-vv raise verbosity (info/debug); parsing failures always warn with a traceback

The refresh takes effect on the next import tacular. Environment variables: TACULAR_DATA_DIR overrides the cache location; TACULAR_DISABLE_CACHE=1 ignores the cache and always uses the bundled data. Equivalent to the CLI: python -m tacular ....

If an ontology release contains an entry tacular can't parse (or a cached file gets corrupted), a warning is logged with the offending id/name, the raw input, the exception type/message, and a full traceback — the root cause should be diagnosable directly from the log without a debugger.

Generate Data

See data_gen/README.md

Generating JSONs

It's possible to generate JSON objects for all parsed data used within tacular. This isn't used within tacular or its downstream packages, but may be useful in other projects, especially those not Python-based. This will be created from the data within the python package, so ensure that this is up to date. See data_gen/README.md for more info.

just gen-jsons

Overview

The following lookups are available:

Amino Acids

• Standard and non-standard amino acid lookups
• Query by single-letter code, three-letter code, or full name
• Access to molecular properties (mass, formula, etc.)

Modifications

• Post-translational modifications (PTMs)
• Query by modification name, ID, or delta mass
• Support for Unimod, PSI-MOD, RESID, XLMOD, GNOme, and UniProt-PTM

Elements

• Chemical element data
• Query by symbol, name
• Isotope information and masses

Additional Data Types

• Fragment ions
• Common neutral deltas (mainly neutral losses)
• mzPAF reference molecules
• Common Proteases

Architecture

Each lookup contains three core components:

• data.py: Auto-generated data file (should not be modified manually)
• dclass.py: Dataclass definitions for the data structures (subclass OboEntity, see obo_entity.py)
• lookup.py: Lookup implementation with query methods (subclass OntologyLookup, see obo_lookup.py)

Each lookup provides multiple query options to enable data retrieval by various means. Lookups are cached for faster repeat queries.

Two more pieces support the 6 ontologies that can be refreshed at runtime (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme -- all OBO-sourced -- and UniProt-PTM, sourced from UniProt's own ptmlist.txt flat file) specifically:

• _datagen/: the parsing logic, one module per ontology. This is the single source of truth — both the developer generators (data_gen/) and the tacular update CLI call into it. See data_gen/README.md.
• _cache.py: resolves each lookup's data from a refreshed per-user cache if present, else the bundled data.py — see "Updating data from the latest ontologies" above.

Usage

import tacular as t

# Query amino acids
alanine = t.AA_LOOKUP['A']
carbon_13 = t.ELEMENT_LOOKUP['13C']

Contributing / working with an AI agent

See CLAUDE.md for an architecture and command reference aimed at AI coding agents (also generally useful for new contributors); AGENTS.md points here for tools that look for that filename instead.