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Peptacular

Peptacular Logo

A Python package for peptide sequence analysis built around ProForma 2.1 notation. Calculate masses, generate fragments, predict isotopic patterns, and more. Peptacular uses type annotations extensively, so it is type safe.

Python package codecov PyPI version Python 3.12+ License: MIT

Documentation/ Examples

ReadTheDocs

Features

  • ProForma 2.1 Parsing
  • Modifiable ProFormaAnnotation Objects (Factory Pattern)
  • Mass/Mz/Composition Calculations
  • Predicted Isotopic Distributions
  • Enzymatic Protein Digestion
  • Fragment Ion Generation
  • Physiochemical Property Calculations
  • Streaming FASTA and Gzip Input
  • Indexed Batch Results and Input Diagnostics
  • Versioned JSON Serialization
  • Optional Pyteomics, psm_utils, and AlphaBase Integrations
  • Built-in Parallel Processing

Installation

pip install peptacular

Optional package adapters can be installed separately:

pip install "peptacular[pyteomics]"
pip install "peptacular[psm-utils]"
pip install "peptacular[alphabase]"

See the interoperability guide and JSON serialization guide for supported conversions and examples.

Quick Start (Object Based)

See docs for more detail.

import peptacular as pt

# Parse a sequence into a ProFormaAnnotation
peptide: pt.ProFormaAnnotation = pt.parse("PEM[Oxidation]TIDE")

# Calculate mass and m/z
mass: float = peptide.mass() # 849.342
mz: float = peptide.mz(charge=2) # 425.678

# Factory pattern
print(peptide.set_charge(2).set_peptide_name("Peptacular").serialize())
# (>Peptacular)PEM[Oxidation]TIDE/2

Quick Start (Functional Based)

Small lists run sequentially. Larger lists automatically use parallel execution, with explicit backend and worker overrides available.

import peptacular as pt

peptides = ['[Acetyl]-PEPTIDES', '<C13>ARE', 'SICK/2']

# Calculate mass and m/z for all peptides
masses: list[float] = pt.mass(peptides) # [928.4026, 374.1914, 451.2454]
mzs: list[float] = pt.mz(peptides, charge=2) # [465.2086, 188.103, 225.6227]

For streaming input, optional batch error collection, and operation diagnostics, see the streaming guide.

results = pt.batch("mass", ["PEPTIDE", "PEP[UnknownModification]TIDE"], errors="collect")
print(results[0].value)
print(results[1].error.code)  # unresolved_modification

Local MCP integration

Peptacular includes 12 optional MCP tools for agents to inspect annotations, calculate theoretical properties, digest protein sequences, and transform annotations. Calls accept small inline batches and return results directly, with no stored data or job setup. Install with pip install "peptacular[mcp]", then check the installation:

peptacular-mcp --check

See the local MCP guide for Claude Code setup, tool examples, limits, and the boundary with Spectacular's spectrum handling.

ProForma 2.1 Compliance

See PROFORMA_COMPLIANCE.md for detailed compliance status.

Contributing

Contributions welcome! See CONTRIBUTING.md for guidelines on setting up the development environment, code style, testing, and submitting pull requests.

License

MIT

Citation

Working on a JOSS submission, but in the meantime use:

https://doi.org/10.5281/zenodo.15054278