peptacular 3.0.0

A ProForma peptide sequence parser and annotation library

Peptacular

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.

Features

• Nearly Complete 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
• Built-in Parallel Processing

Installation

pip install peptacular

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)

When more than one item is passed to the functional API methods, it is automatically parallelized.

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]

ProForma 2.1 Compliance

See PROFORMA_COMPLIANCE.md for detailed compliance status.

Contributing

Contributions welcome! Check the examples directory for code style and documentation patterns.

License

MIT

Citation

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

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