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.
Documentation/ Examples
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
- 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! 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:
1 maintainer
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