uniprotptmpy 0.1.2

Python library for parsing and querying the UniProt PTM controlled vocabulary list.

uniprotptmpy

Python library for parsing and querying the UniProt post-translational modification (PTM) controlled vocabulary.

• Zero dependencies
• Bundled PTM data (748 entries) — works offline out of the box
• Typed, immutable data models (py.typed / PEP 561)

Installation

pip install uniprotptmpy

Or with uv:

uv add uniprotptmpy

Requires Python 3.12+. No third-party dependencies.

Quick Start

from uniprotptmpy import load

# Load the bundled PTM database
db = load()
print(len(db))  # 748

# Look up by accession
entry = db.get_by_id("PTM-0450")
print(entry.name)  # (2-aminosuccinimidyl)acetic acid (Asn-Gly)

# Look up by name (case-insensitive)
entry = db.get_by_name("phosphoserine")
print(entry.id)  # PTM-0253

# Free-text search across name, ID, target, and keywords
results = db.search("acetylation")

# Dict-style access (raises KeyError if not found)
entry = db["PTM-0450"]

# Iterate all entries
for entry in db:
    print(entry.id, entry.name)

Chemical Formulas

entry = db.get_by_id("PTM-0476")  # 3-hydroxyproline
print(entry.correction_formula)   # O1
print(entry.dict_composition)     # {'O': 1}
print(entry.proforma_formula)     # O

Downloading the Latest Data

from uniprotptmpy import download, load

path = download()   # downloads to ~/.cache/uniprotptmpy/ptmlist.txt
db = load(path)     # load from the downloaded file

API Overview

Symbol	Description
load(source=None)	Load the PTM database. Uses bundled data by default.
download(dest=None)	Download the latest ptmlist.txt from UniProt FTP.
parse_ptm_list(path)	Parse a ptmlist.txt file into a PtmDatabase.
PtmDatabase	Indexed collection with get_by_id(), get_by_name(), search(), iteration, and len().
PtmEntry	Frozen dataclass with all PTM fields, plus dict_composition and proforma_formula properties.
FeatureType	StrEnum: CROSSLNK, MOD_RES, LIPID, CARBOHYD, DISULFID.
CrossReference	Frozen dataclass with database and accession fields.
TaxonomicRange	Frozen dataclass with taxon_name, tax_id, description, and raw fields.

Development

just install   # install dependencies with uv
just lint      # ruff check
just format    # ruff format
just ty        # ty type check
just test      # pytest
just check     # lint + type check + test

Related Projects

Package	Description
unimodpy	Parse and query the UNIMOD mass spectrometry modifications database
psimodpy	Parse and query the PSI-MOD protein modification ontology

License

MIT