PepData
Look up shipped amino-acid properties and pairwise matrices, encode peptide sequences, or load peptide assay tables from IEDB. Property lookups work offline; IEDB tables require a download.
Install
python -m pip install pepdata
Python 3.11 or later is required.
Look up a peptide's residue properties
from pepdata.amino_acid_properties import hydropathy
peptide = "ACD"
print([hydropathy[residue] for residue in peptide])
[1.8, 2.5, -3.5]
The values come from the shipped residue-property table. The dictionary maps
single-letter residues to numeric values; it does not predict MHC binding or
clinical immunogenicity. Use uppercase canonical residue letters. A missing
letter raises KeyError.
Find the interface you need
| Task | Module or object |
|---|---|
| Single-residue properties | pepdata.amino_acid_properties |
| BLOSUM substitution matrices | pepdata.blosum |
| PMBEC and contact tables | pepdata.pmbec, pepdata.residue_contact_energies |
| Residue alphabets | pepdata.amino_acid_alphabet, pepdata.reduced_alphabet |
| N-gram features | pepdata.PeptideVectorizer |
| MHC-binding assay tables | pepdata.iedb.mhc |
| T-cell assay tables | pepdata.iedb.tcell |
See residue and pairwise tables, then peptide features and IEDB tables. The API reference follows those same tasks.
Older pepdata documentation placed the property tables in amino_acid and
described a StringTransformer interface. The property dictionaries are
in amino_acid_properties, and there is no StringTransformer class.
Documentation development
Install requirements-docs.txt, run ./docs.sh, then python scripts/check_docs_examples.py.
5 maintainers
Metadata
5 maintainers
Release files for pepdata 1.2.4
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