Metadata-Version: 2.4
Name: pepdata
Version: 1.2.4
Summary: Immunological peptide datasets and amino acid properties
Author-email: Alex Rubinsteyn <alex.rubinsteyn@mssm.edu>
Project-URL: Homepage, https://github.com/openvax/pepdata
Project-URL: Bug Tracker, https://github.com/openvax/pepdata/issues
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: numpy<3.0.0,>=2.0.0
Requires-Dist: scipy>=0.9
Requires-Dist: pandas>=0.17
Requires-Dist: scikit-learn>=0.14.1
Requires-Dist: progressbar33
Requires-Dist: biopython>=1.65
Requires-Dist: datacache>=0.4.4
Requires-Dist: lxml
Dynamic: license-file

# 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

```sh
python -m pip install pepdata
```

Python 3.11 or later is required.

## Look up a peptide's residue properties

```python
from pepdata.amino_acid_properties import hydropathy

peptide = "ACD"
print([hydropathy[residue] for residue in peptide])
```

```text
[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](docs/guides/properties.md), then
[peptide features and IEDB tables](docs/guides/datasets.md). The
[API reference](docs/reference.md) 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`.
