Metadata-Version: 2.4
Name: pepdata
Version: 1.2.2
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: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
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

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PepData
=======

Formerly a repository for diverse peptide datasets, now only contains the [Immune Epitope Database](http://www.iedb.org) and a variety of amino acid property matrices. This package
will probably be eventually split and the IEDB portions placed into something
named `pyiedb`.

**Amino Acid Properties**

The `amino_acid` module contains a variety of physical/chemical properties for both single amino residues and interactions between pairs of residues.

Single residue feature tables are parsed into `StringTransformer` objects, which can be treated as dictionaries or will vectorize a string when you call their method `transform_string`.

Examples of single residue features:
- `hydropathy`
- `volume`
- `polarity`
- `pK_side_chain`
- `prct_exposed_residues`
- `hydrophilicity`
- `accessible_surface_area`
- `refractivity`
- `local_flexibility`
- `accessible_surface_area_folded`
- `alpha_helix_score` (Chou-Fasman)
- `beta_sheet_score` (Chou-Fasman)
- `turn_score` (Chou-Fasman)

Pairwise interaction tables are parsed into nested dictionaries, so that the interaction between amino acids `x` and `y` can be determined from `d[x][y]`.

Pairwise interaction dictionaries:
- `strand_vs_coil` (and its transpose `coil_vs_strand`)
- `helix_vs_strand` (and its transpose `strand_vs_helix`)
- `helix_vs_coil` (and its transpose `coil_vs_helix`)
- `blosum30`
- `blosum50`
- `blosum62`

There is also a function to parse the coefficients of the [PMBEC similarity matrix](http://www.biomedcentral.com/1471-2105/10/394), though this currently lives in the separate `pmbec` module.


