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pepdata

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Python interface to amino acid properties and IEDB

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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.

pepdata

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