PepData
Formerly a repository for diverse peptide datasets, now only contains the Immune Epitope Database 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:
hydropathyvolumepolaritypK_side_chainprct_exposed_residueshydrophilicityaccessible_surface_arearefractivitylocal_flexibilityaccessible_surface_area_foldedalpha_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 transposecoil_vs_strand)helix_vs_strand(and its transposestrand_vs_helix)helix_vs_coil(and its transposecoil_vs_helix)blosum30blosum50blosum62
There is also a function to parse the coefficients of the PMBEC similarity matrix, though this currently lives in the separate pmbec module.
5 maintainers
Metadata
5 maintainers
Release files for pepdata 1.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pepdata-1.2.2.tar.gz | 35.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pepdata-1.2.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 83.4 kB
Release files / pepdata-1.2.2.tar.gz
| Download URL | pepdata-1.2.2.tar.gz |
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| Size | 35.7 kB |
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| Size | 47.6 kB |
| Tags | Python 3 |
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