semvec/pypi-packages huggingface dataset:
mhcnames 0.4.8
Python library for MHC nomenclature parsing
License: http://www.apache.org/licenses/LICENSE-2.0.html

mhcnames
========

All the fun and adventure of MHC nomenclature, now in Python

Example
-------

.. code:: python

    In [1]: mhcnames.parse_allele_name("HLA-A0201")
    Out[1]: AlleleName(species='HLA', gene='A', allele_family='02', allele_code='01')

    In [2]: mhcnames.compact_allele_name("HLA-A*02:01")
    Out[2]: 'A0201'
pepdata 1.0.7
Immunological peptide datasets and amino acid properties
License: http://www.apache.org/licenses/LICENSE-2.0.html

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.