Metadata-Version: 1.1
Name: pepdata
Version: 1.0.4
Summary: Immunological peptide datasets and amino acid properties
Home-page: https://github.com/openvax/pepdata
Author: Alex Rubinsteyn
Author-email: alex.rubinsteyn@mssm.edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description-Content-Type: UNKNOWN
Description: 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.
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
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
