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`peptides.py` |stars|
=====================

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*Physicochemical properties, indices and descriptors for amino-acid sequences.*

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Overview
--------

``peptides.py`` is a pure-Python package to compute common descriptors for
protein sequences. It started as a port of `Peptides <https://cran.r-project.org/web/packages/Peptides/index.html>`_,
the R package written by `Daniel Osorio <https://orcid.org/0000-0003-4424-8422>`_
for the same purpose, but now also provides some more features from
`EMBOSS <http://emboss.bioinformatics.nl/cgi-bin/emboss/>`_,
`ExPASy Protein Identification and Analysis Tools <https://web.expasy.org/protparam/>`_,
and `Rcpi <https://bioconductor.org/packages/release/bioc/html/Rcpi.html>`_. This library has no external dependency and is
available for all modern Python versions (3.6+).

A non-exhaustive list of available features:

- Amino-acid Statistics:

  - Number of occurrences in the peptide sequence
  - Frequency in the peptide sequence

- `QSAR <https://en.wikipedia.org/wiki/Quantitative_structure%E2%80%93activity_relationship>`_ descriptors:

  - `BLOSUM indices <https://doi.org/10.1089/cmb.2008.0173>`_
  - `Cruciani properties <https://doi.org/10.1002/cem.856>`_
  - `FASGAI vectors <https://doi.org/10.1111/j.1747-0285.2008.00641.x>`_
  - `Kidera factors <https://doi.org/10.1007/BF01025492>`_
  - `MS-WHIM scores <https://doi.org/10.1021/ci980211b>`_
  - `PCP descriptors <https://doi.org/10.1007/s00894-001-0058-5>`_
  - `ProtFP descriptors <https://doi.org/10.1186/1758-2946-5-41>`_
  - `Sneath vectors <https://doi.org/10.1016/0022-5193(66)90112-3>`_
  - `ST-scales <https://doi.org/10.1007/s00726-009-0287-y>`_
  - `T-scales <https://doi.org/10.1016/j.molstruc.2006.07.004>`_
  - `VHSE-scales <https://doi.org/10.1002/bip.20296>`_
  - `Z-scales <https://doi.org/10.1021/jm9700575>`_

- Sequence profiles:

  - Hydrophobicity profile using one of 39 proposed scales.
  - Hydrophobic moment profile based on `Eisenberg, Weiss and Terwilliger (1984) <https://doi.org/10.1073/pnas.81.1.140>`_.
  - Membrane position based on `Eisenberg (1984) <https://doi.org/10.1146/annurev.bi.53.070184.003115>`_.

- Physical-chemical properties:

  - Aliphatic index proposed in `Ikai (1980) <https://pubmed.ncbi.nlm.nih.gov/7462208/>`_.
  - Instability index proposed in `Boman (2003) <https://doi.org/10.1046/j.1365-2796.2003.01228.x>`_.
  - Theoretical net charge based on the `Henderson-Hasselbach equation <https://en.wikipedia.org/wiki/Henderson%E2%80%93Hasselbalch_equation>`_.
  - Isoelectric point using one of 8 pKa scales.
  - Molecular weight, taking into account isotope labelling, using one of 3 average weight tables.

- Biological properties:

  - Structural class using methods and reference data from either
    `Nakashima, Nishikawa & Ooi (1985) <https://doi.org/10.1093/oxfordjournals.jbchem.a135454>`_,
    `Chou (1989) <https://doi.org/10.1007/978-1-4613-1571-1>`_,
    `Chou & Zhang (1992) <https://doi.org/10.1111/j.1432-1033.1992.tb17067.x>`_,
    or `Chou, Liu, Maggiora & Zhang (1998) <https://pubmed.ncbi.nlm.nih.gov/9552161/>`_.


Setup
-----

Run ``pip install peptides`` in a shell to download the latest release, or have
a look at the :doc:`Installation page <install>` to find other ways to install
``peptides.py``.


Library
-------

.. toctree::
  :maxdepth: 2

  Installation <install>
  Contributing <contributing>
  API Reference <api>
  Changelog <changes>


License
-------

This library is provided under the `GNU General Public License v3.0 <https://choosealicense.com/licenses/gpl-3.0/>`_.
The original R `Peptides` package was written by `Daniel Osorio <https://orcid.org/0000-0003-4424-8422>`_,
`Paola Rondón-Villarreal <https://orcid.org/0000-0001-8209-3885>`_ and
`Rodrigo Torres <https://orcid.org/0000-0003-1113-3020>`_, and is licensed under
the terms of the `GNU General Public License v2.0 <https://choosealicense.com/licenses/gpl-2.0/>`_.

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original* `Peptides`_ *authors. It was developed by*
`Martin Larralde <https://github.com/althonos>`_ *during his
PhD project at the* `European Molecular Biology Laboratory <https://www.embl.de/>`_
*in the* `Zeller team <https://github.com/zellerlab>`_.