Commit 4714d791 authored by Martin Larralde's avatar Martin Larralde
Browse files

Mention EMBOSS, ExPASy and Rcpi as code and data sources in docs

parent b04efb4c
......@@ -19,8 +19,11 @@
## 🗺️ Overview
`peptides.py` is a pure-Python package to compute common descriptors for
protein sequences. It is 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.
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), but now also provides
some additional 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+).
......@@ -104,6 +107,7 @@ The original R `Peptides` package was written by [Daniel Osorio](https://orcid.o
[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/).
The [EMBOSS] applications are released under the [GNU General Public License v1.0](https://www.gnu.org/licenses/old-licenses/gpl-1.0.html).
*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [original `Peptides` authors](https://github.com/dosorio). It was developed
......
......@@ -57,9 +57,12 @@ Overview
--------
``peptides.py`` is a pure-Python package to compute common descriptors for
protein sequences. It is a port of `Peptides <https://cran.r-project.org/web/packages/Peptides/index.html>`_,
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. This library has no external dependency and is
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:
......@@ -76,6 +79,7 @@ A non-exhaustive list of available features:
- `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>`_
- `ST-scales <https://doi.org/10.1007/s00726-009-0287-y>`_
- `T-scales <https://doi.org/10.1016/j.molstruc.2006.07.004>`_
......@@ -124,7 +128,7 @@ This library is provided under the `GNU General Public License v3.0 <https://cho
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 `GPLv2 <https://choosealicense.com/licenses/gpl-2.0/>`_.
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*
......
......@@ -18,6 +18,7 @@ __license__ = "GPLv3"
__credits__ = """
Daniel Osorio, Paola Rondón-Villarreal and Rodrigo Torres for ``Peptides``.
Alan Bleasby for the ``hmoment`` binary of the EMBOSS.
Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, and Alex F. Chen for ``Rcpi``.
""".strip()
......@@ -1473,13 +1474,13 @@ class Peptide(typing.Sequence[str]):
E5 -0.1059
References:
- Venkatarajan, M. S., and W. Braun.
- Mathura, V. S., and W. Braun.
*New Quantitative Descriptors of Amino Acids Based on
Multidimensional Scaling of a Large Number of
Physical–Chemical Properties*.
Molecular Modeling Annual. Dec 2001;7(12):445–53.
doi:10.1007/s00894-001-0058-5.
- Venkatarajan, M. S., D. Paris, and M. J. Mullan.
- Mathura, V. S., D. Paris, and M. J. Mullan.
*A Novel Physico-Chemical Property Based Model for Studying
the Effects of Mutation on the Aggregation of Peptides*.
Protein and Peptide Letters. 2009;16(8):991–98.
......
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