From 79a63bfc118f9ce6ab66eb3dcbdfe1d7d930315b Mon Sep 17 00:00:00 2001 From: Hubert Date: Tue, 12 Jan 2016 16:26:48 +0100 Subject: [PATCH] Enhances the index file of the documentation. - Add description of Pbxplore - Add authors - Reorganize the TOC --- doc/source/api_cookbook.rst | 12 ++++++ doc/source/api_reference.rst | 16 ++++++++ doc/source/index.rst | 75 +++++++++++++++++++++--------------- 3 files changed, 73 insertions(+), 30 deletions(-) create mode 100644 doc/source/api_cookbook.rst create mode 100644 doc/source/api_reference.rst diff --git a/doc/source/api_cookbook.rst b/doc/source/api_cookbook.rst new file mode 100644 index 0000000..39ff87d --- /dev/null +++ b/doc/source/api_cookbook.rst @@ -0,0 +1,12 @@ +API Cookbook +============ + +This page provides some examples, tutorials as notebooks to help you use the API of ``PBxplore``. + + +.. toctree:: + :maxdepth: 1 + + ./notebooks/Assignement + ./notebooks/WritePB + ./notebooks/Deformability diff --git a/doc/source/api_reference.rst b/doc/source/api_reference.rst new file mode 100644 index 0000000..b0b54f0 --- /dev/null +++ b/doc/source/api_reference.rst @@ -0,0 +1,16 @@ +API Reference +============= + +This page provides the documentation generated from the source files. + + +.. toctree:: + :maxdepth: 1 + + ./pages/PB + ./pages/structure + ./pages/assign + ./pages/io + ./pages/analysis + ./pages/demo + ./pages/pbxplore diff --git a/doc/source/index.rst b/doc/source/index.rst index e260ff7..e0d5284 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -6,10 +6,38 @@ Welcome to PBxplore's documentation! ==================================== -PBxplore is a suite of tools dedicated to Protein Block analysis. +**PBxplore is a suite of tools dedicated to Protein Block analysis.** -PBxplore --------- +Protein Blocks (PBs) are structural prototypes defined by +`de Brevern `_ *et al* in 2000 [#]_. +The 3-dimensional local structure of a protein backbone can be modelized as an 1-dimensional +sequence of PBs. +In principle, any conformation of any amino acid could be represented +by one of the sixteen available Protein Blocks. + +.. _PB-fig: +.. figure:: img/PBs.jpg + :align: center + + Schematic representation of the sixteen protein blocks, labeled from *a* to *p* + (Creative commons CC-BY). + + + + +PBxplore provides both a python library and command-line tools (:doc:`Utilization `). +For some features (reading trajectory, plots), PBxplore requires +some optional dependencies (:doc:`Installation `). +Basically, PBxplore can: + +* **assign PBs** from either a PDB or either a molecular dynamics trajectory (:doc:`PB assignation <./notebooks/Assignement>`). +* use analysis tools to perform **statistical analysis** on PBs (:doc:`Statistics `). +* use analysis tools to **study protein flexibility and deformability** (:doc:`Analyzis <./notebooks/Deformability>`). + + +.. raw:: html + +
.. toctree:: :maxdepth: 1 @@ -21,39 +49,26 @@ PBxplore PBcount PBstat PBclust + api_cookbook + api_reference +.. raw:: html +
-API cookbook ------------- - -.. toctree:: - :maxdepth: 1 - - ./notebooks/Assignement - ./notebooks/WritePB - ./notebooks/Deformability +Contact & Support +----------------- -API reference -------------- - -.. toctree:: - :maxdepth: 1 - - ./pages/PB - ./pages/structure - ./pages/assign - ./pages/io - ./pages/analysis - ./pages/demo - ./pages/pbxplore +PBxplore is a research software and has been developped by: +* Pierre Poulain, DSIMB, Ets Poulain, Pointe-Noire, Congo +* Jonathan Barnoud, University of Groningen, Groningen, The Netherlands +* Hubert Santuz, DSIMB, Paris, France +* Alexandre G. de Brevern, DSIMB, Paris, France -Indices and tables ------------------- +If you want to report a bug, request a feature, +use the `GitHub issue system `_. -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` +.. [#] A. G. de Brevern, C. Etchebest, and S. Hazout. Bayesian Probabilistic Approach for Predicting Backbone Structures in Terms of Protein Blocks. *Proteins* **41**:271-87 (2000).