[WIP] Rewrite of old documentation

.travis.yml

@@ -60,7 +60,7 @@ install:
     - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then pip install "mdanalysis>=0.11" --cache-dir $HOME/.cache/pip; fi
     - pip install -e .
     - if [[ $SETUP == 'doc' ]]; then pip install -r doc_requirements.txt --cache-dir $HOME/.cache/pip; fi
-    - if [[ $SETUP == 'doc' ]]; then ./doc-api/source/install_pandoc.sh; fi
+    - if [[ $SETUP == 'doc' ]]; then ./doc/source/install_pandoc.sh; fi
 
 
 # command to run tests
@@ -69,6 +69,6 @@ script:
     - if [[ $SETUP == 'test' ]]; then yes | ./run_demo1_assignation.sh; fi
     - if [[ $SETUP == 'test' ]]; then yes | ./run_demo2_statistics.sh; fi
     - if [[ $SETUP == 'test' ]]; then yes | ./run_demo2_clusters.sh; fi
-    - if [[ $SETUP == 'doc' ]]; then cd doc-api; sphinx-build -W -b html source build/html; fi
+    - if [[ $SETUP == 'doc' ]]; then cd doc; sphinx-build -W -b html source build/html; fi
 
 #after_success:

README.md

@@ -1,40 +1,68 @@
-Build Status from Travis CI [![Build Status](https://travis-ci.org/pierrepo/PBxplore.svg?branch=master)](https://travis-ci.org/pierrepo/PBxplore)
+# PBxplore [![Build Status](https://travis-ci.org/pierrepo/PBxplore.svg?branch=master)](https://travis-ci.org/pierrepo/PBxplore)
 
 ---
 
-**PBxplore** is a suite of tools dedicated to Protein Block analysis. Protein Blocks are structural prototypes defined by [de Brevern](http://www.dsimb.inserm.fr/~debrevern/index.php) *et al* [1]. 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 (see Figure 1).
+**PBxplore** is a suite of tools dedicated to Protein Block analysis.
+Protein Blocks are structural prototypes defined by
+[de Brevern](http://www.dsimb.inserm.fr/~debrevern/index.php) *et al* [1]. 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 (see Figure 1).
 
-![PBs](doc/img/PBs.jpg "PBs")
+![PBs](doc/source/img/PBs.jpg "PBs")
 
-**Figure 1.** Schematic representation of the sixteen protein blocks, labeled from *a* to *p* (Creative commons CC BY).
+**Figure 1.** Schematic representation of the sixteen protein blocks,
+              labeled from *a* to *p* ([Creative commons 4.0 CC-BY](https://creativecommons.org/licenses/by/4.0/)).
 
-# Download
+
+PBxplore provides both a python library and command-line tools. Basically, PBxplore can:
+
+* **assign PBs** from either a PDB or either a molecular dynamics trajectory.
+* use analysis tools to perform **statistical analysis** on PBs.
+* use analysis tools to **study protein flexibility and deformability**.
+
+For details, see the documentation at [https://pbxplore.readthedocs.org/en/latest/](https://pbxplore.readthedocs.org/en/latest/).
+
+## Download
 
 - [Get latest zip archive](https://github.com/pierrepo/PBxplore/archive/master.zip)
 - Clone repository: `git clone [email protected]:pierrepo/PBxplore.git` or `git clone https://github.com/pierrepo/PBxplore.git`
 
-# Requirements
+## Requirements
 
-PBxplore requires: 
+PBxplore requires:
 
 * Python 2.7 or Python 3.x (>= 3.3)
-* the [NumPy](http://numpy.scipy.org/ "NumPy") Python library, 
-* the R software.
+* the [NumPy](http://numpy.scipy.org/ "NumPy") Python library,
 
 Optionally, PBxplore can use:
 
 * the [MDAnalysis](https://code.google.com/p/mdanalysis/) Python library (version >= 0.11) to read MD trajectories generated by Gromacs (.xtc files),
+* [Mapltolib](http://matplotlib.org/) to generate plots.
 * [WebLogo 3](http://weblogo.threeplusone.com/) to create logo from PB sequences.
 
-# Documentation
+## Documentation
+
+All documentation are hosted by Read The Docs and can be found [here](https://pbxplore.readthedocs.org/en/latest/).
+
+## Contact & Support
+
+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
+
+If you want to report a bug, request a feature,
+use the [GitHub issue system](https://github.com/pierrepo/PBxplore/issues>).
+
+
+## Licence
 
-- [Installation](doc/installation.md)
-- [Introduction to Protein Blocks](doc/intro.PBs.md)
-- [Single structure analysis](doc/single.structure.analysis.md)
-- [Multiple conformation analysis](doc/multiple.conformation.analysis.md)
-* [API documentation](http://pbxplore.readthedocs.org/en/latest/) [![Documentation Status](https://readthedocs.org/projects/pbxplore/badge/?version=latest)](http://pbxplore.readthedocs.org/en/latest/?badge=latest)
+PBxplore is licensed under [The MIT License](https://github.com/pierrepo/PBxplore/blob/master/LICENSE).
 
 
 
-# References
+## References
 [1] A. G. de Brevern, C. Etchebest and S. Hazout. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. *Proteins* **41**: 271-288 (2000).