ProDy documentation is written using reStructuredText markup and prepared using Sphinx. You may install Sphinx using easy_install, i.e. easy_install -U Sphinx, or using package manager on your Linux machine.
ProDy Manual in HTML and PDF formats can be build as follows:
$ cd docs
$ make html
$ make pdf
If all documentation strings and pages are properly formatted according to reStructuredText markup, documentation pages should compile without any warnings. Note that to build PDF files, you need to install latex and pdflatex programs.
Read the Docs
A copy of ProDy manual is hosted on Read the Docs and can be viewed at http://prody.readthedocs.org/. Read the Docs is configured to build manual pages for the devel branch (latest) and the recent stable versions.
ProDy-website source is hosted at https://github.com/prody/ProDy-website This project contains tutorial files and the home pages for other software in the