Documenting ProDy

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.

Building Manual

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 Read the Docs is configured to build manual pages for the devel branch (latest) and the recent stable versions. The user name for Read the Docs is prody.

Building Website

ProDy-website source is hosted at This project contains tutorial files and the home pages for ProDy and other related software.

Latest version

To build website on ProDy server, start with pulling changes:

$ cd ProDy-website
$ git pull

Running the following command will build HTML pages for the latest stable release of ProDy:

$ make html

HTML pages for manual and all tutorials are build as a single project, which allows for referencing from manual to tutorials.

PDF files for the manual and tutorials, and also download files are build as follows:

$ make pdf

PDF and TGZ/ZIP files are copied to appropriate places after they are built.