- This topic has 3 replies, 3 voices, and was last updated 10 years, 1 month ago by Anonymous.
October 23, 2013 at 6:41 am #1737Anonymous
i m very new user of rosetta and pyrosetta i have idea about the algorithms of various molecular simulation programs like Gromacs autodock and other.
i want to know is there any documentation available about all the algorithms and methods used in Rosetta ? more precisely rather then hard core scientific notation i am looking for an easy and more descriptive documentation which can provide the information of various methods available in Rosetta.
Actually i found one very impressive feature of Rosetta and PyRosetta, with the help of various methods i can write my own algorithm to solve a biological problem but it should required a detailed knowledge of various libraries, objects and methods.
October 23, 2013 at 2:27 pm #9443Anonymous
You’ll probably want to start off with http://www.pyrosetta.org/documentation which is the documentation for PyRosetta, and is oriented more toward people just starting out with Rosetta.
The documentation for Rosetta proper can be found at https://www.rosettacommons.org/manual_guide (click on the appropriate version on the left). The main page for each version has links to the documentation for the released applications, and you can get documentation for the classes and files in Rosetta by clicking on the Namespaces/Classes/Files links in the header near the top. These are the same classes that are exposed with the PyRosetta interface, so much of what you can learn from them is applicable to PyRosetta. (From what I understand, much the same documentation should be available through class and function docstrings in Python, accessible through typical python environment help facilities.)
I’ll also recommend the Rosetta tutorials available through http://meilerlab.org/index.php/jobs/resources. These focus on the commandline interface, so don’t have much of the internal plumbing details, but give a good sense of what can be accomplished with Rosetta.
Finally, reading the papers is also sometimes a reasonable way of understanding how things work. If you can be more specific about what sort of things you’re hoping to accomplish, I can make some recommendations.
October 23, 2013 at 2:40 pm #9444Anonymous
Once you go through the PyRosetta tutorials at http://www.pyrosetta.org/tutorials, this command reference is extremely helpful. I have had the newest version of it sitting at my desk for a few years now: http://www.pyrosetta.org/tutorials#TOC-Appendix-A:-Command-Reference
In addition, the paper describing the inner workings of Rosetta3 is a must: ‘ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.’
From my own PyRosetta experience, using the ipython shell is extremely helpful to get code completion and understanding on a more-specific level of the classes and functions available. As Rocco says, it is described in the pyrosetta documentation page.
Finally, once you progress towards understanding how Rosetta works and what you want to do with it, a useful tool is to download the Rosetta C++ code, load it into an IDE, and start exploring. It is a massive software suite; I still find new classes and methods almost everyday. Once you do this, you’ll be surprised how much is there. It’s also helpful to use this to understand exactly how some code works, or get a quick overview of some class you are interested in. Reading C++ can sometimes be tricky, but most of the time you can gather what is happening from your Python knowledge.
Make sure to also go through python tutorials or a book. Writing PyRosetta code is not helpful unless you have a decent knowledge of python….
October 24, 2013 at 10:50 am #9445Anonymous
Thanks for your quick and valuable suggestions, And i really want to thank to the Rosetta community to manage this kind massive support and documentation.
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