The rna_predict Python package models a complete workflow for RNA tertiary
structure prediction using the secondary structure information as well as
optional, additional constraints.
The modelling is done using Rosetta
and its rna_denovo protocol.
Additional constraints, for example from co-evolutional anaylsis, can be included to improve the prediction quality.
A utility to convert residue-residue contacts into atom-atom constraints is included.
rna_predict also comes with tools to cluster and visualize the prediction
results and to compare them to a native crystal strcture, if available.
The rna_predict Python package has the following dependencies:
biopythonmatplotlibnumpy
To install the package (and the dependencies, if necessary), run:
python setup.py install
Additionally, rna_predict depends on Rosetta. However, a few minor
modifications to the Rosetta source are required. For a detailed Rosetta
compilation and installation guide see doc/rosetta.rst or the HTML
documentation.
A few configuration options can be overridden in ~/.rna_predict/sysconfig.
For details refer to the documentation.
rna_predict comes with a command line interface. To see all available
options run:
rna_predict --help
For detailed usage information refer to the documentation.
The HTML documentation can be found here.
A PDF version can be downloaded from here.
If you downloaded a source package or checked out the source from Git,
you can also build the HTML documentation yourself. For that, rna_predict
needs to be installed as well as the Sphinx Python package.
To build the docs run:
python setup.py build_sphinx
After that, the HTML output can be found in build/sphinx/html.