Installation

RSIM is a C++ library for building RNA tertiary structures from a given set of secondary structure constraints. It has been successfully compiled and run on Linux and Mac OSX operating systems. The RSIM code can be downloaded and built using the following commands.

1. Install git

2. Install the boost C++ library

3. Clone the RSIM git repository

    >cd /path_to_project
    >git clone git://github.com/jpbida/RSIM.git
   

   This should create a directory RSIM in the path_to_project director with the RSIM library in it. If you are having trouble at this point check the github documentation for downloading public repositories.

4. If you did not install boost in /usr/include/boost edit the makefiles to point to the boost library

    /path_to_project/rsim/src/makefile
    /path_to_project/rsim/apps/makefile
    
    Change the lines below to point to your boost installation
    
    CPPFLAGS= -O3 -ffast-math -I /usr/include/boost
    CPPFLAGS= -O3 -ffast-math -I /usr/include/boost -I ../src
   

5. Compile the applications by changing into the apps directory and using make.

    cd RSIM/apps
    make all
   

This will create a set of binary files in the /bin directory. A examples for each of the binaries are stored in the tests directory and can be used as a starting point for figuring out how to use the RSIM programs.