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RNA structure prediction program

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README
RSIMS - Is an RNA structure prediction and design C++ library

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. 
      If the directory ./path_to_project/RSIM/bin doesn't exist you need to create it.

      cd RSIM/src
      make all
      cd RSIM/apps
      make all

      This will create a set of binary files in the /bin directory.
   

   6. 
      Then check out the examples in ./examples


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