This is a CPU implementation of ring closure written in 2007, it implements the quadratic combination of half chains with a bin (bucket) search that reduces most jobs to O(N) for sampling N^2 total chains.
The installation via command-line on UNIX-like systems (Linux, OS X) with g++:
cd src
make
The program is installed in the bin folder
The script in the examples folder will run a simulation with the "generic" sequence in the file seq, with the FGH.dat elastic parameters and tp0.dat intrinsic step parameters and output pictures of chains. The protein simulated in the model is based on Nhp6A from yeast.
The program DNAServer presents a web application frontend to these simulation programs for visualizing the resulting graphs and data and will automate running the command-line. However, each program in bin will output a help screen describing the parameters to each command-line executable and the example folder has sample input files.