Tarball of Boltzmann source code

The main algorithm is coded in the file expNumNborTurner.c. The latter is only called 'simple', since I did not yet implement the function ARC(alpha,i,j) described in the paper, which is a precomputation of the number of neighbors due to the addition of a base pair in a loop region. When implemented, the code will be faster, but this will not change numerical values. This code relies on source code, such as energy_par.c from the Vienna RNA Package, in order to access energy terms for stacked base pairs and loops.

C-executables for CentOS Linux, release 5.10

Python code

This code includes a prototype for the C-implementation, in the uniform probability case, drivers for testing, wrapper to enumerate all structures, etc. and subsequently determine the expected number of neighbors by exhaustion. This code requires wrappers to access Vienna RNA Package, given in the section after this section.

Wrappers related to Vienna RNA Package