hermes
All your kinetics are belong to us.
Name Role
-------- ----
FFTbor2D (2D energy landscape parameterized by bp. distance from two input structures for given sequence)
RNAmfpt (Mean first passage time [hitting time] for input matrix in CSV (i, j, x) format)
RNAeq (Population proportion and equilibrium for suboptimal structures of given RNA using spectral decomposition)
FFTmfpt ([--fftbor2d --mfpt] Approximate mean first passage time [hitting time] using 2D energy landscape from FFTbor2D)
FFTeq ([--fftbor2d --mfpt --population] Approximate population proportion and equilibrium using 2D energy landscape from FFTbor2D)
RateEq ([--mfpt --population] Population proportion and equilibrium using row-ordered rate matrix in CSV (i, j, x) format)
Dependencies:
- CMake >= 2.6-patch 4, tested through 3.0.0
- GNU99 compiler, developed with gcc-4.9
- C++98 compiler supporting OpenMP, developed with g++-4.9
- GSL <= 1.15, tested through 1.16
- FFTW3 >= 3.3.3, tested through 3.3.4
- libRNA.a >= 2.0.7, tested through 2.1.7
Installation:
cd build && cmake .. && make
Useful CMake configuration flags:
-DCMAKE_C_COMPILER=/path/to/c/compiler
-DCMAKE_CXX_COMPILER=/path/to/c++/compiler
-DCMAKE_INCLUDE_PATH=~/additional/headers
-DCMAKE_LIBRARY_PATH="~/additional/libraries;/separated/by/semicolons;/and/quoted"
-DCMAKE_INSTALL_PREFIX=/make/install/path/prefix
Note--this project uses the following commands to maintain homogenous styling:
astyle --style=google --indent=spaces=2 --indent-switches --indent-cases --indent-namespaces --indent-labels --indent-col1-comments --break-blocks --pad-oper --pad-header --unpad-paren --fill-empty-lines --align-pointer=type --add-brackets --convert-tabs --recursive *.cpp *.c *.h