LICENSE
MANIFEST.in
README
README.md
VERSION.md
hotknots.py
setup.py
./src/Bands.cpp
./src/Input.cpp
./src/Loop.cpp
./src/LoopList.cpp
./src/Stack.cpp
./src/common.cpp
./src/commonPK.cpp
./src/goodStem.cpp
./src/hotspot.cpp
./src/init.cpp
./src/initPK.cpp
./src/params.cpp
./src/paramsPK.cpp
./src/python.cpp
./src/s_energy_matrix.cpp
./src/s_hairpin_loop.cpp
./src/s_internal_loop.cpp
./src/s_min_folding.cpp
./src/s_multi_loop.cpp
./src/s_multi_loop_sub.cpp
./src/s_partition_function.cpp
./src/s_specific_functions.cpp
./src/s_stacked_pair.cpp
./src/s_sub_folding.cpp
./src/sc.cpp
./src/score.cpp
./src/temp.cpp
./src/timer.cpp
./src/utils.cpp
hotknots/CG_best_parameters_ISMB2007.txt
hotknots/__init__.py
hotknots/coaxial.dat
hotknots/coaxstack.dat
hotknots/mathews-asint1x2-dna.dat
hotknots/mathews-asint1x2-dna.dh
hotknots/mathews-dangle-dna.dat
hotknots/mathews-dangle-dna.dh
hotknots/mathews-loop-dna.dat
hotknots/mathews-loop-dna.dh
hotknots/mathews-miscloop-dna.dat
hotknots/mathews-miscloop-dna.dh
hotknots/mathews-sint2-dna.dat
hotknots/mathews-sint2-dna.dh
hotknots/mathews-sint4-dna.dat
hotknots/mathews-sint4-dna.dh
hotknots/mathews-stack-dna.dat
hotknots/mathews-stack-dna.dh
hotknots/mathews-tloop-dna.dat
hotknots/mathews-tloop-dna.dh
hotknots/mathews-triloop-dna.dat
hotknots/mathews-triloop-dna.dh
hotknots/mathews-tstackh-dna.dat
hotknots/mathews-tstackh-dna.dh
hotknots/mathews-tstacki-dna.dat
hotknots/mathews-tstacki-dna.dh
hotknots/multirnafold.conf
hotknots/parameters_CC06.txt
hotknots/parameters_CC09.txt
hotknots/parameters_DP03.txt
hotknots/parameters_DP09.txt
hotknots/pkenergy.conf
hotknots/pkmodelCC2006.dat
hotknots/pkmodelDP.dat
hotknots/pkmodelRE.dat
hotknots/tstackcoax.dat
hotknots/turner-asint1x2-rna.dat
hotknots/turner-asint1x2-rna.dg
hotknots/turner-asint1x2-rna.dh
hotknots/turner-dangle-rna.dat
hotknots/turner-dangle-rna.dg
hotknots/turner-dangle-rna.dh
hotknots/turner-loop-rna.dat
hotknots/turner-loop-rna.dg
hotknots/turner-loop-rna.dh
hotknots/turner-miscloop-rna.dat
hotknots/turner-miscloop-rna.dg
hotknots/turner-miscloop-rna.dh
hotknots/turner-sint2-rna.dat
hotknots/turner-sint2-rna.dg
hotknots/turner-sint2-rna.dh
hotknots/turner-sint4-rna.dat
hotknots/turner-sint4-rna.dg
hotknots/turner-sint4-rna.dh
hotknots/turner-stack-rna.dat
hotknots/turner-stack-rna.dg
hotknots/turner-stack-rna.dh
hotknots/turner-tloop-rna.dat
hotknots/turner-tloop-rna.dg
hotknots/turner-tloop-rna.dh
hotknots/turner-triloop-rna.dat
hotknots/turner-triloop-rna.dg
hotknots/turner-triloop-rna.dh
hotknots/turner-tstackh-rna.dat
hotknots/turner-tstackh-rna.dg
hotknots/turner-tstackh-rna.dh
hotknots/turner-tstacki-rna.dat
hotknots/turner-tstacki-rna.dg
hotknots/turner-tstacki-rna.dh
hotknots/turner_parameters_fm363_constrdangles.txt
hotknots/turner_partypes_fm363.txt
hotknots/walter-coaxstack-rna.dat
hotknots.egg-info/PKG-INFO
hotknots.egg-info/SOURCES.txt
hotknots.egg-info/dependency_links.txt
hotknots.egg-info/top_level.txt
include/Bands.h
include/Defines.h
include/HotKnotEnergy.h
include/Input.h
include/Loop.h
include/LoopList.h
include/Stack.h
include/common.h
include/commonPK.h
include/constants.h
include/constantsPK.h
include/externs.h
include/externsPK.h
include/globals.h
include/globalsPK.h
include/goodStem.h
include/hotspot.h
include/init.h
include/initPK.h
include/params.h
include/paramsPK.h
include/s_energy_matrix.h
include/s_hairpin_loop.h
include/s_internal_loop.h
include/s_min_folding.h
include/s_multi_loop.h
include/s_multi_loop_sub.h
include/s_partition_function.h
include/s_partition_function_complex.h
include/s_specific_functions.h
include/s_stacked_pair.h
include/s_sub_folding.h
include/sc.h
include/score.h
include/simfold.h
include/structs.h
include/structsPK.h
include/timer.h
include/utils.h
params/CG_best_parameters_ISMB2007.txt
params/coaxial.dat
params/coaxstack.dat
params/mathews-asint1x2-dna.dat
params/mathews-asint1x2-dna.dh
params/mathews-dangle-dna.dat
params/mathews-dangle-dna.dh
params/mathews-loop-dna.dat
params/mathews-loop-dna.dh
params/mathews-miscloop-dna.dat
params/mathews-miscloop-dna.dh
params/mathews-sint2-dna.dat
params/mathews-sint2-dna.dh
params/mathews-sint4-dna.dat
params/mathews-sint4-dna.dh
params/mathews-stack-dna.dat
params/mathews-stack-dna.dh
params/mathews-tloop-dna.dat
params/mathews-tloop-dna.dh
params/mathews-triloop-dna.dat
params/mathews-triloop-dna.dh
params/mathews-tstackh-dna.dat
params/mathews-tstackh-dna.dh
params/mathews-tstacki-dna.dat
params/mathews-tstacki-dna.dh
params/multirnafold.conf
params/multirnafold.conf~
params/parameters_CC06.txt
params/parameters_CC09.txt
params/parameters_DP03.txt
params/parameters_DP09.txt
params/pkenergy.conf
params/pkmodelCC2006.dat
params/pkmodelDP.dat
params/pkmodelRE.dat
params/tstackcoax.dat
params/turner-asint1x2-rna.dat
params/turner-asint1x2-rna.dg
params/turner-asint1x2-rna.dh
params/turner-dangle-rna.dat
params/turner-dangle-rna.dg
params/turner-dangle-rna.dh
params/turner-loop-rna.dat
params/turner-loop-rna.dg
params/turner-loop-rna.dh
params/turner-miscloop-rna.dat
params/turner-miscloop-rna.dg
params/turner-miscloop-rna.dh
params/turner-sint2-rna.dat
params/turner-sint2-rna.dg
params/turner-sint2-rna.dh
params/turner-sint4-rna.dat
params/turner-sint4-rna.dg
params/turner-sint4-rna.dh
params/turner-stack-rna.dat
params/turner-stack-rna.dg
params/turner-stack-rna.dh
params/turner-tloop-rna.dat
params/turner-tloop-rna.dg
params/turner-tloop-rna.dh
params/turner-triloop-rna.dat
params/turner-triloop-rna.dg
params/turner-triloop-rna.dh
params/turner-tstackh-rna.dat
params/turner-tstackh-rna.dg
params/turner-tstackh-rna.dh
params/turner-tstacki-rna.dat
params/turner-tstacki-rna.dg
params/turner-tstacki-rna.dh
params/turner_parameters_fm363_constrdangles.txt
params/turner_partypes_fm363.txt
params/walter-coaxstack-rna.dat
test/NC_000866.fna
test/NC_001416.fna
test/NC_003291.fna
test/phiX174.fna