$ make
to compile the source and obtain the executable "rintc". I succeed to compile them in the following environment:
gcc/7.2.0 on CentOS Linux release 7.5.1804 .
then,
$ ./rintc <rna> <str> <W> <algo>
where
rna: RNA sequence in upper case, e.g. CCCCAAAAGGGG
str: RNA structure enclosed in quotes, e.g. "((((....))))"
W: maximum-span constraint, e.g. 12
algo: name of the algorithm, e.g. RintCwithDFT
For other algos and replicating the experiments, see main.cpp.
example:
./rintc CCCCAAAAGGGG "((((....))))" 12 RintCwithDFT
For reproduce the experiments perfomed in the paper, use the commands below:
$ ./rintc <ComputationTimeExperimentW100>
$ ./rintc <ComputationTimeExperimentWN>
$ ./rintc <HeatResistanceExperiment>
$ ./rintc <AccuracyExperiment151>
$ ./rintc <RrnaAccuracyExperiment>