Implementation of the Ant Colony Optimization meta-heuristic for the Protein Structure Prediction problem using 2D HP model. This approach includes the pull move heuristic for local search.
- gcc
To compile, execute each one of the following commands from the root of the project:
gcc -Wall -O2 -c ./file.c -o ./file.o
gcc -Wall -O2 -c ./main.c -o ./main.o
gcc -Wall -O2 -c ./aco.c -o ./aco.o
gcc -o ./aco-2dhp ./file.o ./main.o ./aco.o -lm -s
After compiling it, you can run the aco-2dhp binary by executing the following command from the root of the project.
./aco-2dhp input sequence8
You can open the input file, located at the root of the project, in a text editor to change the parameters and see other sequences available.
The output will be printed following the template bellow
iterations|protein|directions|energy|final population average|final population standard deviation|convergence|found on iteration|time|iteration,energy/.../iteration,energy/
The script.sh script can be used to run the aco-2dhp binary for all the 8 sequences avaiable in the input file. The script will generate latex tables for all the results obtained. The script will also plot figures representing the best resultant conformation of each protein, as long the 2dhp-plot binary is avaiable in the root of the project (The 2dhp-plot binary avaiable in the root of the project was compiled in a linux x64. To compile a new 2dhp-plot binary, check out this other repository: https://github.com/douglas444/2dhp-plot )
To run the script.sh script, execute the following commands from the root of the project
chmod +x ./script.sh
./script.sh
The results are going to be generated as follows:
./results/outputlog
./results/summary
./results/figures/sequence[1..8]
./results/tables/sequence[1..8]
./results/energy_evolution/sequence[1..8]/run[1..20]
To generate pdf/png from the latex files, execute the following command, changing filename to the path to the latex file that you want to convert to pdf/png
pdflatex --shell-escape filename