DSGA and GA from 'Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding '

Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding Instructions

Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding is a Java application written in Java version 1.7, but it should run on other versions of Java.

There are 10 command line parameters that should be set:

• # position 1 - population size
• # position 2 - number of generations
• # position 3 - mutation rate (decimal)
• # position 4 - initial radius (decimal)
• # position 5 - radius delta (decimal)
• # position 6 - reevaluation loop count
• # position 7 - convergence limit
• # position 8 - protein
• # position 9 - output file location
• # position 10 - log status 0 few logs; 1 more logs; 2 most logs

An output file will be placed in the file location for position 9. 

Here is an example for running the application:

java -jar /Users/mbrown15/NetBeansProjects/DSGAProteinFolding/dist/DSGAProteinFoldingKG.jar 1000 2000 0.03 8.0 -1.0 500 4 PPHPPHHPPHHPPPPPHHHHHHHHHHPPPPPPHHPPHHPPHPPHHHHH //Users//mbrown15//Documents//genetic-algorithm-files// 1

This method allows multiple runs to be placed in a batch file. 

The class called TestAllCombinationsSample will generate a file for Figure 2. 

The file GAProteinFoldingDD has the code for the traditional Genetic Algorithm.