---------------------------------------------------------------------------------------- Instructions: ---------------------------------------------------------------------------------------- Java runtime environment (jre) version 6 or higher should be installed in your computer ---------------------------------------------------------------------------------------- The RGA.jar, EGA.jar, MGA.jar, WGA.jar and GAPlus.jar are the executables for the genetic algorithms variants. a) With no parameter - runs with default values b) With parameters - the.jar files take 6 parameters (5 mandatory and 1 optional). To run this variants the following instructions need to be followed: =============================================================================================== ********** Always ignore the angular braces (<>) ************************ =============================================================================================== For Windows command prompt, you need to run the executable (.jar) as: ----------------------------------------------------------------------------------- 1. java -jar "\GAPlus.jar" "" "" "" 2. Example: Download the .jar in Downloads folder, cd C:\Downloads java -jar "GAPlus.jar" "H1" "HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH" 100 300 101 "." java -jar "GAPlus.jar" "H1" "HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH" 100 300 101 "." -69 3. If sixth value is mentioned (-69) and if the program get the value, it will terminate immediately without completing 300 seconds. 4. It will generate two output files in C:\Downloads\output\ - GAP_H1_101_EnXXX_xyz.txt and GAP_H1_101_EnXXX_data.cml For Linux command prompt, you need to run the executable (.jar) as: ----------------------------------------------------------------------------------- 1. java -jar "/GAPlus.jar" "" "" "" 2. Example: Download the .jar in Downloads folder, cd Downloads java -jar "GAPlus.jar" "H1" "HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH" 100 300 101 "." java -jar "GAPlus.jar" "H1" "HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH" 100 300 101 "." -69 3. If sixth value is mentioned (-69) and if the program achieve the value, it will terminate immediately without completing 300 seconds. 4. It will generate two output files in Downloads/output/ - GAP_H1_101_EnXXX_xyz.txt and GAP_H1_101_EnXXX_data.cml View the structures in Jmol (http://jmol.sourceforge.net/): 1. Run Viewer.jar by double clicking on it: 2. Choose a .cml file (GAP_H1_data.cml) by clicking the "Open File" button 3. Hit on "Show Structure @Jmol" button =============================================================================================== ********** Benchmark sequences ************************ =============================================================================================== //Harvard (H) Instances ==================================================================== H1=HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH H2=HHHHPHHPHHHHHPPHPPHHPPHPPPPPPHPPHPPPHPPHHPPHHHPH H3=PHPHHPHHHHHHPPHPHPPHPHHPHPHPPPHPPHHPPHHPPHPHPPHP H4=PHPHHPPHPHHHPPHHPHHPPPHHHHHPPHPHHPHPHPPPPHPPHPHP H5=PPHPPPHPHHHHPPHHHHPHHPHHHPPHPHPHPPHPPPPPPHHPHHPH H6=HHHPPPHHPHPHHPHHPHHPHPPPPPPPHPHPPHPPPHPPHHHHHHPH H7=PHPPPPHPHHHPHPHHHHPHHPHHPPPHPHPPPHHHPPHHPPHHPPPH H8=PHHPHHHPHHHHPPHHHPPPPPPHPHHPPHHPHPPPHHPHPHPHHPPP H9=PHPHPPPPHPHPHPPHPHHHHHHPPHHHPHPPHPHHPPHPHHHPPPPH H10=PHHPPPPPPHHPPPHHHPHPPHPHHPPHPPHPPHHPPHHHHHHHPPHH S Instances: ==================================================================== S1=HHHHPHHHHHHPPHHPHHHHHHHHPHHPHHHHHHHHHHPPHHPPPPPHHPHHHHHHHHPHPPHHPPPHHHHHHHHPHHHHHHPPHHHHHHHPHPPHHHHHHHHHPPHHPPPHHHHHHHPHHPHHHHHHHPPHHHH S2=HHPPHPHHHHHHHHHHPHPPPPHHHPPPHHHHHPPHHHHHPPHHHHPPHHHHPPHHHHHHPHHHHPPPHHPPPHHHHHHHHPHPPHHHPPPHHHHHPPHHHHHHHPPPHHPPHHHHHPPPHHHHHHHHHPHPPHHHHHHHPPPHHHPPHHP S3=HHHPPPHHPHHPPPPPHHHHHHHHPHPPHHPHHPHHHHHPPPHHHHHHHHHPPHPHPPHPHPPHHHPHPPHPHPPPHHHHHHPHHHHPPPHHHPPPPHHPPPHHHPPHHHHPHHHHHPPHHHHHHPPPHHHHHHPPPHPPHHHHPHHHHHHHPPHHPPHHH S4=HHPPHPHHHHHHHPPHPHPPHPHPPPPHHHPPPHHPHPHHPPHHHHHPPHHHHPPHHHHPPHHHHHHPHHHHPPPHHPPPHHHHHHHHPHPPHHHPPPHHHHHPPHHHHHHPHPPPHHPPHHHPHHPPPHPHHHHHHHPHPPHPPHHHHHHPHPPPHHHPPHHP R Instances: ==================================================================== R1=PPPHPHHPHHPPPHPHPPPPHPHHPPHPHHHHHPPHHPPHHHHHHPPHPPHHPPHPHPHHHHHPHHPHHHPPPHHHPHHPPHPHPPHPPPHPPHPPHPPHHHPHHHPHPPHPHHPHHHHPHPHHHPHHHPPPPPPHHHHHHPPPPPPPPHHHPPHPHPPPHPHPHPHHPPHHPPPPHHHHHHPPPHHPPPPPHPPPHHPP R2=HPHHPPHPPPPPHHPHPHPHHPPHPPPPHHHHHHPPPHPPHHHPPHPPPPHHPPHHHPHPHHHPPHPHHPPHPHHPPPPHHPPHPPHHHHPPPPPHHHPPPPHPPPPPPHPPHHPHHHHPHHHHHHHHPPHHPPPHPHHHPHHHHHPHHPHHHPHPHHPPPPHPHHPHHHPHPPPPHPPPPPPHPHHHHHPHHPPPHPPH R3=HPHHHPHHPHPHPPPHHHHHPHPHPHHHHPPPHHPPPPPPHHPPPPHPHHHPPPPHPPPHHPHHPPPHPPHPPPHHHHPHHPHPPPPHHPPPHHPPHPPPHPPHHHPHHHPHPPHPHHHHPPHHPPPPHHHPHHPPHPPHHHHPPHPHPPHPHPPPPPHPHPHHHHHHHPHPHHHHHHPHHPPPPHPPPPHPPPHHHPHH F90 Instances: ==================================================================== F90_1=PPHHHPPPHHPPPPHHPHHHHHHPHPHPHHPHHHHHPHHHPHPHHHHPHHPPPPHHHPHPHPPHHHPHHPHPHPPHHHPPPPHHPPHPPP F90_2=PHHPPHPHHPHHHPHHHPPHHHHHHPPHPHPPPPHHHPHPPHHHHPHHHHPHHHPHHPPPPPHHPPPPHPHPHPHPHHPPHHHPPPHHHP F90_3=HPHPHHHPHHHHPHHHPPPHPPPHPPPPHHHPPHPPPPHHHPPPPPPPPHPHHPHHHHPHHHPHPHHPPHHHHHPHHPPHHPHHHHHHPH F90_4=PHHHPPHPPHPHPPPPHPPPHPHPPHPHHPHPPPHHHPHHHPPHHHPPHPPPPHPHHHPPHHPPHHHPPHHHHHHPHHHHHHHPHHHHPH F90_5=PPPHPHHHHHHHPPPHPPHHHHHPHHPPHHPPHHHHPHPHPHHPPHHPPPPHPPPHHHPHPHHHHHHHPHHPHPPHHPPPHHHPHPPHPP F180 Instances: ==================================================================== F180_1=HHPPHHHHHPHHHPPPHHHPPHHHPHPPHHHHHPPPHHHPPPHPHHPPPPPHHPPHHPHHPHPHHPPPPPHHHPPPPHPHHHPPHPPPHHHPHHHHPPHHPHPHHHHPHHHHPPHHPHHPHHPHHHPHPPHPHHPHPHHPHHHPHHPPHPPPHPPPPPPPHHHPHHHHHPHHHHHPPHPP F180_2=PHHPHPPPHPPHHPHHHPHPHHPHHHPHHHPPPHHPPHPHPHHPHHHHPPHHPHPHHHHHPHHPPPPHPHPHPPHHHHPHHHHPHHHHHPPHPHHHPPPHPHPPHHPPPHHPHPHPPPPPHPHHPHHHPHPPPPHHPHHHHHPPPHHHHHHHHPHHPPPPPHPPPHPPHPPPHHPHHHHH F180_3=HHHPHPPHHPPPHPPPHPHPHPPHHHHPPHHHHHHPHPHHPPPPPHPPHHPHHHHHHHHHHHPPHPPHPPHHHHHHHHPPPPHPPHHHHHPPHHHPPHHPPHHHHHPPPHHHHHHPHHHPPPHHPPHPPPHPPHPPPHPPPPHHHPPHHPHPPHHHPHHPPHHPHHPHPHPHPHPHPHHP CASP Instances: ==================================================================== 3mse=HPHPHHPPHPPHHPPPPHPPHHHPHHHPPHPHHPPPHPHHPPHHHPHPPPPPHPHPPPPHHPHHHPHHHPPHPHPPHHPHHPHPPPHPHPHPPHHHHPHPHPPHPPPHHPHHHPPHPPPPPHHHPPPPHHPHHPPPHHPPPPHPPHHHPHPPHPPHHHPPPHHPPHPHPPHPPHHHPPH 3mr7=PPHPPPHPHHHHHPHHHHPPHHPPPPPPHHPPPPHHPPPHHPHHHHPHHHPHHPPPHPHHHHPHPPHPHHHPPHHPHPPHHPPPPPPPHPPPPHPHPHHHPHHPHHHPPHPHHHPHHPHHHPHPHHPPHHHHPHPPHHPPHPPPPHPPHHPPHHHPPHPPHPPHHPHHPHHHPHPPPPPPPHPHPPHPP 3mqz=PPHHPHPPHPPHPPHHHHPHHPHHPHHPHPHPHHPHPHPHPHHHHPHHPPHHPHHPPPHHHPHHHHPHHPPHPPPHPHHHPPHHHHHHPPPHHPPHHPPHHHHHHPHHPHPHHHPPPHHPPPPPHHPHHPPPHHHHPPHPPPHHPHPPHHHHPPPHHHPHHPHPHPHPHHHPPHHPHPPHPHPHHHPHPHPPPHHHHHPPHPPHPHHHHPHPPHP 3no6=HPHPPPHPPHPPHHHPPHHPPHHHPPHHHHPHPPPHHPPHHPHPHPHHPPHPPHHHHHHHPHPPHPPHPHHHPPHPHHHPHPHPHPPHHHPHHPPHHPPHHPPPHHHHPHPPHHPPHHHPHHHPPPHHHPHHHHHHPHHHHHHHHPPHHPPHPHPPPPHPPPHHPHHPPPHPPHHPHHPPHHPPHPPPPPPPPPPPHPPPHHPPPHPPPPHHPHHHHPPPHPHHHPPPP 3no3=HPHPPPHHHHHPHHHHHHHHHPPPPPHHHPPHHHPPPHPHPPPHPPHPPHPPHHHHHPPHPHPHPHPPHHHHHPPPPHPHPPHPPPPHPPHPPHPHPPHPPHHPHPPHHPPHPPHPPHPHHHPHPPPPPHPPPPPHHPHPHPHHPPHPHHPPPPHHPHPHPHPPPHHPHPHPPPHPHHPHPHPHHPHPPHHHPHHPHPHPHHPPPHPHHPPPPHHHHPPPHHPHPPHPHHPPHHPHHHPHHPPPHHPPPPPHHPPPHP 3on7=HPHPPHPHPHHPPHPPHHPPHPPPHHHHHPPPHHPPPHHPPHHPPHPHHHPPPHPPPHHHPPPPPPHHHHHPHPPPHPHPPHPPHPPHHPHHHHHPHHPPHPHPHHHHHPPHPPHHPPHHPHHPPHPHPPHPHPHPHHHHPHHHPPPPPHHPHHPHHHHPHPPPHHHHPHHHPPPHPHHPHHHPHPPHHHPHPHPPHPHHPHHPPHHPHHHPHHPHHPPHPPHHHHPPPPPHHPHPHPPPPPPPHPHHHHHPHPHPHHHPPPHPHPPHHHPPHPPHHHH Instances used in the Memetic Algorithm: ==================================================================== B1=HPHPPHHPHHPHPHHPHHPH B2=HHPPHPPHPPHPPHPPHPPHPPHH B3=PPHPPHHPPPPHHPPPPHHPPPPHH B4=PPPHHPPHHPPPPPHHHHHHHPPHHPPPPHHPPHPP B5=PPHPPHHPPHHPPPPPHHHHHHHHHHPPPPPPHHPPHHPPHPPHHHHH B6=HHPHPHPHPHHHHPHHHPHHHPHPPPPHHHPHHHPHPHHHHPHPHPHPHH B7=HHPHPHPHPHHHHPHHHPHHHPHPPPPHHHPHHHPHPHHHHPHPHPHPHH B8=HHHHHHHHHHHHPHPHPPHHPPHHPPHPPHHPPHHPPHPPHHPPHHPPHPHPHHHHHHHHHHHH B9=HHHHPPPPHHHHHHHHHHHHPPPPPPHHHHHHHHHHHHPPPHHHHHHHHHHHHPPPHHHHHHHHHHHHPPPHPPHHPPHHPPHPH B10=PPPPPPHPHHPPPPPHHHPHHHHHPHHPPPPHHPPHHPHHHHHPHHHHHHHHHHPHHPHHHHHHHPPPPPPPPPPPHHHHHHHPPHPHHHPPPPPPHPHH B11=PPPHHPPHHHHPPHHHPHHPHHPHHHHPPPPPPPPHHHHHHPPHHHHHHPPPPPPPPPHPHHPPPPPPPPPPPHPPHHHPHHPHPPHPHHHPPPPPPHHH