Moved the main function under if(__name__) block in sgemme.py.

LICENSE.txt

 MIT License
 
 Copyright (c) 2018: Elodie Laine, Yasaman Karami and Alessandra Carbone.
+Copyright (c) 2022-2023: Mustafa Tekpinar and Alessandra Carbone.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

gemmeAnal.py

@@ -357,6 +357,18 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 			#     	prot+".pdb -o `pwd` -p AVJ   -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
 			jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 					prot+".pdb -o `pwd` -p AVJCG -r "+retMet+" -d chain -n "+n+" -a 5"+" > "+prot+".out"
+		
+		reCode=subprocess.call(jetcmd,shell=True)
+		if os.path.isfile(prot+"/"+prot+"_jet.res"):
+			os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
+		
+		dir_name = prot+"/"
+		if os.path.isdir(dir_name):
+			for f in os.listdir(dir_name): 
+				f_path = os.path.join(dir_name, f)
+				if os.path.isfile(f_path):
+					os.remove(f_path)
+			os.rmdir(dir_name)
 	# print("\nRunning:\n"+jetcmd)
 	# reCode=subprocess.call(jetcmd,shell=True)
 	# if os.path.isfile(prot+"/"+prot+"_jet.res"):

pred.R

 # Copyright (c) 2018: Elodie Laine
-# Copyright (c) 2022: Mustafa Tekpinar
+# Copyright (c) 2022-2023: Mustafa Tekpinar
 # This code is part of the gemme package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.
 

sgemme.py

@@ -657,7 +657,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
             print(df)
         
-    launchPred(prot,inAli,mutFile, normWeightMode, alphabet)
+    launchPred(prot, inAli, mutFile, normWeightMode, alphabet)
 
     #Do Python plotting here
     #TODO: Eventually, I will do the map plotting with a completely independent 
@@ -699,19 +699,16 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
     cleanTheMess(prot,bFile,fFile, chainID=chains[0])
 
-
-def main():
+if (__name__ == '__main__'):
     tic = time.perf_counter()
 
     args = parse_command_line()
-    doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,\
-         args.fastaFile,args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
+    doit(args.input, args.mutations, args.retrievingMethod, args.blastFile,\
+         args.fastaFile, args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
          args.normweightmode, args.alphabet)
 
     toc = time.perf_counter()
     
     print(f"S-GEMME computation finished in {toc - tic:0.4f} seconds!")
     
-if (__name__ == '__main__'):
-    main()