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
@@ -18,4 +19,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.
\ No newline at end of file

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()
+