Increased number of sequences that are perceived by GEMME. Added SC1, SC2,

SC3 calculation options to JET2 calls.

Changed N=20000 to N=40000. Increased CPU load to 2000000 in default.config
file. Finally, modified jetcmd in gemmeAnal.py file so that we can calculate
SC1, SC2 and SC3.

default.conf

@@ -20,7 +20,7 @@ url		http://www.rcsb.org/pdb/downloadFile.do		URL of PDB server
 >Filter
 min_identity	0.20						min sequence identity
 max_identity	0.98						max sequence identity
-
+max_load        2000000                     			max CPU load
 *****************************************
 >Sample
 length_cutoff	0.8						minimum sequence length expressed in number of residues	

gemme.py

@@ -417,7 +417,7 @@ def parse_command_line():
     retMet_args.add_argument(
         '-N', '--NSeqs',
         help='maximum number of sequences to compute the conservation levels',
-        default='20000'
+        default='40000'
     )
         
     retMet_args.add_argument(

gemmeAnal.py

@@ -126,18 +126,22 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	subprocess.call("cp $GEMME_PATH/default.conf .",shell=True)
 	if retMet=="input":
 		if bFile!='':
+			#TODO: I think these two lines must be here as well but I am not sure. 
+			# print(N)
+			# editConfJET(N)
+
 			if(bFile == prot+"_"+chainID+".psiblast"):
 				shutil.copy2(bFile, bFile+".orig")
 				shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast")
 			else:
 				shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
 			if(pdbfile == None):
-				jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 						prot+".pdb -o `pwd` -p J -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
 			else:
-				# jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 				#  		prot+".pdb -o `pwd` -p AVJ   -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
-				jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 					    prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".psiblast -d chain -n "+n+" -a 5"+" > "+prot+".out"
 						#One can also add: -g 'trace,pc,cv,clusters,axs' 
 
@@ -157,22 +161,22 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 			print("\nRunning:\n"+grpcmd)
 			subprocess.call(grpcmd,shell=True)
 			if(pdbfile == None):
-				jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 				     	prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
 			else:
-				# jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 				#      	prot+".pdb -o `pwd` -p AVJ -r input   -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
-				jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+				jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 					    prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 5"+" > "+prot+".out"
 						#One can also add: -g 'trace,pc,cv,clusters,axs' 
 	else:
 		if(pdbfile == None):
-			jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+			jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 			    	prot+".pdb -o `pwd` -p J -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
 		else:
-			# jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+			# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
 			#     	prot+".pdb -o `pwd` -p AVJ   -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
-			jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
+			jetcmd = "java -Xmx2048m -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"
 	print("\nRunning:\n"+jetcmd)
 	reCode=subprocess.call(jetcmd,shell=True)