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Commit 9fa8780f by Mustafa Tekpinar
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Changed java memory from 4096 to 8192 for big proteins.

parent 910931e6
Showing with 10 additions and 10 deletions
esgemme.py
...@@ -221,12 +221,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -221,12 +221,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast") shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx8192m -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" prot+".pdb -o `pwd` -p J -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
else: else:
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ # jetcmd = "java -Xmx8192m -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" # prot+".pdb -o `pwd` -p AVJ -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx8192m -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" 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' #One can also add: -g 'trace,pc,cv,clusters,axs'
...@@ -250,7 +250,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -250,7 +250,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
#subprocess.call(grpcmd,shell=True) #subprocess.call(grpcmd,shell=True)
selectMaxFastaSequences(fFile, prot+"_"+chainID+".fasta", maxNumSeqs=(int(N)+1)) selectMaxFastaSequences(fFile, prot+"_"+chainID+".fasta", maxNumSeqs=(int(N)+1))
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx8192m -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" prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
print("\nRunning command:\n"+jetcmd) print("\nRunning command:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True) reCode=subprocess.call(jetcmd,shell=True)
...@@ -258,7 +258,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -258,7 +258,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
else: else:
# Calculate SC1 # Calculate SC1
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx8192m -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 3"+" > "+prot+".out" prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 3"+" > "+prot+".out"
#One can also add: -g 'trace,pc,cv,clusters,axs' #One can also add: -g 'trace,pc,cv,clusters,axs'
...@@ -278,12 +278,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -278,12 +278,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
else: else:
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx8192m -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" prot+".pdb -o `pwd` -p J -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
else: else:
# jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ # jetcmd = "java -Xmx8192m -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" # 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 "+\ jetcmd = "java -Xmx8192m -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" prot+".pdb -o `pwd` -p AVJCG -r "+retMet+" -d chain -n "+n+" -a 5"+" > "+prot+".out"
reCode=subprocess.call(jetcmd,shell=True) reCode=subprocess.call(jetcmd,shell=True)
...@@ -329,8 +329,8 @@ def cleanTheMess(prot,bFile,fFile, chainID): ...@@ -329,8 +329,8 @@ def cleanTheMess(prot,bFile,fFile, chainID):
if fFile!=prot+"_"+chainID+".fasta": if fFile!=prot+"_"+chainID+".fasta":
if os.path.isfile(prot+"_"+chainID+".fasta"): if os.path.isfile(prot+"_"+chainID+".fasta"):
os.remove(prot+"_"+chainID+".fasta") os.remove(prot+"_"+chainID+".fasta")
if os.path.isfile(prot+"_jet.res"): # if os.path.isfile(prot+"_jet.res"):
os.remove(prot+"_jet.res") # os.remove(prot+"_jet.res")
if os.path.isfile(prot+".pdb"): if os.path.isfile(prot+".pdb"):
os.remove(prot+".pdb") os.remove(prot+".pdb")
......
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