Added ssjetormax normalization weight mode.

computePred.R

@@ -253,6 +253,17 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
   for (row in 1:nrow(jet)) {
     trace<-append(trace, jet[row, "bfactor"]) 
   }
+}else if (normWeightMode=="ssjetormax"){
+  print("Using only ssjetormax")
+  for (row in 1:nrow(jet)) {
+    if(sum(colnames(jet)=="ssjetormax")==1){
+      trace<-append(trace, jet[row, "ssjetormax"])
+    }else{
+      print("No field called ssjetormax in the JET output!")
+      quit(status=-1)
+    } 
+  }
+
 }else{
   print("ERROR: Unknown --normWeightMode selected!")
   print("It can only be 'trace', 'tracemovingaverage', 'pc', 'cv', 'dfi', 'bfactor',")

sgemme.py

@@ -235,17 +235,19 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 
 # Run Rscript to compute predictions
 def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
+    SGEMME_DEV_PATH="/home/tekpinar/research/lcqb/SGEMME-dev-ss-based-jetormax"
+    if (mutFile!=''):
+	    rcmd="Rscript --save "+SGEMME_DEV_PATH+"/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
+    
+    #TODO: remember that there is a problem here!!!! 
+    else:
+        rcmd="Rscript --save "+SGEMME_DEV_PATH+"/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
 
-	if mutFile!='':
-		rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
-	else:
-		rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
-
-	print("\nRunning: \n"+rcmd)
-	reCode=subprocess.call(rcmd,shell=True)
+    print("\nRunning: \n"+rcmd)
+    reCode=subprocess.call(rcmd,shell=True)
 
 	#Add plots here with gemmemore
-	return(reCode)
+    return(reCode)
 
 # Remove temporary files
 def cleanTheMess(prot,bFile,fFile, chainID):
@@ -784,6 +786,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
         (normWeightMode != 'maxtracehalftracecvhalfcvpc') and \
         (normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
         (normWeightMode != 'jetormax') and \
+        (normWeightMode != 'ssjetormax') and \
         (normWeightMode != 'tracemovingaverage') and \
         (normWeightMode != 'maxtracehalfpccv')):
         print("ERROR: normWeightMode can only be 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', bfactor,\n"+\
@@ -835,6 +838,39 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
 
             print(df)
+    if((normWeightMode=='ssjetormax')):
+        if (pdbfile == None):
+            print("ERROR: There is not any pdb file to calculate DFI.")
+            sys.exit(-1)
+        else:
+            #proc=subprocess.Popen("python /home/tekpinar/software/scripts/python_scripts/biotite-secondary-structure.py "+pdbfile+" "+pdbfile+".dssp",stdout=subprocess.PIPE,shell=True)
+            os.system("python /home/tekpinar/software/scripts/python_scripts/biotite-secondary-structure.py "+pdbfile+" "+pdbfile+".dssp")
+            os.system("python /home/tekpinar/software/scripts/python_scripts/count-coil-segments-v2.py "+pdbfile+".dssp >"+pdbfile+".dssp.new")
+            df = pd.read_table(prot+"_jet.res", sep="\s+")
+            print(df['pos'])
+            print(pdbfile+".dssp")
+            print(os.getcwd())
+            df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
+
+            df2.columns = ['pos', 'ss', 'length']
+            print(df2)
+            
+            mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
+            print(mergedRes)
+            ssjetormaxList = []
+            maxCoilLength = 5
+            print("WARNING: Max. coil length = {}".format(maxCoilLength))
+            for index, row in mergedRes.iterrows():
+                if(row['ss']=='C') and (row['length']>maxCoilLength):
+                    ssjetormaxList.append(row['trace'])
+                else:
+                    maxVal = max([((row['trace']+row['pc'])/2.0), ((row['trace']+row['cv'])/2.0), ((row['cv']+row['pc'])/2.0)])
+                    ssjetormaxList.append(maxVal)
+            #ssjetormaxList=rankSortProteinData(ssjetormaxList, inverted=False)
+            df['ssjetormax'] = ssjetormaxList
+            df['ssjetormax'] = df['ssjetormax'].round(decimals = 4)
+            df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
+            #sys.exit(-1)
 
     #If a real pdb file is given, calculate dfi for the residues. 
     if(((normWeightMode=='tracemovingaverage'))):