Final version of Bfactor incorporation.

gemme.py

@@ -76,9 +76,11 @@ def calcPercentDFI(pdbfile, outfile, nmodes=None, attenuate="true", ranksorted="
     else:
         return dfi
 
-def calcBfactors(pdbfile, outfile, nmodes=None, attenuate="true", ranksorted="true"):
+def calcBfactors(pdbfile, outfile, nmodes=None, attenuate="true", 
+                ranksorted="true", inverted=False):
     """
-        Calculate rank normalized dynamic flexibility index. 
+        Calculate rank normalized mean squared fluctuations,
+        which correlate well with Bfactors. 
     """
     
     #confProDy(auto_show=False)
@@ -106,9 +108,15 @@ def calcBfactors(pdbfile, outfile, nmodes=None, attenuate="true", ranksorted="tr
     #     np.savetxt(outfile, dfi)
 
     if(ranksorted.lower()=='true'):
-        return percentBfactors
+        if(inverted==True):
+            return (1.0 - percentBfactors)
+        else:
+            return percentBfactors
     else:
-        return bfactors
+        if(inverted==True):
+            return (np.max(bfactors) - bfactors)
+        else:
+            return bfactors
 
 def getBfactors(pdbfile, outfile, nmodes=None, attenuate="true", ranksorted="true"):
     """
@@ -552,11 +560,13 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
         if (pdbfile == None):
             print("ERROR: There is not any pdb file to calculate or get Bfactors!")
             sys.exit(-1)
-        else:
-            print("Calculating or getting Bfactor data per residue!")
+        else:        
             if (isCalc):
-                bfactors = calcBfactors(pdbfile, outfile=None, nmodes=None, attenuate="true", ranksorted="true")
+                print("Computing Bfactors from the user-provided pdb file using ANM with all modes.")
+                bfactors = calcBfactors(pdbfile, outfile=None, nmodes=None, \
+                            attenuate="true", ranksorted="true", inverted=False)
             else:
+                print("Getting Bfactors from the user-provided pdb file.")
                 bfactors = getBfactors(pdbfile, outfile=None, nmodes=None, attenuate="true", ranksorted="true")
 
             bfactors = bfactors