some more whitespace cleanup

tools/replica/example/parse_ene.py

@@ -15,16 +15,16 @@ for i in range(ntemps):
     logfn = '%s.%d' % (logfnprefix, i)
     with open(logfn, 'r') as of:
         lines = of.readlines()
-    
+
     # extract relevant lines from logfile
     start = [lines.index(line) for line in lines if line.startswith(start_token)][0]
     lines = lines[(start+1) : ]
     stop = [lines.index(line) for line in lines if line.startswith(end_token)][0]
     lines = lines[:stop]
-    
+
     # store the potential energies
     pe = [float(line.strip().split()[-1]) for line in lines]
     u_kn.append(pe)
-    
+
 u_kn = np.array(u_kn)
 np.savetxt('ene.peptide', u_kn, fmt = '%5.5f')

tools/replica/reorder_remd_traj.py

@@ -351,7 +351,7 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
     u_kln = np.zeros([ntemps, ntemps, nframes], float)
     for k in range(ntemps):
         u_kln[k] = np.outer(beta_k, u_kn[k])
-        
+
     # run pymbar and extract the free energies
     print("\nRunning pymbar...")
     mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True)
@@ -368,7 +368,7 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
             denom = f_k - beta_k[k] * u_kn[k,n]
             for l in range(ntemps):
                 logw[l][k,n] = num - logsumexp(denom) - log_nframes
-            
+
     return logw
 
 
@@ -518,7 +518,7 @@ if __name__ == "__main__":
 
     # open all replica files for reading
     infobjs = [readwrite(i, "rb") for i in intrajfns]
-    
+
     # open all byteindex files
     byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) )