Sync copies of pizza

python/examples/pizza/pdbfile.py

@@ -3,7 +3,7 @@
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software.  This software is distributed under 
+# certain rights in this software.  This software is distributed under
 # the GNU General Public License.
 
 # for python3 compatibility
@@ -25,7 +25,7 @@ p = pdbfile("3CRO",d)       read in single PDB file with snapshot data
     if only one 4-char file specified and it is not found,
       it will be downloaded from http://www.rcsb.org as 3CRO.pdb
   d arg is object with atom coordinates (dump, data)
-  
+
 p.one()                     write all output as one big PDB file to tmp.pdb
 p.one("mine")               write to mine.pdb
 p.many()                    write one PDB file per snapshot: tmp0000.pdb, ...
@@ -39,7 +39,7 @@ p.single(N,"new")           write as new.pdb
     if one file in str arg and d: one new PDB file per snapshot
       using input PDB file as template
     multiple input PDB files with a d is not allowed
-    
+
 index,time,flag = p.iterator(0)
 index,time,flag = p.iterator(1)
 
@@ -97,7 +97,7 @@ class pdbfile:
 
     # flist = full list of all PDB input file names
     # append .pdb if needed
-    
+
     if filestr:
       list = filestr.split()
       flist = []
@@ -117,7 +117,7 @@ class pdbfile:
       raise Exception("no input PDB file(s)")
 
     # grab PDB file from http://rcsb.org if not a local file
-    
+
     if len(self.files) == 1 and len(self.files[0]) == 8:
       try:
         open(self.files[0],'r').close()
@@ -127,7 +127,7 @@ class pdbfile:
         urllib.urlretrieve(fetchstr,self.files[0])
 
     if self.data and len(self.files): self.read_template(self.files[0])
-      
+
   # --------------------------------------------------------------------
   # write a single large PDB file for concatenating all input data or files
   # if data exists:
@@ -145,7 +145,7 @@ class pdbfile:
     f = open(file,'w')
 
     # use template PDB file with each snapshot
-    
+
     if self.data:
       n = flag = 0
       while 1:
@@ -163,7 +163,7 @@ class pdbfile:
         print("END",file=f)
         print(file,end='')
         sys.stdout.flush()
-        
+
     f.close()
     print("\nwrote %d datasets to %s in PDB format" % (n,file))
 
@@ -199,7 +199,7 @@ class pdbfile:
         f = open(file,'w')
         self.convert(f,which)
         f.close()
-        
+
         print(time,end='')
         sys.stdout.flush()
         n += 1
@@ -216,13 +216,13 @@ class pdbfile:
         else:
           file = root + str(n)
         file += ".pdb"
-        
+
         f = open(file,'w')
         f.write(open(infile,'r').read())
         f.close()
         print(file,end='')
         sys.stdout.flush()
-        
+
         n += 1
 
     print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
@@ -249,7 +249,7 @@ class pdbfile:
       self.convert(f,which)
     else:
       f.write(open(self.files[time],'r').read())
-      
+
     f.close()
 
   # --------------------------------------------------------------------
@@ -268,8 +268,8 @@ class pdbfile:
 
   # --------------------------------------------------------------------
   # read a PDB file and store ATOM lines
-  
-  def read_template(self,file):  
+
+  def read_template(self,file):
     lines = open(file,'r').readlines()
     self.atomlines = {}
     for line in lines: