added a line to handle empty lines in prep_pdb

Author: sastrys1

pkaani/prep_pdb.py

@@ -33,7 +33,6 @@ def make_apo_pdb(pdbin,pdbout):
 
     with open(pdbin, 'r+') as fd:
        contents = fd.readlines()
-       
        #first find if there is an SSBOND
        for line in contents:
           if('SSBOND' in line):
@@ -57,7 +56,9 @@ def make_apo_pdb(pdbin,pdbout):
 
        for line in contents:
            row=line.strip().split()
-           
+           if (len(row) == 0):
+               continue
+
            if row[0]=='MODEL': 
               model_num = row[-1].strip() 
               if(model_num=='1'): protein.append(line)

pkaani/run.py

@@ -8,6 +8,8 @@
 from urllib.request import urlopen
 from io import StringIO
 
+from pkaani.prep_pdb import prep_pdb
+
 class MyParser(argparse.ArgumentParser):
 	def error(self, message):
 		sys.stderr.write('error: %s\n' % message)
@@ -88,10 +90,9 @@ def main():
 				with open(outfile, 'w') as f2:
 					for line in contents:
 						f2.write(line)
-				
-				from pkaani.prep_pdb import prep_pdb
-				prep_pdb(pdbfile)			 
-				file_exist=True
+			
+			prep_pdb(pdbfile)			 
+			file_exist=True
 
 		#CALCULATER PKA
 		from pkaani.pkaani import calculate_pka