convert to python3

.scripts/fix_smiles.py

@@ -2,6 +2,7 @@
 import sys
 import pubchempy as pcp
 
+
 def query_yes_no(question, default="yes"):
     """Ask a yes/no question via raw_input() and return their answer.
     
@@ -12,9 +13,9 @@ def query_yes_no(question, default="yes"):
 
     The "answer" return value is one of "yes" or "no".
     """
-    valid = {"yes":"yes",   "y":"yes",  "ye":"yes",
-             "no":"no",     "n":"no"}
-    if default == None:
+    valid = {"yes": "yes", "y": "yes", "ye": "yes",
+             "no": "no", "n": "no"}
+    if default is None:
         prompt = " [y/n] "
     elif default == "yes":
         prompt = " [Y/n] "
@@ -25,80 +26,93 @@ def query_yes_no(question, default="yes"):
 
     while 1:
         sys.stdout.write(question + prompt)
-        choice = raw_input().lower()
+        choice = input().lower()
         if default is not None and choice == '':
             return default
         elif choice in valid.keys():
             return valid[choice]
         else:
-            sys.stdout.write("Please respond with 'yes' or 'no' "\
-                             "(or 'y' or 'n').\n")
+            sys.stdout.write("Please respond with 'yes' or 'no' (or 'y' or 'n').\n")
 
 
 def inplace_change(filename, old_string, new_string):
     # Safely read the input filename using 'with'
     with open(filename) as f:
         s = f.read()
         if old_string not in s:
-            print '"{old_string}" not found in {filename}.'.format(**locals())
+            print('"{old_string}" not found in {filename}.'.format(**locals()))
             return
 
     # Safely write the changed content, if found in the file
     with open(filename, 'w') as f:
-        print 'Changing "{old_string}" to "{new_string}" in {filename}'.format(**locals())
+        print('Changing "{old_string}" to "{new_string}" in {filename}'.format(**locals()))
         s = s.replace(old_string, new_string)
         f.write(s)
 
-names=[]
-formula=""
-inchi=""
+
+names = []
+formula = ""
+inchi = ""
 
 for line in open(sys.argv[1]):
- if "CH$NAME" in line:
-   names.append(''.join(line.split(" ")[1:]).strip().lower())
- if "CH$FORMULA" in line:
-   formula=''.join(line.split(" ")[1:]).strip()
- if "CH$IUPAC" in line:
-   inchi=''.join(line.split(" ")[1:]).strip()
- if "CH$SMILES" in line:
-   smiles=''.join(line.split(" ")[1:]).strip()
+    if "CH$NAME" in line:
+        names.append(''.join(line.split(" ")[1:]).strip().lower())
+    if "CH$FORMULA" in line:
+        formula = ''.join(line.split(" ")[1:]).strip()
+    if "CH$IUPAC" in line:
+        inchi = ''.join(line.split(" ")[1:]).strip()
+    if "CH$SMILES" in line:
+        smiles = ''.join(line.split(" ")[1:]).strip()
 
 results = pcp.get_compounds(inchi, namespace=u'inchi')
 
+if smiles == results[0].isomeric_smiles:
+    print('Nothing to do! Exiting.')
+    sys.exit(0)
+
+#clear screen
+print(chr(27) + "[2J")
 if len(results) != 1:
-   print "#results != 1; exiting"
-   sys.exit(1)
+    print("#results != 1; exiting")
+    sys.exit(1)
 
 if results[0].molecular_formula == formula:
-   print 'Formula matches ' + '\033[92m[OK]\033[0m' 
+    print('Formula matches ' + '\033[92m[OK]\033[0m')
+    print(formula)
 else:
-   print results[0].molecular_formula
-   print formula
-   print 'Formulas different ' + '\033[93m[OK]\033[0m'
+    print(f'Formula from pubchem: {results[0].molecular_formula}')
+    print(f'Formula from file: {formula}')
+    print('Formulas different ' + '\033[93m[!!]\033[0m')
 
-synonyms=[x.encode('utf-8').lower() for x in results[0].synonyms]
+print(f'InChI : {inchi}')
 
-common_names=[]
+synonyms = []
+if results[0].synonyms is not None:
+    synonyms = [x.encode('utf-8').lower() for x in results[0].synonyms]
 
+common_names = []
+
+print()
 for name in names:
-   if name in synonyms:
-      print 'Name in synonyms ' + '\033[92m[OK]\033[0m'
-      common_names.append(name)
-   
-print synonyms
-print
-print names
-print '\033[92m'
-print common_names
-print '\033[0m'
-print
-print
+    if name in synonyms:
+        print('Name in synonyms ' + '\033[92m[OK]\033[0m')
+        common_names.append(name)
+
+print(f'Names from pubchem: {synonyms}')
+print(f'Names from file: {names}')
+if len(common_names):
+    print('\033[92m')
+    print(common_names)
+    print('\033[0m')
+print()
+print()
 if (results[0].molecular_formula == formula) and (len(common_names)):
-   inplace_change(sys.argv[1], 'CH$SMILES: '+smiles, 'CH$SMILES: '+results[0].isomeric_smiles)
+    inplace_change(sys.argv[1], 'CH$SMILES: ' + smiles, 'CH$SMILES: ' + results[0].isomeric_smiles)
 else:
-   sub=query_yes_no('Substitute \033[91m' + smiles + '\033[0m by \033[92m ' + results[0].isomeric_smiles + '\033[0m?', default="no")
-   if sub=="yes":
-      inplace_change(sys.argv[1], 'CH$SMILES: '+smiles, 'CH$SMILES: '+results[0].isomeric_smiles)
+    sub = query_yes_no(
+        'Substitute \033[91m' + smiles + '\033[0m by \033[92m ' + results[0].isomeric_smiles + '\033[0m?', default="no")
+    if sub == "yes":
+        inplace_change(sys.argv[1], 'CH$SMILES: ' + smiles, 'CH$SMILES: ' + results[0].isomeric_smiles)
 
-print 
-print
+print()
+print()