Change the way of getting enzyme name

rpg/enzyme.py

@@ -26,16 +26,16 @@
 import os
 import re
 from pathlib import Path
-import core
-import rule
+from rpg import core
+from rpg import rule
 
-DEFENZFILE = "enzymes_definition.py"
 DEFUSERENZFILE = str(Path.home()) + "/rpg_user.py"
 
 # Create the enzymes_user file if it does not exist
 if not os.path.isfile(DEFUSERENZFILE):
     with open(DEFUSERENZFILE, "w") as out_file:
-        out_file.write("import enzyme\nimport rule\nimport enzymes_definition"\
+        out_file.write("from rpg import enzyme\nfrom rpg import rule\n"\
+                       "from rpg import enzymes_definition"\
                        "\n\nAVAILABLE_ENZYMES_USER = []\nCPT_ENZ = enzymes_de"\
                        "finition.CPT_ENZ\n\n### ENZYMES DECLARATION ###\n")
 
@@ -246,7 +246,7 @@ def check_enzyme_name(name_new_enz, all_name_enz):
     return ret
 
 # Not tested
-def user_creation_enzyme():
+def user_creation_enzyme(all_enzymes):
     """Text-mod form to input a new enzyme.
 
     .. warning:: Not tested
@@ -259,21 +259,8 @@ def user_creation_enzyme():
         all_name_enz = set()
 
         # Get all used names
-        # Done here to prevent multiple time opening those files
-        try:
-            with open(DEFENZFILE) as enz_file:
-                for line in enz_file:
-                    if line[0:29] == "ENZYME = enzyme.Enzyme(CPT_ENZ,":
-                        all_name_enz.add(line.split("\"")[1])
-        except IOError:
-            core.handle_errors("fail to open " + DEFENZFILE, 0, "File ")
-        try:
-            with open(DEFUSERENZFILE) as user_enz_file:
-                for line in user_enz_file:
-                    if line[0:29] == "ENZYME = enzyme.Enzyme(CPT_ENZ,":
-                        all_name_enz.add(line.split("\"")[1])
-        except IOError:
-            core.handle_errors("fail to open " + DEFUSERENZFILE, 0, "File ")
+        for enz in all_enzymes:
+            all_name_enz.add(enz.name)
 
         # Name of the enzyme
         name_new_enz = input("Name of the new enzyme?\n")