r27293 - /trunk/user_functions/structure.py -- January 23, 2015 - 17:49

Author: bugman
Date: Fri Jan 23 17:49:29 2015
New Revision: 27293

URL: http://svn.gna.org/viewcvs/relax?rev=27293&view=rev
Log:
Modified the gap penalty arguments for the structure.align user function.

These now must always be supplied, as None is not handled by the backend
lib.sequence_alignment.needleman_wunsch module.  The previous defaults of 
None are now set to 0.0.


Modified:
    trunk/user_functions/structure.py

Modified: trunk/user_functions/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27293&r1=27292&r2=27293&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Fri Jan 23 17:49:29 2015
@@ -227,32 +227,28 @@
     default = 10.0,
     py_type = "float",
     desc_short = "gap opening penalty",
-    desc = "The penalty for introducing gaps, as a positive number.",
-    can_be_none = False
+    desc = "The penalty for introducing gaps, as a positive number."
 )
 uf.add_keyarg(
     name = "gap_extend_penalty",
     default = 1.0,
     py_type = "float",
     desc_short = "gap extension penalty",
-    desc = "The penalty for extending a gap, as a positive number.",
-    can_be_none = False
+    desc = "The penalty for extending a gap, as a positive number."
 )
 uf.add_keyarg(
     name = "end_gap_open_penalty",
-    default = None,
+    default = 0.0,
     py_type = "float",
     desc_short = "end gap opening penalty",
-    desc = "The optional penalty for opening a gap at the end of a 
sequence.",
-    can_be_none = True
+    desc = "The optional penalty for opening a gap at the end of a sequence."
 )
 uf.add_keyarg(
     name = "end_gap_extend_penalty",
-    default = None,
+    default = 0.0,
     py_type = "float",
     desc_short = "end gap extension penalty",
-    desc = "The optional penalty for extending a gap at the end of a 
sequence.",
-    can_be_none = True
+    desc = "The optional penalty for extending a gap at the end of a 
sequence."
 )
 uf.add_keyarg(
     name = "centre_type",