r23393 - in /branches/frame_order_cleanup: ./ pipe_control/ test_suite/system_tests/ user_functions/ -- May 24, 2014 - 08:55

Author: bugman
Date: Sat May 24 08:55:33 2014
New Revision: 23393

URL: http://svn.gna.org/viewcvs/relax?rev=23393&view=rev
Log:
Merged revisions 23392 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk

........
  r23392 | bugman | 2014-05-24 08:53:35 +0200 (Sat, 24 May 2014) | 3 lines
  
  All three file arguments for the pymol.frame_order user function are now 
optional.
........

Modified:
    branches/frame_order_cleanup/   (props changed)
    branches/frame_order_cleanup/pipe_control/pymol_control.py
    branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
    branches/frame_order_cleanup/user_functions/pymol_control.py

Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sat May 24 08:55:33 2014
@@ -1 +1 @@
-/trunk:1-23389
+/trunk:1-23392

Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=23393&r1=23392&r2=23393&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py  (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py  Sat May 24 
08:55:33 2014
@@ -362,13 +362,13 @@
     """Display the frame order results (the geometric object, average 
position and distribution).
 
     @keyword ave_pos_file:  The name of the file for the average molecule 
structure.
-    @type ave_pos_file:     str
+    @type ave_pos_file:     str or None
     @keyword rep_file:      The name of the file of the PDB representation 
of the frame order dynamics to create.
-    @type rep_file:         str
+    @type rep_file:         str or None
     @keyword dist_file:     The name of the file which will contain multiple 
models spanning the full dynamics distribution of the frame order model.
-    @type dist_file:        str
+    @type dist_file:        str or None
     @keyword dir:           The name of the directory to place the PDB file 
into.
-    @type dir:              str
+    @type dir:              str or None
     """
 
     # The path.
@@ -377,9 +377,12 @@
         path = dir + sep
 
     # Set up the respective objects.
-    frame_order_ave_pos(file=path+ave_pos_file)
-    frame_order_geometric(file=path+rep_file)
-    frame_order_distribution(file=path+dist_file)
+    if ave_pos_file:
+        frame_order_ave_pos(file=path+ave_pos_file)
+    if rep_file:
+        frame_order_geometric(file=path+rep_file)
+    if dist_file:
+        frame_order_distribution(file=path+dist_file)
 
 
 def frame_order_ave_pos(file=None):

Modified: branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/frame_order.py?rev=23393&r1=23392&r2=23393&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/frame_order.py 
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/frame_order.py Sat 
May 24 08:55:33 2014
@@ -348,7 +348,7 @@
         """Test the isotropic cone, free rotor frame order model of CaM."""
 
         # The flags, execute the script, and then check the chi2 value.
-        self.flags()
+        self.flags(opt=True)
         self.interpreter.run(script_file=self.cam_path+'iso_cone.py')
         self.check_chi2(4.4891048094666539)
 

Modified: branches/frame_order_cleanup/user_functions/pymol_control.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/pymol_control.py?rev=23393&r1=23392&r2=23393&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/pymol_control.py        
(original)
+++ branches/frame_order_cleanup/user_functions/pymol_control.py        Sat 
May 24 08:55:33 2014
@@ -155,7 +155,8 @@
     desc_short = "average structure file name",
     desc = "The name of the 3D structure PDB file for the molecular 
structure with the moving domains shifted to the average position.",
     wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
-    wiz_filesel_style = FD_OPEN
+    wiz_filesel_style = FD_OPEN,
+    can_be_none = True
 )
 uf.add_keyarg(
     name = "rep_file",
@@ -165,7 +166,8 @@
     desc_short = "PDB representation file name",
     desc = "The name of the PDB file for the geometric object representation 
of the frame order dynamics.",
     wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
-    wiz_filesel_style = FD_OPEN
+    wiz_filesel_style = FD_OPEN,
+    can_be_none = True
 )
 uf.add_keyarg(
     name = "dist_file",
@@ -175,7 +177,8 @@
     desc_short = "distribution file name",
     desc = "The name of the file which will contain multiple models spanning 
the full dynamics distribution of the frame order model.",
     wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
-    wiz_filesel_style = FD_OPEN
+    wiz_filesel_style = FD_OPEN,
+    can_be_none = True
 )
 uf.add_keyarg(
     name = "dir",