r27068 - in /trunk: pipe_control/structure/main.py user_functions/structure.py -- December 11, 2014 - 09:04

Author: bugman
Date: Thu Dec 11 09:04:35 2014
New Revision: 27068

URL: http://svn.gna.org/viewcvs/relax?rev=27068&view=rev
Log:
Changed the argument order for the structure.align user function.

The standardised order will now be pipes, models, molecules, atom_id, etc.


Modified:
    trunk/pipe_control/structure/main.py
    trunk/user_functions/structure.py

Modified: trunk/pipe_control/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27068&r1=27067&r2=27068&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Thu Dec 11 09:04:35 2014
@@ -105,19 +105,19 @@
     print("Created the empty model number %s." % model_num)
 
 
-def align(pipes=None, molecules=None, models=None, method='fit to mean', 
atom_id=None, centre_type="centroid", centroid=None):
+def align(pipes=None, models=None, molecules=None, atom_id=None, method='fit 
to mean', centre_type="centroid", centroid=None):
     """Superimpose a set of related, but not identical structures.
 
     @keyword pipes:         The data pipes to include in the alignment and 
superimposition.
     @type pipes:            None or list of str
+    @keyword models:        The list of models to for each data pipe 
superimpose.  The number of elements must match the pipes argument.  If set 
to None, then all models will be used.
+    @type models:           list of lists of int or None
     @keyword molecules:     The molecule names to include in the alignment 
and superimposition.
     @type molecules:        None or list of str
-    @keyword models:        The list of models to for each data pipe 
superimpose.  The number of elements must match the pipes argument.  If set 
to None, then all models will be used.
-    @type models:           list of lists of int or None
+    @keyword atom_id:       The molecule, residue, and atom identifier 
string.  This matches the spin ID string format.
+    @type atom_id:          str or None
     @keyword method:        The superimposition method.  It must be one of 
'fit to mean' or 'fit to first'.
     @type method:           str
-    @keyword atom_id:       The molecule, residue, and atom identifier 
string.  This matches the spin ID string format.
-    @type atom_id:          str or None
     @keyword centre_type:   The type of centre to superimpose over.  This 
can either be the standard centroid superimposition or the CoM could be used 
instead.
     @type centre_type:      str
     @keyword centroid:      An alternative position of the centroid to allow 
for different superpositions, for example of pivot point motions.

Modified: trunk/user_functions/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27068&r1=27067&r2=27068&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Thu Dec 11 09:04:35 2014
@@ -183,6 +183,13 @@
     can_be_none = True
 )
 uf.add_keyarg(
+    name = "atom_id",
+    py_type = "str",
+    desc_short = "atom ID string",
+    desc = "The atom identification string.",
+    can_be_none = True
+)
+uf.add_keyarg(
     name = "method",
     default = "fit to mean",
     py_type = "str",
@@ -191,13 +198,6 @@
     wiz_element_type = "combo",
     wiz_combo_choices = ["fit to mean", "fit to first"],
     wiz_read_only = True
-)
-uf.add_keyarg(
-    name = "atom_id",
-    py_type = "str",
-    desc_short = "atom ID string",
-    desc = "The atom identification string.",
-    can_be_none = True
 )
 uf.add_keyarg(
     name = "centre_type",