r27721 - in /branches/frame_order_cleanup: specific_analyses/frame_order/uf.py user_functions/frame_order.py -- February 25, 2015 - 14:16

Author: bugman
Date: Wed Feb 25 14:16:04 2015
New Revision: 27721

URL: http://svn.gna.org/viewcvs/relax?rev=27721&view=rev
Log:
Added the new 'atom_id' argument to the frame_order.distribute user function.

This uses the new inverse selection functionality recently introduced into 
the trunk to delete all
structural data not matching the atom_id from the copy of the loaded 
structural data string prior to
generating the distribution of structures.


Modified:
    branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
    branches/frame_order_cleanup/user_functions/frame_order.py

Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=27721&r1=27720&r2=27721&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py    
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py    Wed 
Feb 25 14:16:04 2015
@@ -47,13 +47,15 @@
 from specific_analyses.frame_order.parameters import assemble_param_vector, 
update_model
 
 
-def distribute(file="distribution.pdb.bz2", dir=None, total=1000, 
max_rotations=100000, model=1, force=True):
+def distribute(file="distribution.pdb.bz2", dir=None, atom_id=None, 
total=1000, max_rotations=100000, model=1, force=True):
     """Create a uniform distribution of structures for the frame order 
motions.
 
     @keyword file:          The PDB file for storing the frame order 
motional distribution.  The compression is determined automatically by the 
file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
     @type file:             str
     @keyword dir:           The directory name to place the file into.
     @type dir:              str or None
+    @keyword atom_id:       The atom identification string to allow the 
distribution to be a subset of all atoms.
+    @type atom_id:          None or str
     @keyword total:         The total number of states/model/structures in 
the distribution.
     @type total:            int
     @keyword max_rotations: The maximum number of rotations to generate the 
distribution from.  This prevents an execution for an infinite amount of time 
when a frame order amplitude parameter is close to zero so that the subset of 
all rotations within the distribution is close to zero.
@@ -108,6 +110,14 @@
 
     # The motional eigenframe.
     frame = generate_axis_system()
+
+    # Only work with a subset.
+    if atom_id:
+        # The inverted selection.
+        selection = structure.selection(atom_id=atom_id, inv=True)
+
+        # Delete the data.
+        structure.delete(selection=selection, verbosity=0)
 
     # Create the distribution.
     uniform_distribution(file=file, model=cdp.model, structure=structure, 
parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(), 
total=total, max_rotations=max_rotations)

Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=27721&r1=27720&r2=27721&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py  (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py  Wed Feb 25 
14:16:04 2015
@@ -83,6 +83,13 @@
     arg_type = "dir",
     desc_short = "directory name",
     desc = "The directory where the files are to be located.",
+    can_be_none = True
+)
+uf.add_keyarg(
+    name = "atom_id",
+    py_type = "str",
+    desc_short = "atom identification string",
+    desc = "The atom identification string to allow the distribution to be a 
subset of all atoms.",
     can_be_none = True
 )
 uf.add_keyarg(