r14910 - /1.3/prompt/structure.py -- October 25, 2011 - 11:08

Author: bugman
Date: Tue Oct 25 11:08:47 2011
New Revision: 14910

URL: http://svn.gna.org/viewcvs/relax?rev=14910&view=rev
Log:
Added the atom_id arg to the new structure.displacement user function front 
end.

This will be used to restrict the calculation to subsets of all atoms.


Modified:
    1.3/prompt/structure.py

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14910&r1=14909&r2=14910&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Tue Oct 25 11:08:47 2011
@@ -195,30 +195,35 @@
     _build_doc(delete)
 
 
-    def displacement(self, model_from=None, model_to=None):
+    def displacement(self, model_from=None, model_to=None, atom_id=None):
         # Function intro text.
         if self._exec_info.intro:
             text = self._exec_info.ps3 + "structure.displacement("
             text = text + "model_from=" + repr(model_from)
-            text = text + ", model_to=" + repr(model_to) + ")"
+            text = text + ", model_to=" + repr(model_to)
+            text = text + ", atom_id=" + repr(atom_id) + ")"
             print(text)
 
         # The argument checks.
         arg_check.is_int(model_from, 'model from', can_be_none=True)
         arg_check.is_int(model_to, 'model to', can_be_none=True)
-
-        # Execute the functional code.
-        generic_fns.structure.main.displacement(model_from=model_from, 
model_to=model_to)
+        arg_check.is_str(atom_id, 'atom identification string', 
can_be_none=True)
+
+        # Execute the functional code.
+        generic_fns.structure.main.displacement(model_from=model_from, 
model_to=model_to, atom_id=atom_id)
 
     # The function doc info.
     displacement._doc_title = "Determine the rotational and translational 
displacement between a set of models."
     displacement._doc_title_short = "Rotational and translational 
displacement."
     displacement._doc_args = [
         ["model_from", "The optional model number for the starting position 
of the displacement."],
-        ["model_to", "The optional model number for the ending position of 
the displacement."]
+        ["model_to", "The optional model number for the ending position of 
the displacement."],
+        ["atom_id", "The atom identification string."]
     ]
     displacement._doc_desc = """
         This user function allows the rotational and translational 
displacement between two models of the same structure to be calculated.  The 
information will be printed out in various formats and held in the relax data 
store.  This is directional, so there is a starting and ending position for 
each displacement.  If the starting and ending models are not specified, then 
the displacements in all directions between all models will be calculated.
+
+        The atom ID, which uses the same notation as the spin ID strings, 
can be used to restrict the displacement calculation to certain molecules, 
residues, or atoms.  This is useful if studying domain motions, secondary 
structure rearrangements, amino acid side chain rotations, etc.
         """
     displacement._doc_examples = """
         To determine the rotational and translational displacements between 
all sets of models, type: