r28220 - /trunk/user_functions/structure.py -- June 02, 2016 - 19:09

Author: bugman
Date: Thu Jun  2 19:09:34 2016
New Revision: 28220

URL: http://svn.gna.org/viewcvs/relax?rev=28220&view=rev
Log:
Addition of the atomic boolean argument to the structure.rmsd user function 
front end.

This will be used to enable the calculation of per-atom RMSDs.

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=28220&r1=28219&r2=28220&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Thu Jun  2 19:09:34 2016
@@ -1284,15 +1284,26 @@
     desc = "The atom identification string of the coordinates of interest.",
     can_be_none = True
 )
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows the root mean squared deviation 
(RMSD) between all structures to be calculated.  The RMSDs for individual 
structures to the mean structure will be calculated and reported, and then 
these values averaged for the global RMSD.  This will be stored in the 
structural object of the current data pipe.")
+uf.add_keyarg(
+    name = "atomic",
+    default = False,
+    py_type = "bool",
+    desc_short = "atomic-level RMSD flag",
+    desc = "A flag which if if True will allow for per-atom RMSDs to be 
additionally calculated."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This allows the root mean squared deviation 
(RMSD) between all structures to be calculated.  The RMSDs for individual 
structures to the mean structure will be calculated and reported.  These 
values averaged to produce a global RMSD stored in the structural object of 
the current data pipe.  If the 'atomic' argument is set, per-atom RMSDs will 
additionally be calculated stored in spin containers.")
 uf.desc[-1].add_paragraph(paragraph_multi_struct)
 uf.desc[-1].add_paragraph(paragraph_atom_id)
 # Prompt examples.
 uf.desc.append(Desc_container("Prompt examples"))
 uf.desc[-1].add_paragraph("To determine the RMSD of all models in the 
current data pipe, simply type:")
 uf.desc[-1].add_prompt("relax> structure.rmsd()")
+uf.desc[-1].add_paragraph("For the backbone heavy atom RMSD of all models in 
the current data pipe, simply type:")
+uf.desc[-1].add_prompt("relax> structure.rmsd(atom_id='@N,C,CA,O')")
+uf.desc[-1].add_paragraph("To calculate the C-alpha backbone RMSDs of all 
models in the current data pipe, type:")
+uf.desc[-1].add_prompt("relax> structure.rmsd(atom_id='CA', atomic=True)")
 uf.backend = pipe_control.structure.main.rmsd
 uf.menu_text = "&rmsd"
 uf.wizard_height_desc = 400