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
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