r24365 - in /trunk: pipe_control/structure/main.py user_functions/structure.py -- June 30, 2014 - 18:10

Author: bugman
Date: Mon Jun 30 18:10:09 2014
New Revision: 24365

URL: http://svn.gna.org/viewcvs/relax?rev=24365&view=rev
Log:
Created the very basic structure.com user function for calculating the centre 
of mass.

This is to simply allow an easy interface to the 
pipe_control.structure.mass.pipe_centre_of_mass()
function.


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=24365&r1=24364&r2=24365&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py        (original)
+++ trunk/pipe_control/structure/main.py        Mon Jun 30 18:10:09 2014
@@ -119,6 +119,20 @@
 
     # Add the atoms.
     cdp.structure.connect_atom(index1=index1, index2=index2)
+
+
+def com(model=None):
+    """Calculate the centre of mass of all structures.
+
+    @keyword model: Only use a specific model.
+    @type model:    int or None
+    """
+
+    # Test if the current data pipe exists.
+    pipes.test()
+
+    # Calculate and store the centre of mass.
+    cdp.com = pipe_centre_of_mass(model=model)
 
 
 def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):

Modified: trunk/user_functions/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=24365&r1=24364&r2=24365&view=diff
==============================================================================
--- trunk/user_functions/structure.py   (original)
+++ trunk/user_functions/structure.py   Mon Jun 30 18:10:09 2014
@@ -145,6 +145,30 @@
 uf.menu_text = "&add_model"
 uf.gui_icon = "oxygen.actions.list-add-relax-blue"
 uf.wizard_size = (700, 400)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
+
+
+# The structure.com user function.
+uf = uf_info.add_uf('structure.com')
+uf.title = "Calculate the centre of mass for all structures."
+uf.title_short = "Centre of mass calculation."
+uf.add_keyarg(
+    name = "model",
+    py_type = "int",
+    desc_short = "model",
+    desc = "The optional structural model number to restrict the calculation 
of the centre of mass to.",
+    can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This user function will calculate the centre of 
mass (CoM) for all loaded structures, printing out the position and storing 
it in the current data pipe.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To determine the centre of mass of all structure, 
simply type:")
+uf.desc[-1].add_prompt("relax> structure.com()")
+uf.backend = pipe_control.structure.main.com
+uf.menu_text = "co&m"
+uf.wizard_size = (600, 400)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'