r24373 - in /branches/frame_order_cleanup: pipe_control/pymol_control.py specific_analyses/frame_order/geometric.py -- July 01, 2014 - 12:42

Author: bugman
Date: Tue Jul  1 12:42:41 2014
New Revision: 24373

URL: http://svn.gna.org/viewcvs/relax?rev=24373&view=rev
Log:
The motional pivots for the frame order models are now labelled in the 
geometric representation.

The pivot points are now added as a new molecule called 'pivots' in the 
frame_order.pdb_model user
function.  The atoms all belong to the PIV residue.  The pymol.frame_order 
user function now selects
this residue, hides its atoms, and then shows the atom name 'Piv' as the 
label.  For the double
rotor model, the atom names 'Piv1' and 'Piv2' are used to differentiate the 
pivots.


Modified:
    branches/frame_order_cleanup/pipe_control/pymol_control.py
    branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py

Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=24373&r1=24372&r2=24373&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py  (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py  Tue Jul  1 
12:42:41 2014
@@ -381,6 +381,9 @@
     # The object ID.
     id = file_root(file)
 
+    # Set up the pivot points.
+    represent_pivots(id=id)
+
     # Set up the rotor objects.
     represent_rotor_object(id=id)
 
@@ -618,6 +621,30 @@
     pymol_obj.exec_cmd("cmd.delete('sele')")
 
 
+def represent_pivots(id=None):
+    """Set up the PyMOL pivot object representation.
+
+    @keyword id:    The PyMOL object ID.
+    @type id:       str
+    """
+
+    # Sanity check.
+    if id == None:
+        raise RelaxError("The PyMOL object ID must be supplied.")
+
+    # Select the PIV residues.
+    pymol_obj.exec_cmd("select (%s & resn PIV)" % id)
+
+    # Hide the atom.
+    pymol_obj.exec_cmd("hide ('sele')")
+
+    # Label using the atom name.
+    pymol_obj.exec_cmd("cmd.label(\"sele\",\"name\")")
+
+    # Remove the selection.
+    pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
 def represent_rotor_object(id=None):
     """Set up the PyMOL rotor object representation.
 

Modified: 
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24373&r1=24372&r2=24373&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py   
  (original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py   
  Tue Jul  1 12:42:41 2014
@@ -227,6 +227,31 @@
         cone(mol=mol_neg, cone_obj=cone_obj, start_res=1, apex=pivot, 
R=R_neg, inc=inc, distribution='regular', axis_flag=False)
 
 
+def add_pivots(structure=None):
+    """Add the pivots for the current frame order model to the structural 
object.
+
+    @keyword structure: The internal structural object to add the rotor 
objects to.
+    @type structure:    lib.structure.internal.object.Internal instance
+    """
+
+    # The pivot point.
+    pivot1 = generate_pivot(order=1)
+    pivot2 = generate_pivot(order=2)
+
+    # Create the molecule.
+    mol_name = 'pivots'
+    structure.add_molecule(name=mol_name)
+
+    # Add the pivots for the double motion models.
+    if cdp.model in ['double rotor']:
+        structure.add_atom(mol_name=mol_name, pdb_record='HETATM', 
atom_num=1, atom_name='Piv1', res_name='PIV', res_num=1, pos=pivot1, 
element='C')
+        structure.add_atom(mol_name=mol_name, pdb_record='HETATM', 
atom_num=2, atom_name='Piv2', res_name='PIV', res_num=1, pos=pivot2, 
element='C')
+
+    # Add the pivot for the single motion models.
+    else:
+        structure.add_atom(mol_name=mol_name, pdb_record='HETATM', 
atom_num=1, atom_name='Piv', res_name='PIV', res_num=1, pos=pivot1, 
element='C')
+
+
 def add_rotors(structure=None):
     """Add all rotor objects for the current frame order model to the 
structural object.
 
@@ -401,6 +426,9 @@
     if cdp.model not in ['rotor', 'free rotor', 'double rotor']:
         model_neg = structure.add_model(model=2)
 
+    # Add the pivots.
+    add_pivots(structure=structure)
+
     # Add all rotor objects.
     add_rotors(structure=structure)