r18013 - /branches/frame_order_testing/auto_analyses/frame_order.py -- November 21, 2012 - 08:41

Author: bugman
Date: Wed Nov 21 08:41:46 2012
New Revision: 18013

URL: http://svn.gna.org/viewcvs/relax?rev=18013&view=rev
Log:
Added some code to allow for results visualisation in the frame order 
auto-analysis.

This creates the 'cone.pdb' file representation of the motion and a relax 
script for launching the
visualisation later on.


Modified:
    branches/frame_order_testing/auto_analyses/frame_order.py

Modified: branches/frame_order_testing/auto_analyses/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/auto_analyses/frame_order.py?rev=18013&r1=18012&r2=18013&view=diff
==============================================================================
--- branches/frame_order_testing/auto_analyses/frame_order.py (original)
+++ branches/frame_order_testing/auto_analyses/frame_order.py Wed Nov 21 
08:41:46 2012
@@ -38,6 +38,7 @@
 from maths_fns.coord_transform import spherical_to_cartesian
 from prompt.interpreter import Interpreter
 from relax_errors import RelaxError
+from relax_io import open_write_file
 from status import Status; status = Status()
 
 
@@ -138,6 +139,9 @@
             # Finish.
             self.interpreter.results.write(file='results', force=True)
 
+            # Results visualisation.
+            self.visualisation()
+
         # Clean up.
         finally:
             # Finish and unlock execution.
@@ -499,3 +503,43 @@
 
         # Success.
         return True
+
+
+    def visualisation(self):
+        """Create visual representations of the frame order results.
+
+        This includes a PDB representation of the motions (the 'cone.pdb' 
file located in each model directory) together with a relax script for 
displaying the average domain positions together with the cone/motion 
representation in PyMOL (the 'pymol_display.py' file, also created in the 
model directory).
+        """
+
+        # Loop over all models.
+        for pipe_name in self.models.values() + ['final']:
+            # The directory to place files into.
+            if pipe_name == 'final':
+                results_dir = pipe_name
+            else:
+                results_dir = cdp.model
+
+            # Switch to the data pipe.
+            self.interpreter.pipe.switch(pipe_name)
+
+            # Create a PDB file representation of the motions.
+            if cdp.model != 'rigid':
+                self.interpreter.frame_order.cone_pdb(file='cone.pdb', 
dir=results_dir, force=True)
+
+            # Create the visualisation script.
+            script = open_write_file(file_name='pymol_display.py', 
dir=results_dir, force=True)
+
+            # Add a comment for the user.
+            script.write("# relax script for displaying the frame order 
results of this '%s' model in PyMOL.\n\n" % results_dir)
+
+            # The script contents.
+            script.write("# Load the relax state file.\n")
+            script.write("state.load('results')\n")
+            script.write("\n")
+            script.write("# PyMOL visualisation.\n")
+            script.write("pymol.view()\n")
+            script.write("pymol.command('show spheres')\n")
+            script.write("pymol.cone_pdb('cone.pdb')\n")
+
+            # Close the file.
+            script.close()