r23883 - /branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py -- June 12, 2014 - 15:57

Author: bugman
Date: Thu Jun 12 15:57:22 2014
New Revision: 23883

URL: http://svn.gna.org/viewcvs/relax?rev=23883&view=rev
Log:
Removed the structure loading and transformation from the CaM frame order 
system tests.

This was mimicking the old behaviour of the auto-analysis.  However as that 
behaviour has been
shifted into the backend of the frame_order.pdb_model user function, which is 
called by these system
tests as well, the code is now redundant and is wasting test suite time.


Modified:
    
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py

Modified: 
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=23883&r1=23882&r2=23883&view=diff
==============================================================================
--- 
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
 (original)
+++ 
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
 Thu Jun 12 15:57:22 2014
@@ -106,12 +106,6 @@
 
         # Optimise.
         self.optimisation()
-
-        # Load the original structure.
-        self.original_structure()
-
-        # Domain transformation.
-        self.transform()
 
         # Display in pymol.
         self.pymol_display()
@@ -216,29 +210,8 @@
         self._execute_uf(uf_name='results.write', file='devnull', dir=None, 
force=True)
 
 
-    def original_structure(self):
-        """Load the original structure into a dedicated data pipe."""
-
-        # Delete the data pipe (if a loaded state has been used).
-        if self.LOAD_STATE:
-            self._execute_uf(uf_name='pipe.delete', pipe_name='orig pos')
-
-        # Create a special data pipe for the original rigid body position.
-        self._execute_uf(uf_name='pipe.create', pipe_name='orig pos', 
pipe_type='frame order')
-
-        # Load the structure.
-        self._execute_uf(uf_name='structure.read_pdb', 
file='1J7P_1st_NH_rot.pdb', dir=BASE_PATH)
-
-
     def pymol_display(self):
         """Display the results in PyMOL."""
-
-        # Switch back to the main data pipe.
-        self._execute_uf(uf_name='pipe.switch', pipe_name='frame order')
-
-        # Load the PDBs of the 2 domains.
-        self._execute_uf(uf_name='structure.read_pdb', 
file='1J7O_1st_NH.pdb', dir=BASE_PATH)
-        self._execute_uf(uf_name='structure.read_pdb', 
file='1J7P_1st_NH_rot.pdb', dir=BASE_PATH)
 
         # Create the PDB representation.
         self._execute_uf(uf_name='frame_order.pdb_model', 
ave_pos_file='devnull', rep_file='devnull', dist_file='devnull', force=True)
@@ -328,37 +301,3 @@
             self._execute_uf(uf_name='rdc.delete')
         if hasattr(status, 'flag_pcs') and not status.flag_pcs:
             self._execute_uf(uf_name='pcs.delete')
-
-
-    def transform(self):
-        """Transform the domain to the average position."""
-
-        # Switch back to the main data pipe.
-        self._execute_uf(uf_name='pipe.switch', pipe_name='frame order')
-
-        # The rotation matrix.
-        R = zeros((3, 3), float64)
-        if hasattr(cdp, 'ave_pos_alpha'):
-            euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta, 
cdp.ave_pos_gamma, R)
-        else:
-            euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
-        print("Rotation matrix:\n%s\n" % R)
-        R = transpose(R)
-        print("Inverted rotation:\n%s\n" % R)
-        pivot = array([cdp.pivot_x, cdp.pivot_y, cdp.pivot_z])
-
-        # Delete the data pipe (if a loaded state has been used).
-        if self.LOAD_STATE:
-            self._execute_uf(uf_name='pipe.delete', pipe_name='ave pos')
-
-        # Create a special data pipe for the average rigid body position.
-        self._execute_uf(uf_name='pipe.create', pipe_name='ave pos', 
pipe_type='frame order')
-
-        # Load the structure.
-        self._execute_uf(uf_name='structure.read_pdb', 
file='1J7P_1st_NH_rot.pdb', dir=BASE_PATH)
-
-        # Rotate all atoms.
-        self._execute_uf(uf_name='structure.rotate', R=R, origin=pivot)
-
-        # Write out the new PDB.
-        self._execute_uf(uf_name='structure.write_pdb', file='devnull')