r18865 - /branches/frame_order_testing/specific_fns/frame_order.py -- March 18, 2013 - 18:01

Author: bugman
Date: Mon Mar 18 18:01:05 2013
New Revision: 18865

URL: http://svn.gna.org/viewcvs/relax?rev=18865&view=rev
Log:
Implemented the average structure creation component of the 
frame_order.pdb_model user function.

This is the implementation of the _pdb_ave_pos() frame order specific method. 
 The loaded structure
is simply copied, rotated, translated, and then written out as a PDB file.


Modified:
    branches/frame_order_testing/specific_fns/frame_order.py

Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18865&r1=18864&r2=18865&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Mon Mar 18 
18:01:05 2013
@@ -956,6 +956,26 @@
         @keyword force: Flag which if set to True will cause any 
pre-existing file to be overwritten.
         @type force:    bool
         """
+
+        # Make a copy of the structural object (so as to preserve the 
original structure).
+        structure = deepcopy(cdp.structure)
+
+        # First rotate the moving domain to the average position.
+        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)
+        structure.rotate(R=R, origin=cdp.pivot, 
atom_id=self._domain_moving())
+
+        # Then translate the moving domain.
+        if not self._translation_fixed():
+            structure.translate(T=[cdp.ave_pos_x, cdp.ave_pos_y, 
cdp.ave_pos_z], atom_id=self._domain_moving())
+
+        # Write out the PDB file.
+        file = open_write_file(file_name=file, dir=dir, force=force)
+        structure.write_pdb(file=file)
+        file.close()
 
 
     def _pdb_distribution(self, file=None, dir=None, force=False):