r11529 - /1.3/generic_fns/pymol_control.py -- August 17, 2010 - 18:40

Author: bugman
Date: Tue Aug 17 18:40:03 2010
New Revision: 11529

URL: http://svn.gna.org/viewcvs/relax?rev=11529&view=rev
Log:
pymol.cone_pdb() is now rotating the moving domain to the average position 
for the frame order theory.


Modified:
    1.3/generic_fns/pymol_control.py

Modified: 1.3/generic_fns/pymol_control.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol_control.py?rev=11529&r1=11528&r2=11529&view=diff
==============================================================================
--- 1.3/generic_fns/pymol_control.py (original)
+++ 1.3/generic_fns/pymol_control.py Tue Aug 17 18:40:03 2010
@@ -29,12 +29,14 @@
 # Python module imports.
 if dep_check.pymol_module:
     import pymol
+from numpy import float64, zeros
 from os import sep
 from subprocess import PIPE, Popen
 
 # relax module imports.
 from generic_fns.mol_res_spin import exists_mol_res_spin_data
 from generic_fns import pipes
+from maths_fns.rotation_matrix import euler_to_R_zyz, R_to_axis_angle
 from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError
 from relax_io import file_root, open_write_file, test_binary
 from specific_fns.setup import get_specific_fn
@@ -279,6 +281,25 @@
 
     # Remove the selection.
     pymol_obj.exec_cmd("cmd.delete('sele')")
+
+
+    # Rotate to the average position.
+    #################################
+
+    # The average position rotation.
+    ave_pos_R = zeros((3, 3), float64)
+    euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta, cdp.ave_pos_gamma, 
ave_pos_R)
+
+    # Convert to axis-angle notation.
+    axis, angle = R_to_axis_angle(ave_pos_R)
+
+    # The PDB file to rotate.
+    for i in range(len(cdp.domain_to_pdb)):
+        if cdp.domain_to_pdb[i][0] != cdp.ref_domain:
+            pdb = cdp.domain_to_pdb[i][1]
+
+    # Execute the pymol command to rotate.
+    pymol_obj.exec_cmd("cmd.rotate([%s, %s, %s], %s, '%s', origin=[%s, %s, 
%s])" % (axis[0], axis[1], axis[2], angle, pdb, cdp.pivot[0], cdp.pivot[1], 
cdp.pivot[2]))
 
 
 def create_macro(data_type=None, style="classic", colour_start=None, 
colour_end=None, colour_list=None):