r24478 - /branches/frame_order_cleanup/lib/structure/represent/rotor.py -- July 08, 2014 - 12:08

Author: bugman
Date: Tue Jul  8 12:08:28 2014
New Revision: 24478

URL: http://svn.gna.org/viewcvs/relax?rev=24478&view=rev
Log:
Added model support for the rotor geometric object.

This is the structural object used in the frame order analysis to create PDB 
representations of
rotor motions.  The number of atoms created for the rotor is now constant, 
allowing for models
whereby the atom number and connectivity must be preserved between all models.


Modified:
    branches/frame_order_cleanup/lib/structure/represent/rotor.py

Modified: branches/frame_order_cleanup/lib/structure/represent/rotor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/represent/rotor.py?rev=24478&r1=24477&r2=24478&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/represent/rotor.py       
(original)
+++ branches/frame_order_cleanup/lib/structure/represent/rotor.py       Tue 
Jul  8 12:08:28 2014
@@ -116,8 +116,11 @@
             mol.atom_add(pdb_record='HETATM', atom_name=label, 
res_name='RTL', res_num=res_num, pos=label_pos2, element='H')
 
 
-def rotor_propellers(mol=None, rotor_angle=None, centre=None, axis=None, 
blade_length=5.0, staggered=False):
+def rotor_propellers(mol=None, rotor_angle=None, centre=None, axis=None, 
blade_length=5.0, step_angle=2.0, staggered=False):
     """Create a PDB representation of a rotor motional model.
+
+    This function will create a fixed number of atoms, placing the propeller 
blade steps outside of the rotor angle on the edge.  This is to allow for 
model support whereby the rotor angle between models can be different but the 
atomic count and connectivity must be the same in all models.
+
 
     @keyword mol:           The internal structural object molecule 
container to add the atoms to.
     @type mol:              MolContainer instance
@@ -129,12 +132,15 @@
     @type axis:             numpy rank-1, 3D array
     @keyword blade_length:  The length of the representative rotor blades in 
Angstrom.
     @type blade_length:     float
+    @keyword step_angle:    The angle between propeller blades, in degrees.
+    @type step_angle:       float
     @keyword staggered:     A flag which if True will cause the rotor blades 
to be staggered.  This is used to avoid blade overlap.
     @type staggered:        bool
     """
 
     # Init.
-    step_angle = 2.0 / 360.0 * 2.0 * pi
+    step_angle = step_angle / 360.0 * 2.0 * pi
+    step_num = int(pi / step_angle)
     R = zeros((3, 3), float64)
     res_num = mol.last_residue() + 1
 
@@ -172,11 +178,11 @@
         angle = 0.0
         pos_last_index = mid_pt_index
         neg_last_index = mid_pt_index
-        while True:
+        for j in range(step_num):
             # Increase the angle.
             angle += step_angle
 
-            # The edge rotation.
+            # The edge rotation (place all points outside of the rotor angle 
on the edge).
             if angle > rotor_angle:
                 axis_angle_to_R(axis, rotor_angle, R)
 
@@ -200,9 +206,5 @@
             pos_last_index = pos_index
             neg_last_index = neg_index
 
-            # Finish.
-            if angle > rotor_angle:
-                break
-
         # Increment the residue number.
         res_num += 1