r10954 - in /1.3/specific_fns: frame_order.py n_state_model.py -- March 09, 2010 - 11:51

Author: bugman
Date: Tue Mar  9 11:51:38 2010
New Revision: 10954

URL: http://svn.gna.org/viewcvs/relax?rev=10954&view=rev
Log:
The frame order and N-state model cone_pdb() methods now use the isotropic 
cone object.


Modified:
    1.3/specific_fns/frame_order.py
    1.3/specific_fns/n_state_model.py

Modified: 1.3/specific_fns/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=10954&r1=10953&r2=10954&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Mar  9 11:51:38 2010
@@ -38,6 +38,7 @@
 from float import isNaN, isInf
 from generic_fns import pipes
 from generic_fns.angles import wrap_angles
+from generic_fns.structure.cones import Iso_cone
 from generic_fns.structure.geometric import cone_edge, generate_vector_dist, 
generate_vector_residues, stitch_cone_to_edge
 from generic_fns.structure.internal import Internal
 from maths_fns import frame_order, order_parameters
@@ -166,6 +167,9 @@
             if factor == -1:
                 R = -R
 
+            # The isotropic cone object.
+            cone = Iso_cone(cdp.theta_cone)
+
             # Create the structural object.
             structure = Internal()
 
@@ -185,7 +189,7 @@
             # Generate the cone outer edge.
             print("\nGenerating the cone outer edge.")
             edge_start_atom = mol.atom_num[-1]+1
-            cone_edge(mol=mol, res_name='CON', res_num=3+num_sim, 
apex=cdp.pivot, R=R, angle=cdp.theta_cone, length=size, inc=inc)
+            cone_edge(mol=mol, res_name='CON', res_num=3+num_sim, 
apex=cdp.pivot, R=R, phi_max_fn=cone.phi_max, length=size, inc=inc)
 
             # Generate the cone cap, and stitch it to the cone edge.
             print("\nGenerating the cone cap.")

Modified: 1.3/specific_fns/n_state_model.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=10954&r1=10953&r2=10954&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Tue Mar  9 11:51:38 2010
@@ -40,6 +40,7 @@
 import generic_fns
 from generic_fns.mol_res_spin import return_spin, spin_loop
 from generic_fns import pcs, pipes, rdc
+from generic_fns.structure.cones import Iso_cone
 import generic_fns.structure.geometric
 from generic_fns.structure.internal import Internal
 import generic_fns.structure.mass
@@ -382,6 +383,13 @@
         R = zeros((3, 3), float64)
         two_vect_to_R(array([0, 0, 1], float64), 
cdp.ave_pivot_CoM/norm(cdp.ave_pivot_CoM), R)
 
+        # The isotropic cone object.
+        if cone_type == 'diff in cone':
+            angle = cdp.theta_diff_in_cone
+        elif cone_type == 'diff on cone':
+            angle = cdp.theta_diff_on_cone
+        cone = Iso_cone(angle)
+
         # Create the structural object.
         structure = Internal()
 
@@ -403,12 +411,8 @@
 
         # Generate the cone outer edge.
         print("\nGenerating the cone outer edge.")
-        if cone_type == 'diff in cone':
-            angle = cdp.theta_diff_in_cone
-        elif cone_type == 'diff on cone':
-            angle = cdp.theta_diff_on_cone
         cap_start_atom = mol.atom_num[-1]+1
-        generic_fns.structure.geometric.cone_edge(mol=mol, res_name='CON', 
res_num=3, apex=cdp.pivot_point, R=R, angle=angle, 
length=norm(cdp.pivot_CoM), inc=inc)
+        generic_fns.structure.geometric.cone_edge(mol=mol, res_name='CON', 
res_num=3, apex=cdp.pivot_point, R=R, phi_max_fn=cone.phi_max, 
length=norm(cdp.pivot_CoM), inc=inc)
 
         # Generate the cone cap, and stitch it to the cone edge.
         if cone_type == 'diff in cone':